Showing papers by "Bar-Ilan University published in 2020"

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Vaccine hesitancy: the next challenge in the fight against COVID-19.

Abstract: Vaccine hesitancy remains a barrier to full population inoculation against highly infectious diseases. Coincident with the rapid developments of COVID-19 vaccines globally, concerns about the safety of such a vaccine could contribute to vaccine hesitancy. We analyzed 1941 anonymous questionnaires completed by healthcare workers and members of the general Israeli population, regarding acceptance of a potential COVID-19 vaccine. Our results indicate that healthcare staff involved in the care of COVID-19 positive patients, and individuals considering themselves at risk of disease, were more likely to self-report acquiescence to COVID-19 vaccination if and when available. In contrast, parents, nurses, and medical workers not caring for SARS-CoV-2 positive patients expressed higher levels of vaccine hesitancy. Interventional educational campaigns targeted towards populations at risk of vaccine hesitancy are therefore urgently needed to combat misinformation and avoid low inoculation rates.

GW190814: Gravitational Waves from the Coalescence of a 23 Solar Mass Black Hole with a 2.6 Solar Mass Compact Object

Abstract: We report the observation of a compact binary coalescence involving a 222–243 M ⊙ black hole and a compact object with a mass of 250–267 M ⊙ (all measurements quoted at the 90% credible level) The gravitational-wave signal, GW190814, was observed during LIGO's and Virgo's third observing run on 2019 August 14 at 21:10:39 UTC and has a signal-to-noise ratio of 25 in the three-detector network The source was localized to 185 deg2 at a distance of ${241}_{-45}^{+41}$ Mpc; no electromagnetic counterpart has been confirmed to date The source has the most unequal mass ratio yet measured with gravitational waves, ${0112}_{-0009}^{+0008}$, and its secondary component is either the lightest black hole or the heaviest neutron star ever discovered in a double compact-object system The dimensionless spin of the primary black hole is tightly constrained to ≤007 Tests of general relativity reveal no measurable deviations from the theory, and its prediction of higher-multipole emission is confirmed at high confidence We estimate a merger rate density of 1–23 Gpc−3 yr−1 for the new class of binary coalescence sources that GW190814 represents Astrophysical models predict that binaries with mass ratios similar to this event can form through several channels, but are unlikely to have formed in globular clusters However, the combination of mass ratio, component masses, and the inferred merger rate for this event challenges all current models of the formation and mass distribution of compact-object binaries

GW190521: A Binary Black Hole Merger with a Total Mass of 150 M

Abstract: On May 21, 2019 at 03:02:29 UTC Advanced LIGO and Advanced Virgo observed a short duration gravitational-wave signal, GW190521, with a three-detector network signal-to-noise ratio of 14.7, and an estimated false-alarm rate of 1 in 4900 yr using a search sensitive to generic transients. If GW190521 is from a quasicircular binary inspiral, then the detected signal is consistent with the merger of two black holes with masses of 85_{-14}^{+21} M_{⊙} and 66_{-18}^{+17} M_{⊙} (90% credible intervals). We infer that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65 M_{⊙}. We calculate the mass of the remnant to be 142_{-16}^{+28} M_{⊙}, which can be considered an intermediate mass black hole (IMBH). The luminosity distance of the source is 5.3_{-2.6}^{+2.4} Gpc, corresponding to a redshift of 0.82_{-0.34}^{+0.28}. The inferred rate of mergers similar to GW190521 is 0.13_{-0.11}^{+0.30} Gpc^{-3} yr^{-1}.

Current status and future directions of multivalent metal-ion batteries

Abstract: Batteries based on multivalent metals have the potential to meet the future needs of large-scale energy storage, due to the relatively high abundance of elements such as magnesium, calcium, aluminium and zinc in the Earth’s crust. However, the complexity of multivalent metal-ion chemistries has led to rampant confusions, technical challenges, and eventually doubts and uncertainties about the future of these technologies. In this Review, we clarify the key strengths as well as common misconceptions of multivalent metal-based batteries. We then examine the growth behaviour of metal anodes, which is crucial for their safety promises but hitherto unestablished. We further discuss scrutiny of anode efficiency and cathode storage mechanism pertaining to complications arising from electrolyte solutions. Finally, we critically review existing cathode materials and discuss design strategies to enable genuine multivalent metal-ion-based energy storage materials with competitive performance. Batteries based on multivalent metal anodes hold great promise for large-scale energy storage but their development is still at an early stage. This Review surveys the main complexity arising from anodes, electrolytes and cathodes, and offers views on the progression path of these technologies.

GW190412: Observation of a binary-black-hole coalescence with asymmetric masses

Abstract: We report the observation of gravitational waves from a binary-black-hole coalescence during the first two weeks of LIGO’s and Virgo’s third observing run. The signal was recorded on April 12, 2019 at 05∶30∶44 UTC with a network signal-to-noise ratio of 19. The binary is different from observations during the first two observing runs most notably due to its asymmetric masses: a ∼30 M⊙ black hole merged with a ∼8 M⊙ black hole companion. The more massive black hole rotated with a dimensionless spin magnitude between 0.22 and 0.60 (90% probability). Asymmetric systems are predicted to emit gravitational waves with stronger contributions from higher multipoles, and indeed we find strong evidence for gravitational radiation beyond the leading quadrupolar order in the observed signal. A suite of tests performed on GW190412 indicates consistency with Einstein’s general theory of relativity. While the mass ratio of this system differs from all previous detections, we show that it is consistent with the population model of stellar binary black holes inferred from the first two observing runs.

Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future

Abstract: The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal-air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal-air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li-O2 cells but include Na-O2, K-O2, and Mg-O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li-O2 cells.

Traumatic stress in the age of COVID-19: A call to close critical gaps and adapt to new realities.

Abstract: THE ISSUE: Coronavirus-19 (COVID-19) is transforming every aspect of our lives. Identified in late 2019, COVID-19 quickly became characterized as a global pandemic by March of 2020. Given the rapid acceleration of transmission, and the lack of preparedness to prevent and treat this virus, the negative impacts of COVID-19 are rippling through every facet of society. Although large numbers of people throughout the world will show resilience to the profound loss, stress, and fear associated with COVID-19, the virus will likely exacerbate existing mental health disorders and contribute to the onset of new stress-related disorders for many. RECOMMENDATIONS: The field of traumatic stress should address the serious needs that will emerge now and well into the future. However, we propose that these efforts may be limited, in part, by ongoing gaps that exist within our research and clinical care. In particular, we suggest that COVID-19 requires us to prioritize and mobilize as a research and clinical community around several key areas: (a) diagnostics, (b) prevention, (c) public outreach and communication, (d) working with medical staff and mainstreaming into nonmental health services, and (e) COVID-19-specific trauma research. As members of our community begin to rapidly develop and test interventions for COVID-19-related distress, we hope that those in positions of leadership in the field of traumatic stress consider limits of our current approaches, and invest the intellectual and financial resources urgently needed in order to innovate, forge partnerships, and develop the technologies to support those in greatest need. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

Health equity and COVID-19: global perspectives.

Abstract: The COVID-19 is disproportionally affecting the poor, minorities and a broad range of vulnerable populations, due to its inequitable spread in areas of dense population and limited mitigation capacity due to high prevalence of chronic conditions or poor access to high quality public health and medical care. Moreover, the collateral effects of the pandemic due to the global economic downturn, and social isolation and movement restriction measures, are unequally affecting those in the lowest power strata of societies. To address the challenges to health equity and describe some of the approaches taken by governments and local organizations, we have compiled 13 country case studies from various regions around the world: China, Brazil, Thailand, Sub Saharan Africa, Nicaragua, Armenia, India, Guatemala, United States of America (USA), Israel, Australia, Colombia, and Belgium. This compilation is by no-means representative or all inclusive, and we encourage researchers to continue advancing global knowledge on COVID-19 health equity related issues, through rigorous research and generation of a strong evidence base of new empirical studies in this field.

Resilience, COVID-19-related stress, anxiety and depression during the pandemic in a large population enriched for healthcare providers.

Abstract: COVID-19 pandemic is a global calamity posing an unprecedented opportunity to study resilience. We developed a brief resilience survey probing self-reliance, emotion-regulation, interpersonal-relationship patterns and neighborhood-environment, and applied it online during the acute COVID-19 outbreak (April 6–15, 2020), on a crowdsourcing research website ( www.covid19resilience.org ) advertised through social media. We evaluated level of stress (worries) regarding COVID-19: (1) contracting, (2) dying from, (3) currently having, (4) family member contracting, (5) unknowingly infecting others with (6) experiencing significant financial burden following. Anxiety (GAD7) and depression (PHQ2) were measured. Totally, 3042 participants (n = 1964 females, age range 18–79, mean age = 39) completed the resilience and COVID-19-related stress survey and 1350 of them (mean age = 41, SD = 13; n = 997 females) completed GAD7 and PHQ2. Participants significantly endorsed more distress about family contracting COVID-19 (48.5%) and unknowingly infecting others (36%), than getting COVID-19 themselves (19.9%), p 10, 22.2%) and depression (PHQ2 > 2, 16.1%) did not differ between healthcare providers and non-healthcare providers. Higher resilience scores were associated with lower COVID-19 related worries (main effect F1,3054 = 134.9; p < 0.00001, covarying for confounders). Increase in 1 SD on resilience score was associated with reduced rate of anxiety (65%) and depression (69%), across healthcare and non-healthcare professionals. Findings provide empirical evidence on mental health associated with COVID-19 outbreak in a large convenience sample, setting a stage for longitudinal studies evaluating mental health trajectories following COVID-19 pandemic.

Human Trust in Artificial Intelligence: Review of Empirical Research

Abstract: Artificial intelligence (AI) characterizes a new generation of technologies capable of interacting with the environment and aiming to simulate human intelligence. The success of integrating AI into...

Properties and Astrophysical Implications of the 150 M Binary Black Hole Merger GW190521

Abstract: The gravitational-wave signal GW190521 is consistent with a binary black hole (BBH) merger source at redshift 0.8 with unusually high component masses, 85-14+21 M o˙ and 66-18+17 M o˙, compared to previously reported events, and shows mild evidence for spin-induced orbital precession. The primary falls in the mass gap predicted by (pulsational) pair-instability supernova theory, in the approximate range 65-120 M o˙. The probability that at least one of the black holes in GW190521 is in that range is 99.0%. The final mass of the merger (142-16+28 M o˙) classifies it as an intermediate-mass black hole. Under the assumption of a quasi-circular BBH coalescence, we detail the physical properties of GW190521's source binary and its post-merger remnant, including component masses and spin vectors. Three different waveform models, as well as direct comparison to numerical solutions of general relativity, yield consistent estimates of these properties. Tests of strong-field general relativity targeting the merger-ringdown stages of the coalescence indicate consistency of the observed signal with theoretical predictions. We estimate the merger rate of similar systems to be 0.13-0.11+0.30 Gpc-3 yr-1. We discuss the astrophysical implications of GW190521 for stellar collapse and for the possible formation of black holes in the pair-instability mass gap through various channels: via (multiple) stellar coalescences, or via hierarchical mergers of lower-mass black holes in star clusters or in active galactic nuclei. We find it to be unlikely that GW190521 is a strongly lensed signal of a lower-mass black hole binary merger. We also discuss more exotic possible sources for GW190521, including a highly eccentric black hole binary, or a primordial black hole binary.

Low plasma 25(OH) vitamin D level is associated with increased risk of COVID-19 infection: an Israeli population-based study.

Abstract: Vitamin D deficiency is a worldwide pandemic. The aim of this study was to evaluate associations of plasma 25(OH)D levels with the likelihood of coronavirus disease 2019 (COVID-19) infection and hospitalization. The study population included the 14 000 members of Leumit Health Services, who were tested for COVID-19 infection from February 1st to April 30th , 2020, and who had at least one previous blood test for the plasma 25(OH)D level. 'Suboptimal' or 'low' plasma 25(OH)D level was defined as plasma 25-hydroxyvitamin D, or 25(OH)D, concentration below the level of 30 ng/mL. Of 7807 individuals, 782 (10.02%) were COVID-19-positive, and 7025 (89.98%) COVID-19-negative. The mean plasma vitamin D level was significantly lower among those who tested positive than negative for COVID-19 [19.00 ng/mL1 (95% confidence interval (CI) 18.41-19.59) vs. 20.55 (95% CI: 20.32-20.78)]. Univariate analysis demonstrated an association between the low plasma 25(OH)D level and increased likelihood of COVID-19 infection [crude odds ratio (OR) of 1.58 (95% CI: 1.24-2.01, P < 0.001)], and of hospitalization due to the SARS-CoV-2 virus [crude OR of 2.09 (95% CI: 1.01-4.30, P < 0.05)]. In multivariate analyses that controlled for demographic variables, and psychiatric and somatic disorders, the adjusted OR of COVID-19 infection [1.45 (95% CI: 1.08-1.95, P < 0.001)] and of hospitalization due to the SARS-CoV-2 virus [1.95 (95% CI: 0.98-4.845, P = 0.061)] were preserved. In the multivariate analyses, age over 50 years, male gender and low-medium socioeconomic status were also positively associated with the risk of COVID-19 infection; age over 50 years was positively associated with the likelihood of hospitalization due to COVID-19. We concluded that low plasma 25(OH)D levels appear to be an independent risk factor for COVID-19 infection and hospitalization.

Charge-transfer materials for electrochemical water desalination, ion separation and the recovery of elements

Abstract: Reversible electrochemical processes are a promising technology for energy-efficient water treatment. Electrochemical desalination is based on the compensation of electric charge by ionic species, through which the ions are immobilized and, thereby, removed from a feed-water stream flowing through a desalination cell. For decades, electrochemical desalination has focused on the use of carbon electrodes, but their salt-removal ability is limited by the mechanism of ion electrosorption at low molar concentrations and low charge-storage capacity. Recently, charge-transfer materials, often found in batteries, have demonstrated much larger charge-storage capacities and energy-efficient desalination at both low and high molar strengths. In this Review, we assess electrochemical-desalination mechanisms and materials, including ion electrosorption and charge-transfer processes, namely, ion binding with redox-active polymers, ion insertion, conversion reactions and redox-active electrolytes. Furthermore, we discuss performance metrics and cell architectures, which we decouple from the nature of the electrode material and the underlying mechanism to show the versatility of cell-design concepts. These charge-transfer processes enable a wealth of environmental applications, ranging from potable-water generation and industrial-water remediation to lithium recovery and heavy-metal-ion removal. Electrochemical processes enable energy-efficient desalination of water and the separation and recovery of elements. In this Review, we discuss the mechanisms and materials of this emerging generation of water-remediation technology.

Towards Faithfully Interpretable NLP Systems: How Should We Define and Evaluate Faithfulness?

Abstract: With the growing popularity of deep-learning based NLP models, comes a need for interpretable systems. But what is interpretability, and what constitutes a high-quality interpretation? In this opinion piece we reflect on the current state of interpretability evaluation research. We call for more clearly differentiating between different desired criteria an interpretation should satisfy, and focus on the faithfulness criteria. We survey the literature with respect to faithfulness evaluation, and arrange the current approaches around three assumptions, providing an explicit form to how faithfulness is "defined" by the community. We provide concrete guidelines on how evaluation of interpretation methods should and should not be conducted. Finally, we claim that the current binary definition for faithfulness sets a potentially unrealistic bar for being considered faithful. We call for discarding the binary notion of faithfulness in favor of a more graded one, which we believe will be of greater practical utility.

oLMpics-On What Language Model Pre-training Captures

Abstract: Recent success of pre-trained language models (LMs) has spurred widespread interest in the language capabilities that they possess. However, efforts to understand whether LM representations are useful for symbolic reasoning tasks have been limited and scattered. In this work, we propose eight reasoning tasks, which conceptually require operations such as comparison, conjunction, and composition. A fundamental challenge is to understand whether the performance of a LM on a task should be attributed to the pre-trained representations or to the process of fine-tuning on the task data. To address this, we propose an evaluation protocol that includes both zero-shot evaluation (no fine-tuning), as well as comparing the learning curve of a fine-tuned LM to the learning curve of multiple controls, which paints a rich picture of the LM capabilities. Our main findings are that: (a) different LMs exhibit qualitatively different reasoning abilities, e.g., RoBERTa succeeds in reasoning tasks where BERT fails completely; (b) LMs do not reason in an abstract manner and are context-dependent , e.g., while RoBERTa can compare ages, it can do so only when the ages are in the typical range of human ages; (c) On half of our reasoning tasks all models fail completely. Our findings and infrastructure can help future work on designing new datasets, models and objective functions for pre-training.

Evaluating Models’ Local Decision Boundaries via Contrast Sets

Abstract: Standard test sets for supervised learning evaluate in-distribution generalization. Unfortunately, when a dataset has systematic gaps (e.g., annotation artifacts), these evaluations are misleading: a model can learn simple decision rules that perform well on the test set but do not capture the abilities a dataset is intended to test. We propose a more rigorous annotation paradigm for NLP that helps to close systematic gaps in the test data. In particular, after a dataset is constructed, we recommend that the dataset authors manually perturb the test instances in small but meaningful ways that (typically) change the gold label, creating contrast sets. Contrast sets provide a local view of a model’s decision boundary, which can be used to more accurately evaluate a model’s true linguistic capabilities. We demonstrate the efficacy of contrast sets by creating them for 10 diverse NLP datasets (e.g., DROP reading comprehension, UD parsing, and IMDb sentiment analysis). Although our contrast sets are not explicitly adversarial, model performance is significantly lower on them than on the original test sets—up to 25% in some cases. We release our contrast sets as new evaluation benchmarks and encourage future dataset construction efforts to follow similar annotation processes.

Null It Out: Guarding Protected Attributes by Iterative Nullspace Projection

Abstract: The ability to control for the kinds of information encoded in neural representation has a variety of use cases, especially in light of the challenge of interpreting these models. We present Iterative Null-space Projection (INLP), a novel method for removing information from neural representations. Our method is based on repeated training of linear classifiers that predict a certain property we aim to remove, followed by projection of the representations on their null-space. By doing so, the classifiers become oblivious to that target property, making it hard to linearly separate the data according to it. While applicable for multiple uses, we evaluate our method on bias and fairness use-cases, and show that our method is able to mitigate bias in word embeddings, as well as to increase fairness in a setting of multi-class classification.

Elevated rates of autism, other neurodevelopmental and psychiatric diagnoses, and autistic traits in transgender and gender-diverse individuals

Abstract: It is unclear whether transgender and gender-diverse individuals have elevated rates of autism diagnosis or traits related to autism compared to cisgender individuals in large non-clinic-based cohorts. To investigate this, we use five independently recruited cross-sectional datasets consisting of 641,860 individuals who completed information on gender, neurodevelopmental and psychiatric diagnoses including autism, and measures of traits related to autism (self-report measures of autistic traits, empathy, systemizing, and sensory sensitivity). Compared to cisgender individuals, transgender and gender-diverse individuals have, on average, higher rates of autism, other neurodevelopmental and psychiatric diagnoses. For both autistic and non-autistic individuals, transgender and gender-diverse individuals score, on average, higher on self-report measures of autistic traits, systemizing, and sensory sensitivity, and, on average, lower on self-report measures of empathy. The results may have clinical implications for improving access to mental health care and tailoring adequate support for transgender and gender-diverse individuals. It is unclear if rates of autism and other neurodevelopmental and psychiatric diagnoses are elevated in transgender and gender-diverse individuals compared to cisgender individuals. Here, the authors use data from five different large-scale datasets to identify elevated rates of autism diagnoses, diagnoses of other neurodevelopmental and psychiatric conditions, and elevated traits related to autism in transgender and gender-diverse individuals, compared to cisgender individuals.

The m6A epitranscriptome: transcriptome plasticity in brain development and function

Abstract: The field of epitranscriptomics examines the recently deciphered form of gene expression regulation that is mediated by type- and site-specific RNA modifications. Similarly to the role played by epigenetic mechanisms - which operate via DNA and histone modifications - epitranscriptomic modifications are involved in the control of the delicate gene expression patterns that are needed for the development and activity of the nervous system and are essential for basic and higher brain functions. Here we describe the mechanisms that are involved in the writing, erasing and reading of N6-methyladenosine, the most prevalent internal mRNA modification, and the emerging roles played by N6-methyladenosine in the nervous system.

A community-based transcriptomics classification and nomenclature of neocortical cell types

Abstract: To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.

Layered Cathode Materials for Lithium-Ion Batteries: Review of Computational Studies on LiNi1–x–yCoxMnyO2 and LiNi1–x–yCoxAlyO2

Abstract: At present the most successful rechargeable battery is the Li-ion battery, due to the small size, high energy density, and low reduction potential of Li. Computational materials science has become ...

Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers.

Abstract: Recent reports suggest that 10 to 30% of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) infected patients are asymptomatic and that viral shedding may occur before symptom onset. Therefore, there is an urgent need to increase diagnostic testing capabilities to prevent disease spread. We developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, which identifies all positive subjects within a set of samples using a single round of testing. Each sample is assigned into multiple pools using a combinatorial pooling strategy based on compressed sensing. We pooled sets of 384 samples into 48 pools, providing both an eightfold increase in testing efficiency and an eightfold reduction in test costs, while identifying up to five positive carriers. We then used P-BEST to screen 1115 health care workers using 144 tests. P- BEST provides an efficient and easy-to-implement solution for increasing testing capacity that can be easily integrated into diagnostic laboratories.

Equivalency of the diagnostic accuracy of the PHQ-8 and PHQ-9: A systematic review and individual participant data meta-analysis

Abstract: BACKGROUND: Item 9 of the Patient Health Questionnaire-9 (PHQ-9) queries about thoughts of death and self-harm, but not suicidality. Although it is sometimes used to assess suicide risk, most positive responses are not associated with suicidality. The PHQ-8, which omits Item 9, is thus increasingly used in research. We assessed equivalency of total score correlations and the diagnostic accuracy to detect major depression of the PHQ-8 and PHQ-9. METHODS: We conducted an individual patient data meta-analysis. We fit bivariate random-effects models to assess diagnostic accuracy. RESULTS: 16 742 participants (2097 major depression cases) from 54 studies were included. The correlation between PHQ-8 and PHQ-9 scores was 0.996 (95% confidence interval 0.996 to 0.996). The standard cutoff score of 10 for the PHQ-9 maximized sensitivity + specificity for the PHQ-8 among studies that used a semi-structured diagnostic interview reference standard (N = 27). At cutoff 10, the PHQ-8 was less sensitive by 0.02 (-0.06 to 0.00) and more specific by 0.01 (0.00 to 0.01) among those studies (N = 27), with similar results for studies that used other types of interviews (N = 27). For all 54 primary studies combined, across all cutoffs, the PHQ-8 was less sensitive than the PHQ-9 by 0.00 to 0.05 (0.03 at cutoff 10), and specificity was within 0.01 for all cutoffs (0.00 to 0.01). CONCLUSIONS: PHQ-8 and PHQ-9 total scores were similar. Sensitivity may be minimally reduced with the PHQ-8, but specificity is similar.

There is nothing new under the sun: ageism and intergenerational tension in the age of the COVID-19 outbreak.

Abstract: At the time of this writing, 203 countries and territories have been affected by the COVID-19 outbreak (Worldometer, 2020a). Older adults, in particular, are negatively impacted by this pandemic (Lipsitch et al., 2020). Current estimates suggest that the COVID-19 mortality rate stands at 15% for those over the age of 80, but 0 for those under the age of 10 (Worldometer, 2020b). Hence, there is no doubt that age poses a major risk for COVID-19 mortality. At the same time, there are incidental reports of centenarians, who recovered from COVID-19, and of younger adults, who have not (Coffey and Oransky, 2020; Lanese and Writer, 2020). Moreover, the prevalence of younger people infected by the virus is higher than that of older adults (Surveillances, 2020). Hence, age alone is likely an insufficient criterion for predicting the direct medical impact of the outbreak. In this commentary, I argue that the portrayal of all older adults as a homogenous, vulnerable group, rather than the use of a more refined discourse, which stresses the heterogeneity inherited in old age and the potential impact of the pandemic on society at large, has resulted in increased ageism and intergenerational tension, worldwide. Ageism is defined as stereotypes, prejudice, and discrimination toward people because of their age (Ayalon and Tesch-Römer, 2018; Officer and de la FuenteNúñez, 2018). Although ageism can be both positive and negative (Ayalon and Tesch-Römer, 2018), in the context of the COVID-19 outbreak, we have seen an out surge of negative manifestations of ageism. Intergenerational tension, characterized as conflict between people of different generations, also has been intensified as a result of the outbreak and has fuelled the response to the pandemic. It is argued here that the psychosocial implications of the COVID-19 pandemic exacerbate and oftentimes supersede its direct medical impact, which to date, has received a substantial amount of research attention (World Health Organization, 2020). From the get-go, the COVID-19 outbreak has been portrayed as “the problem of older adults” and a clear age division, separating young from old has been promoted (Zhou et al., 2020). In China, where the COVID-19 outbreak had started, the tension between the generations has been manifested in anger toward older adults because of the refusal of some older adults to wear face masks (Eckersley, 2020). This is consistent with the prediction that at times of scarce resources, symbolic threats, manifested in disputes over values and beliefs, intensify (Stephan and Stephan, 2017). Overtime, the public focus has shifted to financial donations made by poor older adults, who sacrificed their living in an effort to support the fight against the pandemic. Both in the case of face masks and in the case of financial donations, older adults were portrayed as a separate, homogenous group in society, defined by its chronological age. In the former example, older adults were seen as a threat to society, as they “selfishly” refused to conform to current societal practices. In the latter example, on the other hand, older adults were presented as a selfless, yet vulnerable group, which is willing to risk its own being in order to help society at large. In other countries, the division between young and old resulted in somewhat different manifestations, depending on the sociocultural background of the country and its ability to address the pandemic. In Israel, the Ministry of Defense had issued a statement that “the single most important insight : : : is to separate old people from young people. The single most lethal combination cocktail is when grandma meets her grandchild and hugs him” (Gross and TOI Staff, 2020). This statement explicitly argues for an age division between the generations and portrays intergenerational contact as THE problem. Following the same logic, in the UK, the first response to the outbreak was “business as usual.” In fact, the Prime Minister, Boris Johnson, had suggested that older adults over the age of 70 should self-isolate for a period of 4 months, while all other age groups continue as usual (Sparrow, 2020). A similar approach has been advocated in other countries, which had stressed the importance of socially isolating older adults, rather than the entire population (Armitage and Nellums, 2020). This approach was attributed to the fact that older adults already have their pensions and thus are not likely to be impacted financially by social isolation. International Psychogeriatrics: page 1 of 4© International Psychogeriatric Association 2020. This is anOpen Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. doi:10.1017/S1041610220000575

Risk factors for psychological distress during the COVID-19 pandemic in Israel: Loneliness, age, gender, and health status play an important role.

Abstract: Objective Research on the psychological toll of the COVID-19 pandemic is being conducted in various countries. This study aimed to examine risk factors for mental health problems among Israeli adults during this crisis. Methods A total of 204 participants took part in the study. They completed self-report questionnaires assessing perceived stress, anxiety, quality of life, and various questions related to quarantine, pre-existing health issues, and worries related to the virus. The study took place during the last two weeks of March 2020. Results The majority of participants reported relatively high levels of perceived stress and corona-related worries, but low levels of anxiety. Female gender, younger age, corona-related loneliness, and pre-existing chronic illness were all related to higher levels of psychological distress and lower levels of quality of life. Conclusions While considering the preliminary nature of these results, the current study highlights risk factors for psychological distress in light of the corona pandemic. Attention should be given to sociodemographic variables that were identified as related to psychological distress, as well as to the important role of loneliness, when screening and treating people during this crisis. More research is needed in order to fully understand the scope and correlates of psychological difficulties during these challenging times.

Break It Down: A Question Understanding Benchmark

Abstract: Understanding natural language questions entails the ability to break down a question into the requisite steps for computing its answer. In this work, we introduce a Question Decomposition Meaning Representation (QDMR) for questions. QDMR constitutes the ordered list of steps, expressed through natural language, that are necessary for answering a question. We develop a crowdsourcing pipeline, showing that quality QDMRs can be annotated at scale, and release the Break dataset, containing over 83K pairs of questions and their QDMRs. We demonstrate the utility of QDMR by showing that (a) it can be used to improve open-domain question answering on the HotpotQA dataset, (b) it can be deterministically converted to a pseudo-SQL formal language, which can alleviate annotation in semantic parsing applications. Last, we use Break to train a sequence-to-sequence model with copying that parses questions into QDMR structures, and show that it substantially outperforms several natural baselines.