Showing papers by "San Francisco State University published in 2022"

Symmetry, Confinement, and the Higgs Phase

Abstract: We show that the Higgs and confinement phases of a gauge Higgs theory, with the Higgs field in the fundamental representation of the gauge group, are distinguished both by a broken or unbroken realization of the global center subgroup of the gauge group, and by the type of confinement in each phase. This is color confinement in the Higgs phase, and a stronger property, which we call “separation-of-charge” confinement, in the confining phase.

Matroid psi classes

Abstract: Motivated by the intersection theory of moduli spaces of curves, we introduce psi classes in matroid Chow rings and prove a number of properties that naturally generalize properties of psi classes in Chow rings of Losev-Manin spaces. We use these properties of matroid psi classes to give new proofs of (1) a Chow-theoretic interpretation for the coefficients of the reduced characteristic polynomials of matroids, (2) explicit formulas for the volume polynomials of matroids, and (3) Poincaré duality for matroid Chow rings.

Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs

Abstract: Abstract The dynamics of adaptation, reversion, and compensation have been central topics in microbial evolution, and several studies have attempted to resolve the population genetics underlying how these dynamics occur. However, questions remain regarding how certain features—the evolution of mutators and whether compensatory mutations alleviate costs fully or partially—may influence the evolutionary dynamics of compensation and reversion. In this study, we attempt to explain findings from experimental evolution by utilizing computational and theoretical approaches toward a more refined understanding of how mutation rate and the fitness effects of compensatory mutations influence adaptive dynamics. We find that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation is associated with a dramatically decreased probability of reversion to the wild type. These findings help to explain specific results from experimental evolution, where compensation was observed in nonmutator strains, but reversion (sometimes with compensation) was observed in mutator strains, indicating that real-world compensatory mutations are often unable to fully alleviate the costs associated with adaptation. Our findings emphasize the potential role of the supply and quality of mutations in crafting the dynamics of adaptation and reversal, with implications for theoretical population genetics and for biomedical contexts like the evolution of antibiotic resistance.

Host blood meal identity modifies vector gene expression and competency

Abstract: A vector's susceptibility and ability to transmit a pathogen—termed vector competency—determines disease outcomes, yet the ecological factors influencing tick vector competency remain largely unknown. Ixodes pacificus, the tick vector of Borrelia burgdorferi (Bb) in the western U.S., feeds on rodents, birds, and lizards. Rodents and birds are reservoirs for Bb and infect juvenile ticks, while lizards are refractory to Bb and cannot infect feeding ticks. Additionally, the lizard bloodmeal contains borreliacidal properties, clearing previously infected feeding ticks of their Bb infection. Despite I. pacificus feeding on a range of hosts, it is undetermined how the host identity of the larval bloodmeal affects future nymphal vector competency. We experimentally evaluate the influence of larval host bloodmeal on Bb acquisition by nymphal I. pacificus. Larval I. pacificus were fed on either lizards or mice and after molting, nymphs were fed on Bb-infected mice. We found that lizard-fed larvae were significantly more likely to become infected with Bb during their next bloodmeal than mouse-fed larvae. We also conducted the first RNA-seq analysis on whole-bodied I. pacificus and found significant upregulation of tick antioxidants and antimicrobial peptides in the lizard-fed group. Our results indicate that the lizard bloodmeal significantly alters vector competency and gene regulation in ticks, highlighting the importance of host bloodmeal identity in vector-borne disease transmission and upends prior notions about the role of lizards in Lyme disease community ecology.

Fungi of São Tomé and Príncipe Islands: Basidiomycete Mushrooms and Allies

Abstract: Abstract Mushrooms and allies belong to the Agaricomycetes lineage of Basidiomycota. A total of 260 species, belonging in 109 genera, 51 families and 13 orders have been reported from São Tomé and Príncipe between 1851 and 2020, of which 66 were described as new species. They range in body forms from agarics and boletes to polyporoid, clavarioid, coralloid, thelephoroid, stereoid, corticioid, hydnoid, cantherelloid, gasteroid, and jelly fungi. The vast majority are saprotrophs, a small number are plant pathogens, and a rare few may be ectomycorrhizal. Sixty species, 23%, can be classified putative endemics. The current state of knowledge of the Agaricomycetes from the nation is based on fewer than ten expeditions in the past 170 years and represents only a snapshot of the actual diversity that is likely present.

Novel RNA viruses associated with avian haemosporidian parasites

Abstract: Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect haemosporidian parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon . By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus . MaRNAV3 had ~59% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and ~63% amino acid identity to MaRNAV2. MaRNAV4 had ~44% amino acid identity to MaRNAV1 and ~47% amino acid identity to MaRNAV2. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax , and now two genera of avian haemosporidians.

A Fatal Attraction to Normalizing

Abstract: This chapter identifies and theorizes the sin of synecdoche: that of making a value judgment about a person on the basis of a single aspect of their identity. Asch and Wasserman are interested in how synecdoche factors into decisions to terminate pregnancies after the fetus is identified as having or being likely to develop some kind of disability. They argue that the sin of synecdoche involves a moral failing.

Evaluation of a Brief Stress Management Workshop for Incoming Nursing Students

Abstract: The purpose of this study was to evaluate the effectiveness of a brief stress management workshop on nursing students' perceived stress and resilience. Students who received the stress management intervention during orientation had significantly higher resilience scores and lower stress scores 1 year later during COVID-19 than the comparison group.

Anarchist Prophets

Abstract: In Anarchist Prophets James R. Martel juxtaposes anarchism with what he calls archism in order to theorize the potential for a radical democratic politics. He shows how archism—a centralized and hierarchical political form that is a secularization of ancient Greek and Hebrew prophetic traditions—dominates contemporary politics through a prophet’s promises of peace and prosperity or the threat of violence. Archism is met by anarchism, in which a community shares a collective form of judgment and vision. Martel focuses on the figure of the anarchist prophet, who leads efforts to regain the authority for the community that archism has stolen. The goal of anarchist prophets is to render themselves obsolete and to cede power back to the collective so as to not become archist themselves. Martel locates anarchist prophets in a range of philosophical, literary, and historical examples, from Hobbes and Nietzsche to Mary Shelley and Octavia Butler to Kurdish resistance in Syria and the Spanish Revolution. In so doing, Martel highlights how anarchist forms of collective vision and action can provide the means to overthrow archist authority.

Walking in the Ivory Tower: Differential Belonging and the Architexture of Home:

Abstract: Deploying Carrillo Rowe’s concept of differential belonging and extending McCune’s notion of architexture to encompass transnational sensory registers, affective valences and intensities, relationa...

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus

Abstract: Like many viruses, Hepatitis C Virus (HCV) has a high nutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be site and virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.

The Illusions of Time Passage: Why Time Passage Is Real

Abstract: The passage of time pertains to the dynamic happening of anticipated future events merging into a present actuality and subsequently becoming the past. Philosophers and scientists alike often endorse the view that the passage of time is an illusion. Here we instead account for the phenomenology of time passage as a real psycho-biological phenomenon. We argue that the experience of time passage has a real and measurable basis as it arises from an internal generative model for anticipating upcoming events. The experience of passage is not merely a representation by a passive recipient of sensory stimulation but is generated by predictive processes of the brain and proactive sensorimotor activity of the whole body. Although some philosophical approaches to time consider some psycho-biological evidence, the biological basis of the passage of time has not been examined in detail from a thorough scientific perspective. This paper proposes to remedy this omission.

What about hybrids? Supplemental methods for skeletal muscle fibre typing

Abstract: Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

A deficiency screen of the 3^rdchromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal

Abstract: Abstract The mechanism surrounding chromosome inheritance during cell division has been well documented, however, organelle inheritance during mitosis is less understood. Recently, the Endoplasmic Reticulum (ER) has been shown to reorganize during mitosis, dividing asymmetrically in proneuronal cells prior to cell fate selection, indicating a programmed mechanism of inheritance. ER asymmetric partitioning in proneural cells relies on the highly conserved ER integral membrane protein, Jagunal (Jagn). Knockdown of Jagn in the compound Drosophila eye displays a pleotropic rough eye phenotype in 48% of the progeny. To identify genes involved in Jagn dependent ER partitioning pathway, we performed a dominant modifier screen of the 3 rd chromosome for enhancers and suppressors of this Jagn RNAi-induced rough eye phenotype. We screened through 181 deficiency lines covering the 3L and 3R chromosomes and identified 12 suppressors and 10 enhancers of the Jagn RNAi phenotype. Based on the functions of the genes covered by the deficiencies, we identified genes that displayed a suppression or enhancement of the Jagn RNAi phenotype. These include Division Abnormally Delayed (Dally), an heparan sulfate proteoglycan, the γ-secretase subunit Presenilin, and the ER resident protein Sec63. Based on our understanding of the function of these targets, there is a connection between Jagn and the Notch signaling pathway. Further studies will elucidate the role of Jagn and identified interactors within the mechanisms of ER partitioning during mitosis.

In the Shadow of Mistrust

Abstract: Abstract Since the 1979 Iranian Revolution, the normalization of relations between Iran and America has appeared unrealistic if not inconceivable, given that the Iranian state has vigorously pursued an anti-American ideology. This account of US–Iranian relations examines the efficacy of external pressure such as sanctions, as well as domestic grassroots reform movements within the Islamic Republic. The Obama presidency marked a rare high point in the Washington–Tehran relationship, as negotiations between the two countries and other powers produced an unprecedented nuclear deal, the Joint Comprehensive Plan of Action. However, the Trump administration's unilateral withdrawal from the JCPOA, and re-imposition of new sanctions in pursuit of "maximum pressure", had devastating economic consequences, undermining the Iranian middle class, which has consistently been the voice of political moderation and supported Iran's integration into the global economy. Crucially, sanctions have also driven Iran further into the arms of China, while rendering it an even more recalcitrant and aggressive adversary. Monshipouri's central conviction is that negotiations are pivotal to dismantling the mistrust that has long characterised US–Iranian relations, and to seeking détente between Iran and its Arab neighbours--a critical priority, since gradual US withdrawal from the region is all but certain.

An Improved Harmony Search Approach for Block Placement for VLSI Design Automation

Abstract: Level of knowledge with the field for VLSI IC Design’s Placement and Routing and in the area of Wireless Communication is rapidly evolving; Hence the process designing in the above fields is critical to assimilate a higher quantity of computation elements or nodes into a very compact size in VLSI Area and also the same is applicable in Wireless Communications to cover more number of nodes in a specific area. Prior to completing the placement, the physical and technical arranging of the computation elements or nodes in the chip area is planned, which is nothing more than Placement step and analogous with coverage of nodes in Wireless communication. Floorplanning must be done properly for reduce given placement area in physical ICDie. The proposed work suggests an ImprovisedHarmonySearch-IHS Optimization Algorithm, which is an Sequential combination of the HarmonySearch (HS) Algorithm and the most effective Particle Swarm Optimization (PSO) Algorithm to achieve the major objective of the VLSI Placement approach and applicable to the field of Wireless Communication. The aim at this point is to reduce the gap between the standard area of the benchmark circuit to the obtained area of the corresponding benchmark circuit. The MATLAB code for the ImprovisedHarmonySearch-IHS Algorithm is recreated, and discoveries are tested for better inspection using standard MCNC, or North Carolina Microelectronics Center benchmark circuits and suggest to adopt the corresponding results to the area of Wireless communication.

Hobbes Reading Hobbes

Abstract: Abstract This chapter argues that Hobbes’s instructions for how to read a text can be applied to Hobbes’s own writings. When we do this, our reading changes from one in which we must obey the sovereign in all things to one in which individual interpretations are valued over and above one centralizing interpreter’s. Following an analogy that Hobbes himself made between the author and the reader of the text on the one hand and the sovereign and subject of the nation on the other, we see that the way Hobbes subverts his own textual authority has implications for the politics that his books promote as well.