scispace - formally typeset

Showing papers in "Journal of the Indian Institute of Science in 2020"


Journal ArticleDOI

[...]

TL;DR: This article reviews some of the important mathematical models used to support the ongoing planning and response efforts in the COVID-19 pandemic and discusses their use, their mathematical form and their scope.
Abstract: COVID-19 pandemic represents an unprecedented global health crisis in the last 100 years. Its economic, social and health impact continues to grow and is likely to end up as one of the worst global disasters since the 1918 pandemic and the World Wars. Mathematical models have played an important role in the ongoing crisis; they have been used to inform public policies and have been instrumental in many of the social distancing measures that were instituted worldwide. In this article, we review some of the important mathematical models used to support the ongoing planning and response efforts. These models differ in their use, their mathematical form and their scope.

40 citations


Journal ArticleDOI

[...]

TL;DR: This article argues that communication engineers in the post-5G era should extend the scope of their activity in terms of design objectives and constraints beyond connectivity to encompass the semantics of the transferred bits within the given applications and use cases.
Abstract: The traditional role of a communication engineer is to address the technical problem of transporting bits reliably over a noisy channel. With the emergence of 5G, and the availability of a variety of competing and coexisting wireless systems, wireless connectivity is becoming a commodity. This article argues that communication engineers in the post-5G era should extend the scope of their activity in terms of design objectives and constraints beyond connectivity to encompass the semantics of the transferred bits within the given applications and use cases. To provide a platform for semantic-aware connectivity solutions, this paper introduces the concept of a semantic-effectiveness (SE) plane as a core part of future communication architectures. The SE plane augments the protocol stack by providing standardized interfaces that enable information filtering and direct control of functionalities at all layers of the protocol stack. The advantages of the SE plane are described in the perspective of recent developments in 5G, and illustrated through a number of example applications. The introduction of a SE plane may help replacing the current “next-G paradigm” in wireless evolution with a framework based on continuous improvements and extensions of the systems and standards.

28 citations


Journal ArticleDOI

[...]

TL;DR: The transfer of the bridging proton from one molecule to another can occur not only in the ground electronic state, but also in various excited states as discussed by the authors, and a great deal has been learned about the nature, properties, and applications of the H-bond.
Abstract: Since its original inception, a great deal has been learned about the nature, properties, and applications of the H-bond. This review summarizes some of the unexpected paths that inquiry into this phenomenon has taken researchers. The transfer of the bridging proton from one molecule to another can occur not only in the ground electronic state, but also in various excited states. Study of the latter process has developed insights into the relationships between the nature of the state, the strength of the H-bond, and the height of the transfer barrier. The enormous broadening of the range of atoms that can act as both proton donor and acceptor has led to the concept of the CH···O HB, whose properties are of immense importance in biomolecular structure and function. The idea that the central bridging proton can be replaced by any of various electronegative atoms has fostered the rapidly growing exploration of related noncovalent bonds that include halogen, chalcogen, pnicogen, and tetrel bonds.

12 citations


Journal ArticleDOI

[...]

TL;DR: In this article, it was shown that if polarization is minor and the hydrogen bonds relatively weak, then their interaction energies correlate well with the product of the most positive electrostatic potential on the hydrogen and the most negative one on the negative site.
Abstract: Molecular electrostatic potentials, in conjunction with polarization, provide the key to understanding hydrogen bonding. As required by the Hellmann–Feynman theorem, hydrogen bonding is a Coulombic interaction between (a) a positive electrostatic potential associated with a region of lower electronic density on the hydrogen (a σ-hole), and (b) a negative site on the hydrogen-bond acceptor. The charge distributions of both the hydrogen-bond donor and the acceptor reflect the polarizing effects of each other’s electric fields. The greater the polarization, the stronger the interaction. This interpretation of hydrogen bonding applies to all of the different categories into which it has been subdivided; they are fundamentally similar. We show that if polarization is minor and the hydrogen bonds relatively weak, then their interaction energies correlate well with the product of the most positive electrostatic potential on the hydrogen and the most negative one on the negative site. It is argued that the partial covalent character that is often attributed to hydrogen bonds simply reflects a greater degree of polarization.

11 citations


Journal ArticleDOI

[...]

TL;DR: A plethora of such H bonds have been investigated over past several decades through high-resolution laser spectroscopy, microwave and quantum chemical calculations as discussed by the authors, and these H bonds not only play important roles in biological systems, but are increasingly being tuned in nature and strength to construct artificial models that can aid our mechanistic understanding of noncovalent interactions and also help in modulation of activity, detection, and combat of diseases.
Abstract: Compared to conventional hydrogen bonds like (O–H···N, N–H···O, O–H···O, N–H···N), hydrogen bonds involving heavier chalcogens like sulfur, selenium, and tellurium have been considered weaker owing to less electronegativity of these elements. However, various instances exist to prove that these hydrogen bonds (H bonds) are of similar strength of conventional hydrogen bonds, although the nature of hydrogen bonding could be different depending on a combination of electronegativity, polarizability, and dispersion effects. We have presented a plethora of such H bonds that have been investigated over past several decades through high-resolution laser spectroscopy, microwave spectroscopy, and quantum chemical calculations. These H bonds not only play important roles in biological systems, but are increasingly being tuned in nature and strength to construct artificial models that can aid our mechanistic understanding of non-covalent interactions and also help in modulation of activity, detection, and combat of diseases. We have discussed how these interactions could be exploited for applications in crystal engineering, superconductivity, gas capture, and field-effect transistor studies.

10 citations


Journal ArticleDOI

[...]

TL;DR: In this paper, the authors develop an agent-based simulation framework in Python that can simulate various testing policies as well as interventions such as lockdown based on them and compare the performance of three testing policies: Random Symptomatic Testing (RST), Contact Tracing (CT), and a new Location-Based Testing policy (LBT).
Abstract: The number of confirmed cases of COVID-19 is often used as a proxy for the actual number of ground truth COVID-19-infected cases in both public discourse and policy making. However, the number of confirmed cases depends on the testing policy, and it is important to understand how the number of positive cases obtained using different testing policies reveals the unknown ground truth. We develop an agent-based simulation framework in Python that can simulate various testing policies as well as interventions such as lockdown based on them. The interaction between the agents can take into account various communities and mobility patterns. A distinguishing feature of our framework is the presence of another 'flu'-like illness with symptoms similar to COVID-19, that allows us to model the noise in selecting the pool of patients to be tested. We instantiate our model for the city of Bengaluru in India, using census data to distribute agents geographically, and traffic flow mobility data to model long-distance interactions and mixing. We use the simulation framework to compare the performance of three testing policies: Random Symptomatic Testing (RST), Contact Tracing (CT), and a new Location-Based Testing policy (LBT). We observe that if a sufficient fraction of symptomatic patients come out for testing, then RST can capture the ground truth quite closely even with very few daily tests. However, CT consistently captures more positive cases. Interestingly, our new LBT, which is operationally less intensive than CT, gives performance that is comparable with CT. In another direction, we compare the efficacy of these three testing policies in enabling lockdown, and observe that CT flattens the ground truth curve maximally, followed closely by LBT, and significantly better than RST.

9 citations


Journal ArticleDOI

[...]

TL;DR: In this paper, the authors present an overview of the state-of-the-art DL architectures and algorithms used for CSI acquisition and feedback in massive MIMO systems and provide further research directions.
Abstract: Massive multiple-input multiple-output (MIMO) systems are a main enabler of the excessive throughput requirements in 5G and future generation wireless networks as they can serve many users simultaneously with high spectral and energy efficiency. To achieve this massive MIMO systems require accurate and timely channel state information (CSI), which is acquired by a training process that involves pilot transmission, CSI estimation, and feedback. This training process incurs a training overhead, which scales with the number of antennas, users, and subcarriers. Reducing the training overhead in massive MIMO systems has been a major topic of research since the emergence of the concept. Recently, deep learning (DL)-based approaches have been proposed and shown to provide significant reduction in the CSI acquisition and feedback overhead in massive MIMO systems compared to traditional techniques. In this paper, we present an overview of the state-of-the-art DL architectures and algorithms used for CSI acquisition and feedback, and provide further research directions.

9 citations


Journal ArticleDOI

[...]

TL;DR: In this article, a spectroscopic overview of the C-H···Y (Y = hydrogen bond acceptors) hydrogen bonded (HB or H-bond) complexes is presented.
Abstract: We present a spectroscopic overview of the C–H···Y (Y = hydrogen bond acceptors) hydrogen bonded (HB or H-bond) complexes in this article. Although C–H···Y interactions have been recognized as H-bonding interactions for quite some time, they have not been investigated spectroscopically until recently. Recent results indicated that unlike the conventional hydrogen bond, C–H···Y H-bond has interesting spectroscopic characteristics, i.e. it shows both red as well as blue shift in C–H stretching frequency upon H-bond formation. This review presents examples of red, blue, and zero shifted C–H···Y H-bonds investigated in our laboratory that were characterized using laser-based IR and UV spectroscopic techniques applied to the cold isolated molecular complexes formed under supersonic expansion conditions. Along with spectroscopic information, ab initio/DFT-predicted geometry optimized structures of various conformers, harmonic frequency calculations of the optimized structures, and a number of properties such as electron densities at the bond critical points, orbital interaction energies, binding energies of the C–H···Y bound complexes are also summarized for better understanding of this type of H-bond. Not only the spectroscopic shift in C–H stretching frequency, but also the role of C–H···O H-bonds in microsolvation of several organic molecules has been highlighted. It has been found that depending upon activation of C–H moiety, C–H···Y H-bonds can provide primary or secondary stabilization for the growth of the primary solvation shell around organic molecules.

8 citations


Journal ArticleDOI

[...]

TL;DR: In this article, the authors survey the data landscape around COVID-19, with a focus on how such datasets have aided modeling and response through different stages so far in the pandemic.
Abstract: Some of the key questions of interest during the COVID-19 pandemic (and all outbreaks) include: where did the disease start, how is it spreading, who are at risk, and how to control the spread. There are a large number of complex factors driving the spread of pandemics, and, as a result, multiple modeling techniques play an increasingly important role in shaping public policy and decision-making. As different countries and regions go through phases of the pandemic, the questions and data availability also change. Especially of interest is aligning model development and data collection to support response efforts at each stage of the pandemic. The COVID-19 pandemic has been unprecedented in terms of real-time collection and dissemination of a number of diverse datasets, ranging from disease outcomes, to mobility, behaviors, and socio-economic factors. The data sets have been critical from the perspective of disease modeling and analytics to support policymakers in real time. In this overview article, we survey the data landscape around COVID-19, with a focus on how such datasets have aided modeling and response through different stages so far in the pandemic. We also discuss some of the current challenges and the needs that will arise as we plan our way out of the pandemic.

8 citations


Journal ArticleDOI

[...]

TL;DR: This article surveys the existing green sensing and communication approaches to realize sustainable IoT systems for various applications and presents a few case studies that aim to generate sensed traffic data intelligently as well as prune it efficiently without sacrificing the required service quality.
Abstract: With the advent of Internet of Things (IoT) devices, their reconfigurability, networking, task automation, and control ability have been a boost to the evolution of traditional industries such as health-care, agriculture, power, education, and transport. However, the quantum of data produced by the IoT devices poses serious challenges on its storage, communication, computation, security, scalability, and system’s energy sustainability. To address these challenges, the concept of green sensing and communication has gained importance. This article surveys the existing green sensing and communication approaches to realize sustainable IoT systems for various applications. Further, a few case studies are presented that aim to generate sensed traffic data intelligently as well as prune it efficiently without sacrificing the required service quality. Challenges associated with these green techniques, various open issues, and future research directions for improving the energy efficiency of the IoT systems are also discussed.

8 citations


Journal ArticleDOI

[...]

TL;DR: The review article provides an overview of the emergence of IoT in healthcare globally, the intricacies of different factors impinging its current status and recommends policy intervention for an optimal roadmap of Internet of Things-IoT in healthcare in the Indian context.
Abstract: The digitization of data including health data (referred to as Internet of Things-IoT in Healthcare) and its usage in delivery of healthcare has been growing rapidly across the world. The COVID-19 pandemic has been a pivot for exponential growth of IoT in healthcare. Several rapidly evolving technologies are converging to influence the trajectory of IoT in healthcare. There are several challenges in technology development, healthcare delivery as well as issues related to privacy of data, digital divide, role of government and other stakeholders, behaviour and adoption by medical doctors and hospitals. The review article provides an overview of the emergence of IoT in healthcare globally, the intricacies of different factors impinging its current status and recommends policy intervention for an optimal roadmap of IoT in healthcare in the Indian context.

Journal ArticleDOI

[...]

TL;DR: The field of intra-and intermolecular interactions has received a major boost in the past one decade as mentioned in this paper, and significant advances in both instrumentation (for experimental purposes) and computational resources (development of theoretical models) have provided strong impetus to this area of research.
Abstract: The field of intra- and intermolecular interactions has received a major boost in the past one decade. Significant advances in both instrumentation (for experimental purposes) and computational resources (development of theoretical models) have provided strong impetus to this area of research. The understanding of the nature, energetics and the topological characteristics of these interactions are the driving forces which govern intermolecular recognition. This is strongly dependent on the state of aggregation of the substance. The environment (solid, liquid and gas) plays an extremely crucial and subtle role in deciphering the mechanism via which molecules interact with each other. In the past two decades, there has been rigorous development in the understanding of strong hydrogen bonds. The focus has now shifted towards the quantitative assessment of weak intermolecular interactions, of the type C–H···X (X = F in particular), X···X, X(lp)···π along with σ–hole-directed intermolecular interactions involving tetrels, chalcogens, pnictogens, halogens and the aerogens. In addition, there is increasing evidence for the assessment of the relevance of π–hole-based interactions in tetrels, chalcogens, and pnictogens as well. The current perspective highlights the importance of the above-mentioned interactions and their associated electronic features. This has strong implications in the area of materials and related applied sciences with relevance towards the technological applications of these interactions in terms of understanding structure–property correlation in the mechanical, optical and electrical properties of matter.

Journal ArticleDOI

[...]

TL;DR: In this paper, a remarkable match was confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction.
Abstract: Formic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.

Journal ArticleDOI

[...]

TL;DR: MIMO-OTFS systems are shown to achieve significantly better performance compared to MIMo-OFDM in high-Doppler environments operating in 4 GHz and 28 GHz frequency bands.
Abstract: Among the several emerging use case families in 5G, high-mobility use case family is a technologically challenging one. It is expected that there will be a growing demand for mobile services in vehicles, high-speed trains, and even aircraft. The degree of mobility support required (i.e., speed) will depend upon the specific use case (e.g., 500 km/h in bullet trains and 1000 km/h in airplanes). Mobility-on-demand, ranging from very high mobility to low or no mobility, need to be supported. The currently used waveforms fail to perform well in high-mobility scenarios where the Doppler shifts witnessed are quite high (e.g., several kHz of Doppler). Orthogonal time–frequency space (OTFS) is a recently proposed radio access technology waveform suited very well for high-mobility environments. It is a two-dimensional modulation scheme in which information symbols are multiplexed in the delay–Doppler domain. We present an overview of delay–Doppler representation of wireless channels and introduce OTFS modulation along with OTFS basis functions. We illustrate the slow variability and sparse nature of the delay–Doppler channel using an urban multi-lane scenario. Focusing on MIMO-OTFS systems, we present signal detection and channel estimation schemes and their performance. MIMO-OTFS is shown to achieve significantly better performance compared to MIMO-OFDM in high-Doppler environments operating in 4 GHz and 28 GHz frequency bands.

Journal ArticleDOI

[...]

TL;DR: This work studies the propagation in a factory floor using ray tracing, which shows that received signal strength is sufficiently large even when the line-of-sight (LoS) signal is blocked, and proposes an adaptive beam selection method that chooses the best set of beams across multiple users to improve the latency performance.
Abstract: Automation enabled by ultra-reliable and low latency 5G connectivity is expected to transform the industrial landscape over the next decade. Given the spectrum crunch in bands below 6 GHz, there is significant interest in exploring the use of millimeter wave (mmWave) bands for industrial automation. The harsh propagation conditions at high frequencies raise questions about the viability of providing ultra-reliable and low latency connectivity in these bands. Furthermore, the use of analog beamforming with narrow beams implies limited frequency multiplexing opportunity despite the wider bandwidths available, which in turn results in larger waiting times for packet transmission. We study the propagation in a factory floor using ray tracing, which shows that received signal strength is sufficiently large even when the line-of-sight (LoS) signal is blocked. To improve the latency performance, we propose an adaptive beam selection method that chooses the best set of beams across multiple users to reduce the overall latency for all users. We show through simulations that our proposed greedy algorithm performs better than the state-of-the-art algorithm, and that there is more improvement possible.

Journal ArticleDOI

[...]

TL;DR: It is concluded that 6 months into the pandemic, the quality of COVID-19 data reporting across India continues to be highly disparate, which could hinder public health efforts.
Abstract: India reported its first case of COVID-19 on January 30, 2020. Six months since then, COVID-19 continues to be a growing crisis in India with over 1.6 million reported cases. In this communication, we assess the quality of COVID-19 data reporting done by the state and union territory governments in India between July 12 and July 25, 2020. We compare our findings with those from an earlier assessment conducted in May 2020. We conclude that 6 months into the pandemic, the quality of COVID-19 data reporting across India continues to be highly disparate, which could hinder public health efforts.

Journal ArticleDOI

[...]

TL;DR: GoCoronaGo as mentioned in this paper is an institutional contact tracing app developed by the Indian Institute of Science campus in Bangalore, which is used for monitoring the COVID-19 pandemic.
Abstract: The COVID-19 pandemic is imposing enormous global challenges in managing the spread of the virus. A key pillar to mitigation is contact tracing, which complements testing and isolation. Digital apps for contact tracing using Bluetooth technology available in smartphones have gained prevalence globally. In this article, we discuss various capabilities of such digital contact tracing, and its implication on community safety and individual privacy, among others. We further describe the GoCoronaGo institutional contact tracing app that we have developed, and the conscious and sometimes contrarian design choices we have made. We offer a detailed overview of the app, backend platform and analytics, and our early experiences with deploying the app to over 1000 users within the Indian Institute of Science campus in Bangalore. We also highlight research opportunities and open challenges for digital contact tracing and analytics over temporal networks constructed from them.

Journal ArticleDOI

[...]

TL;DR: In this paper, the authors highlight the usefulness of city-scale agent-based simulators in studying various non-pharmaceutical interventions to manage an evolving pandemic and demonstrate the power of the simulator via several exploratory case studies in two metropolises.
Abstract: We highlight the usefulness of city-scale agent-based simulators in studying various non-pharmaceutical interventions to manage an evolving pandemic. We ground our studies in the context of the COVID-19 pandemic and demonstrate the power of the simulator via several exploratory case studies in two metropolises, Bengaluru and Mumbai. Such tools may in time become a common-place item in the tool kit of the administrative authorities of large cities.

Journal ArticleDOI

[...]

TL;DR: In this article, the authors discuss how an intricate interplay among infected cells and cells of innate and adaptive immune system can lead to such diverse clinicopathological outcomes and discuss how the emergent nonlinear dynamics of interaction among the components of adaptive and immune system components and virally infected cells can drive different disease severity.
Abstract: The disease caused by SARS-CoV-2-CoVID-19-is a global pandemic that has brought severe changes worldwide. Approximately 80% of the infected patients are largely asymptomatic or have mild symptoms such as fever or cough, while rest of the patients display varying degrees of severity of symptoms, with an average mortality rate of 3-4%. Severe symptoms such as pneumonia and acute respiratory distress syndrome may be caused by tissue damage, which is mostly due to aggravated and unresolved innate and adaptive immune response, often resulting from a cytokine storm. Here, we discuss how an intricate interplay among infected cells and cells of innate and adaptive immune system can lead to such diverse clinicopathological outcomes. Particularly, we discuss how the emergent nonlinear dynamics of interaction among the components of adaptive and immune system components and virally infected cells can drive different disease severity. Such minimalistic yet rigorous mathematical modeling approaches are helpful in explaining how various co-morbidity risk factors, such as age and obesity, can aggravate the severity of CoVID-19 in patients. Furthermore, such approaches can elucidate how a fine-tuned balance of infected cell killing and resolution of inflammation can lead to infection clearance, while disruptions can drive different severe phenotypes. These results can help further in a rational selection of drug combinations that can effectively balance viral clearance and minimize tissue damage.

Journal ArticleDOI

[...]

TL;DR: This work shows that both the discovery latency and energy consumption can be significantly reduced using fully digital front-ends, and proposes the use of digital beamformers with low-resolution analog to digital converters (4 bits), which brings the power consumption to the same level as analog beamforming for data transmissions while benefiting from the spatial multiplexing capabilities of fully digital beamforming.
Abstract: Future millimeter-wave systems, 5G cellular or WiFi, must rely on highly directional links to overcome severe pathloss in these frequency bands. Establishing such links requires the mutual discovery of the transmitter and the receiver, potentially leading to a large latency and high energy consumption. In this work, we show that both the discovery latency and energy consumption can be significantly reduced using fully digital front-ends. In fact, we establish that by reducing the resolution of the fully digital front-ends we can achieve lower energy consumption compared to both analog and high-resolution digital beamforming. Since beamforming through analog front-ends allows sampling in only one direction at a time, the mobile device is “on” for a longer time compared to a digital beamformer, which can get spatial samples from all directions in one shot. We show that the energy consumed by the analog front-end can be four to six times more than that of the digital front-ends, depending on the size of the employed antenna arrays. We recognize, however, that using fully digital beamforming post beam discovery, i.e., for data transmission, is not viable from a power consumption standpoint. To address this issue, we propose the use of digital beamformers with low-resolution analog to digital converters (4 bits). This reduction in resolution brings the power consumption to the same level as analog beamforming for data transmissions while benefiting from the spatial multiplexing capabilities of fully digital beamforming, thus reducing initial discovery latency and improving energy efficiency.

Journal ArticleDOI

[...]

TL;DR: This work describes the basic idea behind pooling of samples and different methods for reconstructing the result for each individual from the test of pooled samples, and describes the potential advantages of the combinatorial pooling method named Tapestry Pooling that relies on compressed sensing techniques.
Abstract: As SARS-CoV-2 continues to propagate around the world, it is becoming increasingly important to scale up testing. This is necessary both at the individual level, to inform diagnosis, treatment and contract tracing, as well as at the population level to inform policies to control spread of the infection. The gold-standard RT-qPCR test for the virus is relatively expensive and takes time, so combining multiple samples into "pools" that are tested together has emerged as a useful way to test many individuals with less than one test per person. Here, we describe the basic idea behind pooling of samples and different methods for reconstructing the result for each individual from the test of pooled samples. The methods range from simple pooling, where each pool is disjoint from the other, to more complex combinatorial pooling where each sample is split into multiple pools and each pool has a specified combination of samples. We describe efforts to validate these testing methods clinically and the potential advantages of the combinatorial pooling method named Tapestry Pooling that relies on compressed sensing techniques.

Journal ArticleDOI

[...]

TL;DR: In this paper, the authors assess the relative significance of strong and weak interactions in the macromolecular recognition processes and find that the weaker interactions can be made and broken more easily than stronger interactions.
Abstract: The hydrogen bond has justifiably been termed the ‘master key of molecular recognition’. It is an interaction that is weaker than the covalent bond and stronger than the van der Waals interaction. The ubiquity and flexibility of hydrogen bonds make them the most important physical interaction in systems of biomolecules in aqueous solution. Hydrogen bonding plays a significant role in many chemical and biological processes, including ligand binding and enzyme catalysis. In biological processes, both specificity and reversibility are important. Weaker interactions can be made and broken more easily than stronger interactions. In this context, it is of interest to assess the relative significance of strong and weak interactions in the macromolecular recognition processes. Is protein–ligand binding governed by conventional, that is, electrostatic N–H…O and O–H…O hydrogen bonds, or do weaker interactions with a greater dispersive component such as C–H…O hydrogen bonds also play a role? If so, to what extent are they significant? Most proteins, involving as they do, main chains, side chains, and differently bound forms of water, do not really have a static fixed structure, but rather have a dynamic, breathing nature. This tendency may to some extent be lessened by the ligands which are small molecules, but in the end, it is reasonable to expect that the strong and weak hydrogen bonds inside the protein and also at the protein–ligand interface will also have dynamic character; arguably, the weaker the hydrogen bond, the greater its dynamic character. These are often central to the much debated mechanisms of binding such as conformational selection and induced fit. All protein–ligand interactions must compete with interactions with water; both the protein and the ligand are solvated before complexation and lose their solvation shell on complex formation. Conversely, the entropic cost of trapping highly mobile water molecules in the binding site is large. However, in favorable cases, these losses are suitably compensated by the enthalpic gain resulting from water-mediated hydrogen bonds. In effect, the enthalpy–entropy balance is a fine one, and for a water molecule to be able to contribute to binding affinity, it has to be in a binding site that provides the maximum number of hydrogen-bond partners at the optimum distance and orientation. In summary, hydrogen bonds are crucial to the recognition of ligands by proteins. Integration of knowledge gained from more high-quality protein–ligand structures into theoretical and computational molecular models will be an exciting challenge in the coming years.

Journal ArticleDOI

[...]

TL;DR: This review discusses the current state-of-art of scRNA-seq analysis step-by-step including filtering, normalization and analysis and discusses the brief history of experimental methods, followed by data processing and implications in precision oncology.
Abstract: Tumors exhibit genetic and phenotypic diversity leading to intra-tumor heterogeneity (ITH). Further complex ecosystem (stromal and immune cells) of tumors contributes into the ITH. This ITH allows tumors to overcome various selection pressures such as anti-cancer therapies and metastasis at distant organs. Single-cell RNA-seq (scRNA-seq) has provided unprecedented insights into ITH and its implications in drug resistance and metastasis. As scRNA-seq technology grows and provides many new findings, new tools on different programming platforms are frequently generated. Here, we aim to provide a framework and guidelines for new entrants into the field of scRNA-seq. In this review, we discuss the current state-of-art of scRNA-seq analysis step-by-step including filtering, normalization and analysis. First, we discuss the brief history of experimental methods, followed by data processing and implications in precision oncology.

Journal ArticleDOI

[...]

TL;DR: Molecular and metabolic plasticity in matrix-attached and -detached states of cancer cells that aid in metastatic cancer progression are discussed and cancer heterogeneity is discussed—an emerging evil that needs to be tackled for overcoming therapy failure and achieving better treatment outcomes.
Abstract: The ability of cells to assume different phenotypes without changing their genotype : The complete genetic constitution of an organism. is referred to as cellular plasticity. It is increasingly being recognized as a fundamental and essential property of cancer cells, which enables their adaptation to the changing environmental conditions, imposed by both disease progression and therapeutic intervention. Epithelial–mesenchymal transition (EMT) is a classical well-studied example of cellular plasticity during cancer progression that aids cancer spread by metastasis. A closely associated phenomenon that entails metastatic progression is the detachment of cancer cells from the extracellular matrix (ECM) at the primary tumor site, their passage and survival in the circulation in an anchorage-independent form, and subsequent re-attachment at a distant site to establish new tumor growth. In this review, we discuss molecular and metabolic plasticity in matrix-attached and -detached states of cancer cells that aid in metastatic cancer progression. Further, cellular plasticity enables cancer cells within a population to assume different phenotypic states, thus leading to cancer heterogeneity—an emerging evil that needs to be tackled for overcoming therapy failure and achieving better treatment outcomes.

Journal ArticleDOI

[...]

TL;DR: An overview of the field of mass-resolved laser spectroscopy applied to nucleobases, peptides, and monosaccharides to demonstrate that despite the different environment the molecules encounter in the jet, such experiments yield important structural information that helps understanding the role played by hydrogen bond in biology as discussed by the authors.
Abstract: Life makes extensive use of non-covalent interactions, as they are a convenient way to build complex structures that can be assembled or disassembled quickly, with a minimum energy consumption. Among the inter-molecular interactions, hydrogen bond plays a central role, and it is the main responsible of the structure of proteins, DNA, and several other superstructures in the cell. Characterization of hydrogen bond in biologic environment is not an easy task, and several complex and imaginative techniques have been developed to circumvent the technical challenges of such studies. We present here an overview of the field of mass-resolved laser spectroscopy applied to nucleobases, peptides, and monosaccharides to demonstrate that despite the different environment the molecules encounter in the jet, such experiments yield important structural information that helps understanding the role played by hydrogen bond in biology.

Journal ArticleDOI

[...]

TL;DR: An overview of the integration of NOMA with several other leading technologies for 5G and beyond networks to enhance the connectivity is presented, thereby achieving multi-fold enhancement in connectivity.
Abstract: Two of the most challenging goals for the fifth generation (5G) and beyond communication systems are massive connectivity and higher capacity. The use of traditional orthogonal multiple access techniques limits the number of users that can be served using available resources due to orthogonality constraint. Moreover, the available resources may not be utilized effectively by alloted users thereby resulting in inefficiency and user unfairness. This imposes a severe drawback in cases where the number of users to be served are high, like in the Internet of Things or ultra-dense 5G networks. Hence, introducing non-orthogonality to multiple access scheme is advocated as a superior methodology to serve multiple users simultaneously, thereby achieving multi-fold enhancement in connectivity. In scenarios with massive number of users, non-orthogonal multiple access scheme (NOMA) increases the number of active connections by superimposing signals of multiple users on the same resource block, thereby also utilizing the available resources efficiently. This article presents an overview of the integration of NOMA with several other leading technologies for 5G and beyond networks to enhance the connectivity.

Journal ArticleDOI

[...]

TL;DR: This review discusses both the generalized physical principles and associated mathematical models developed to understand phenotypic state transition and the opportunities to connect these two approaches and the limitations of the current understanding and mathematical methods.
Abstract: Change in the phenotype of a cell is considered as a transition of a cell from one cellular state to another. Cellular state transition can be driven by an external cue or by the noise in molecular processes. Over the years, generalized physical principles, and associated mathematical models have been developed to understand phenotypic state transition. Starting with Waddington’s epigenetic landscape, phenotypic state transition is seen as a movement of cells on a potential landscape. Though the landscape model is close to the thermodynamic principles of state change, it is difficult to envisage it from experimental observations. Therefore, phenotypic state transition is often considered as a discrete state jump process. This approach is particularly useful to estimate the paths of state transition from experimental observations. In this review, we discuss both of these approaches and the associated mathematical formulations. Furthermore, we explore the opportunities to connect these two approaches and the limitations of our current understanding and mathematical methods.

Journal ArticleDOI

[...]

TL;DR: A new waveform with low peak-to-average power ratio that has been introduced in 5G for coverage enhancement and is looked at by taking a case study from the Indian rural setting.
Abstract: In most developing countries across the world, cellular rural users are predominantly pedestrian and indoor users within village homes, and much less from vehicles, let alone fast-moving ones. Specifically, in India, 85% of the villages in the plains are spaced 2–3 km apart uniformly in every direction. The base station required for providing coverage in rural areas is starkly different from the base station along highways to provide coverage for fast-moving vehicles. Till IMT-2020, ITU did not have a rural use case suited to rural needs of developing countries. Hence, the IMT advanced technology development (such as 4G LTE) did not meet the rural requirements in countries like India. To avoid such a situation for 5G, a new test case requirement, named low-mobility large cell (LMLC) was included as a mandatory use case with performance requirements that must be met by every specification that is approved as an IMT-2020 compliant standard. In this paper, we describe the reasons why such a test case requirement is crucial by taking a case study from the Indian rural setting. In addition, we also describe various technical solutions that can be considered to satisfy such stringent requirements. In particular, we look at a new waveform with low peak-to-average power ratio that has been introduced in 5G for coverage enhancement.

Journal ArticleDOI

[...]

TL;DR: In this article, molecular dynamics simulations of benzene and 12 fluorobenzenes with various degrees of fluorine substitution in water reveal that the accumulation of water in the first solvent shell decreases with an increase in number of fluorines relative to benzene, with the exception of hexafluorobenzene.
Abstract: Molecular dynamics simulations of benzene and 12 fluorobenzenes with various degrees of fluorine substitution in water reveal that the accumulation of water in the first solvent shell decreases with increase in number of fluorine atoms relative to benzene, with an exception of hexafluorobenzene. Further, the solute–solute radial density function indicates that partially substituted fluorobenzenes sample $$ \uppi $$-stacked and T-shaped geometries. In contrast benzene and hexafluorobenzene sample only the T-shaped geometries. Comparison of solute–solute and solute–solvent radial density functions suggests that solute–solute interactions is preferred over solute–solvent interaction, which suggests the hydrophobic nature of fluorobenzenes, which increases with increase in number of fluorine atoms on the phenyl ring. The spatial distribution of water around the fluorobenzenes suggests that water avoids the C–F bond group, which indicates increase in hydrophobicity of fluorobenzenes with number of fluorine atoms.

Journal ArticleDOI

[...]

TL;DR: In this article, a multipole formalism developed for accurate X-ray diffraction data is routinely utilized in conjunction with the concept of atoms in molecules to obtain quantitative estimates of the topological properties in molecular crystals which allow the evaluation of both bonded and non-bonded contacts.
Abstract: Mapping of charge densities in molecular crystals has been contemplated ever since it was recognized that X-rays are scattered by the electron density in the crystal. The methodology both from the experimental and theoretical perspective was standardized and applied extensively only during the last few decades, as technological advances were a prerequisite in both data collection and computation. Multipole formalism developed for accurate X-ray diffraction data is routinely utilized in conjunction with the concept of atoms in molecules to obtain quantitative estimates of the topological properties in molecular crystals which allow the evaluation of both bonded and non-bonded contacts. Recently, with the advent of quantum crystallography, combining Hirshfeld atom refinement along with libraries of extremely localized molecular orbitals, HAR–ELMOs, has emerged as an alternate approach. Apart from the weak hydrogen bonds, other highly directional non-bonded contacts like halogen, pnicogen, chalcogen and carbon bonds have been subjected to charge density analysis to experimentally observe and quantify σ-holes using experimental high-resolution X-ray diffraction data. The recognition of lack of directional preferences in hydrophobic interactions is demonstrated experimentally which might have far reaching consequences in the areas of materials and biology.