Faculty/ Researcher Works: Recent submissions
Now showing items 41-60 of 3966
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Recommendations Emerging from Carbon Emissions Estimations of the Society for Neuroscience Annual MeetingThe annual Society for Neuroscience (SfN) meeting yields significant, measurable impacts that conflict with the environmental commitment of the Society and the Intergovernmental Panel on Climate Change (IPCC) recommendations to address the climate emergency (IPCC, 2018). We used 12,761 presenters’ origins, two online carbon calculators, and benchmark values to estimate 2018 meeting-related travel, event venue operations, and hotel accommodation emissions. Presenters’ conference travel resulted in between 17,298 and 8690 tons of atmospheric carbon dioxide (t CO2), with or without radiative forcing index factors. Over 92% of authors traveled by air and were responsible for >99% of total travel-related emissions. Extrapolations based on 28,691 registrants yielded between 69,592.60 metric tons of carbon dioxide equivalents (t CO2e) and 38,010.85 t CO2 from travel. Comparatively, authors’ and registrants’ hotel accommodation emissions equaled 429 and 965 t CO2e, whereas operation of the San Diego Convention Center equaled ∼107 t CO2e. We relate SfN meeting-related emissions to potential September Arctic Sea ice loss, labor productivity loss in lower-income equatorial countries, and future temperature-related deaths. We estimate emissions reductions of between 23% and 78% by incentivizing between 10% and 50% of the most distant registrants to attend virtually or connecting between two and seven in-person hubs virtually. Completely virtual meetings may yield a reduction of >99% relative to centralized in-person meetings and increase participation of women, queer and transgender scientists, and scientists from low- and middle-income countries. We strongly recommend adopting alternative meeting modes such as four or more in-person global hubs connected virtually by 2030 and fully virtual by 2050.
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The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygenThe origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1–0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43–2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2–1.5 Ga, with an even narrower core interval of 2.0–1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.
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Improving cellular phylogenies through the integrated use of mutation order and optimality principlesThe study of tumor evolution is being revolutionalized by single-cell sequencing technologies that survey the somatic variation of cancer cells. In these endeavors, reliable inference of the evolutionary relationship of single cells is a key step. However, single-cell sequences contain many errors and missing bases, which necessitate advancing standard molecular phylogenetics approaches for applications in analyzing these datasets. We have developed a computational approach that integratively applies standard phylogenetic optimality principles and patterns of co-occurrence of sequence variations to produce more expansive and accurate cellular phylogenies from single-cell sequence datasets. We found the new approach to also perform well for CRISPR/Cas9 genome editing datasets, suggesting that it can be useful for various applications. We apply the new approach to some empirical datasets to showcase its use for reconstructing recurrent mutations and mutational reversals as well as for phylodynamics analysis to infer metastatic cell migrations between tumors.
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Master Nian念法師 as the “Westerner”: Re-Establishing Orthodoxy in Chinese AbhidharmaSarvāstivāda Abhidharma treatises started to be carefully studied and commented on by monks in early medieval China with the translation of hṛdaya treatises, the *Aṣṭagrantha, and the *Vibhāṣas. However, with the “new” translations undertaken by Xuanzang and his clique, these were regarded as “old” translations and the thoughts of these scholars were gradually marginalized. Examining a doctrinal debate in Puguang’s Jushe lun ji, this article delves into the construction of authority by Xuanzang and his disciples in the field of Abhidharma. In this debate, Puguang criticizes Zhinian’s viewpoint solely based on its similarity with the view of “westerners” (xifang shi). The evidence Puguang presents is a quote from the newly translated *Mahavibhāṣa, which he uses to extol the value of Xuanzang’s “new” translation. It shows how Xuanzang and his team use the orthodoxy constructed by Kashmiri Vaibhāsikas to justify their own authority. Their success comes at a sacrifice of diversity of Abhidharma studies in China.
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Successful use of a phage endolysin for treatment of chronic pelvic pain syndrome/chronic bacterial prostatitisChronic prostatitis (CP) is a common inflammatory condition of the prostate that is estimated to effect 2%–10% of the world’s male population. It can manifest as perineal, suprapubic, or lower back pain and urinary symptoms occurring with either recurrent bacterial infection [chronic bacterial prostatitis (CBP)] or in the absence of evidence of bacterial infection [chronic pelvic pain syndrome (CPPS)]. Here, in the case of a 39 years-old CBP patient, we report the first successful use of a bacteriophage-derived muralytic enzyme (endolysin) to treat and resolve the disease. Bacteriological analysis of the patient’s prostatic secretion and semen samples revealed a chronic Enterococcus faecalis prostate infection, supporting a diagnosis of CBP. The patient’s E. faecalis strain was resistant to several antibiotics and developed resistance to others during the course of treatment. Previous treatment with multiple courses of antibiotics, bacteriophages, probiotics, and immunologic stimulation had failed to achieve long term eradication of the infection or lasting mitigation of the symptoms. A cloned endolysin gene, encoded by E. faecalis bacteriophage ϕEf11, was expressed, and the resulting gene product was purified to electrophoretic homogeneity. A seven-day course of treatment with the endolysin resulted in the elimination of the E. faecalis infection to below culturally detectable levels, and the abatement of symptoms to near normal levels. Furthermore, during the endolysin treatment, the patient experienced no untoward reactions. The present report demonstrates the effectiveness of an endolysin as a novel modality in managing a recalcitrant infection that could not be controlled by conventional antibiotic therapy.
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Habitat isolation interacts with top-down and bottom-up processes in a seagrass ecosystemHabitat loss is accelerating at unprecedented rates, leading to the emergence of smaller, more isolated habitat remnants. Habitat isolation adversely affects many ecological processes independently, but little is known about how habitat isolation may interact with ecosystem processes such as top-down (consumer-driven) and bottom-up (resource-driven) effects. To investigate the interactive influence of habitat isolation, resource availability and consumer distribution and impact on community structure, we tested two hypotheses using invertebrate and algal epibionts on temperate seagrasses, an ecosystem of ecological and conservation importance. First, we hypothesized that habitat isolation will change the structure of the seagrass epibiont community, and isolated patches of seagrass will have lower epibiont biomass and different epibiont community composition than contiguous meadows. Second, we hypothesized that habitat isolation would mediate top-down (i.e., herbivory) and bottom-up (i.e., nutrient enrichment) control for algal epibionts. We used observational studies in natural seagrass patches and experimental artificial seagrass to examine three levels of habitat isolation. We further manipulated top-down and bottom-up processes in artificial seagrass through consumer reductions and nutrient additions, respectively. We indeed found that habitat isolation of seagrass patches decreased epibiont biomass and modified epibiont community composition. This pattern was largely due to dispersal limitation of invertebrate epibionts that resulted in a decline in their abundance and richness in isolated patches. Further, habitat isolation reduced consumer abundances, weakening top-down control of algal epibionts in isolated seagrass patches. Nutrient additions, however, reversed this pattern, and allowed a top-down effect on algal richness to emerge in isolated habitats, demonstrating a complex interaction between patch isolation and top-down and bottom-up processes. Habitat isolation may therefore shape the relative importance of central processes in ecosystems, leading to changes in community composition and food web structure in marine habitats.
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Disparities in sport participation of transgender women: a systematic and scoping review protocolIntroduction: Transgender women experience disparities in sport participation that are exacerbated by policies from sport organisations and legislation in the USA regulating the participation of transgender women in the category that best aligns with their gender identity. Both transgender and cisgender women are affected by these policies because sport organisations do not have a clear understanding of the effects of gender-affirming hormone therapy on transgender women and the unfair advantage they may have over cisgender women athletes. This article describes a review protocol to understand disparities in sport participation of transgender women. Methods and analysis: A systematic and scoping review is being conducted. Studies are included if they explore disparities in sport participation (ie, participation rates, real and/or perceived barriers to participation) of transgender women of any age. A search strategy has been developed for PubMed, EMBASE, Web of Science, Cochrane Library and CINAHL. Relevant grey literature will also be scanned. The planned search dates are July and August 2023. Ethics and dissemination: This review does not directly involve human subjects, so ethical approval is not required. Findings from the systematic review will be disseminated via publications in peer-reviewed journals and conferences.
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Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse LearningPhylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
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Human HspB1, HspB3, HspB5 and HspB8: Shaping these disease factors during vertebrate evolutionSmall heat shock proteins (sHSPs) emerged early in evolution and occur in all domains of life and nearly in all species, including humans. Mutations in four sHSPs (HspB1, HspB3, HspB5, HspB8) are associated with neuromuscular disorders. The aim of this study is to investigate the evolutionary forces shaping these sHSPs during vertebrate evolution. We performed comparative evolutionary analyses on a set of orthologous sHSP sequences, based on the ratio of non-synonymous: synonymous substitution rates for each codon. We found that these sHSPs had been historically exposed to different degrees of purifying selection, decreasing in this order: HspB8 > HspB1, HspB5 > HspB3. Within each sHSP, regions with different degrees of purifying selection can be discerned, resulting in characteristic selective pressure profiles. The conserved α-crystallin domains were exposed to the most stringent purifying selection compared to the flanking regions, supporting a 'dimorphic pattern' of evolution. Thus, during vertebrate evolution the different sequence partitions were exposed to different and measurable degrees of selective pressures. Among the disease-associated mutations, most are missense mutations primarily in HspB1 and to a lesser extent in the other sHSPs. Our data provide an explanation for this disparate incidence. Contrary to the expectation, most missense mutations cause dominant disease phenotypes. Theoretical considerations support a connection between the historic exposure of these sHSP genes to a high degree of purifying selection and the unusual prevalence of genetic dominance of the associated disease phenotypes. Our study puts the genetics of inheritable sHSP-borne diseases into the context of vertebrate evolution.
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To go or not to go: multiple identities and the effects of ambivalenceThis study unpacks how a person’s multiple identities affect their decision making when selecting a tourism destination. We propose that different aspects of identity yield distinct yet competing emotions. For instance, perceived social audience admiration combined with animosity might produce ambivalence, leading to greater decision-making uncertainty. Findings show that tourists with greater ambivalence towards particular destination countries are more likely to cancel or postpone their travel decisions. Additionally, the destination country’s economic development and a tourist’s pursuit of material happiness interact as moderators in the relationships between identities, emotions, and travel intention. Recommendations are provided for tourism product development and marketing communications for destination countries.
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Updated QCD global analysis of single transverse-spin asymmetries: Extracting ˜H, and the role of the Soffer bound and lattice QCDWe present an update to the QCD global analysis of single transverse-spin asymmetries presented in [J. Cammarota et al. (Jefferson Lab Angular Momentum Collaboration), Phys. Rev. D 102, 054002 (2020).] (JAM3D-20). JAM3D-20 simultaneously included transverse momentum dependent and collinear twist-3 observables, both of which are sensitive to quark-gluon-quark correlations in hadrons. In this study we extract for the first time the twist-3 chiral odd fragmentation function ˜H by incorporating the sinϕs modulation data from semi-inclusive deep-inelastic scattering along with its contribution to the single transverse-spin asymmetry in pion production from proton-proton collisions. We also explore the impact of lattice QCD tensor charge calculations and the Soffer bound on our global analysis. We find that both constraints can be accommodated within our results, with ˜H playing a key role in maintaining agreement with the data from proton-proton collisions.
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Context-dependent amygdala-prefrontal connectivity in youths with autism spectrum disorderBackground: The amygdala-prefrontal cortex circuit is involved in processing socio-emotional cues and may partially mediate social impairment in autism spectrum disorder (ASD). Past task-based fMRI studies in ASD indicate a mix of hypo- and hyper-connectivity in response to socio-emotional stimuli whereas resting state studies report hypoconnectivity between these regions. However, it is still unknown whether ASD-related alterations in amygdala-prefrontal circuitry are present across socio-emotional tasks and resting state contexts within the same sample or instead, depend on context. Method: ASD (n = 47) and typically developing individuals (TD; n = 72) underwent fMRI during an implicit emotional face processing task and during rest, and whole-brain amygdala connectivity was calculated to determine patterns that differed by context and diagnosis. Results: Relative to TD, the ASD group demonstrated weaker left amygdala connectivity with the medial frontal gyrus and the left superior frontal gyrus during rest, but stronger connectivity during task. Furthermore, across both contexts, ASD vs. TD had stronger right amygdala connectivity with the left insula/superior temporal gyrus. Conclusion: Findings suggest some alterations in amygdala connectivity of ASD may depend on context while others are pervasive across task and rest conditions. Understanding context-dependent brain alterations in ASD may help disambiguate the mechanisms subserving social impairment and provide targets for treatment.
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Studies of the symmetric binding mode of daclatasvir and analogs using a new homology model of HCV NS5A GT-4aContext: Egypt has a high prevalence of the hepatitis C virus (HCV) genotype 4a (GT-4a). Unfortunately, the high resistance it exhibited still was not given the deserved attention in the scientific community. There is currently no consensus on the NS5A binding site because the crystal structure of HCV NS5A has not been resolved. The prediction of the binding modes of direct-acting antivirals (DAA) with the NS5A is a point of controversy due to the fact that several research groups presented different interaction models to elucidate the NS5A binding site. Consequently, a 3D model of HCV NS5A GT-4a was constructed and evaluated using molecular dynamics (MD) simulations. The generated model implies an intriguing new orientation of the AH relative to domain I. Additionally, the probable binding modes of marketed NS5A inhibitors were explored. MD simulations validated the stability of the predicted protein–ligand complexes. The suggested model predicts that daclatasvir and similar drugs bind symmetrically to HCV NS5A GT-4a. This will allow for the development of new NS5A-directed drugs, which may result in reduced resistance and/or a wider range of effectiveness against HCV. Methods: The 3D model of HCV NS5A GT-4a was constructed using the comparative modeling approach of the web-based application Robetta. Its stability was tested with 200-ns MD simulations using the Desmond package of Schrodinger. The OPLS2005 force field was assigned for minimization, and the RMSD, RMSF, and rGyr were tracked throughout the MD simulations. Fpocket was used to identify druggable protein pockets (cavities) over the simulation trajectories. The binding modes of marketed NS5A inhibitors were then generated and refined with the aid of docking predictions made by FRED and AutoDock Vina. The stability of these drugs in complex with GT-4a was investigated by using energetic and structural analyses over MD simulations. The Prime MM-GBSA (molecular mechanics/generalized Born surface area) method was used as a validation tool after the docking stage and for the averaged clusters after the MD simulation stage. We utilized PyMOL and VMD to visualize the data.
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ATHENA detector proposal — a totally hermetic electron nucleus apparatus proposed for IP6 at the Electron-Ion ColliderATHENA has been designed as a general purpose detector capable of delivering the full scientific scope of the Electron-Ion Collider. Careful technology choices provide fine tracking and momentum resolution, high performance electromagnetic and hadronic calorimetry, hadron identification over a wide kinematic range, and near-complete hermeticity. This article describes the detector design and its expected performance in the most relevant physics channels. It includes an evaluation of detector technology choices, the technical challenges to realizing the detector and the R&D required to meet those challenges.
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Burkhardt-Cottingham-type sum rules for light-cone and quasi-PDFsThe Burkhardt-Cottingham (BC) sum rule connects the twist-3 light-cone parton distribution function (PDF) gT(x) to the twist-2 helicity PDF g1(x). The chiral-odd counterpart of the BC sum rule relates the twist-3 light-cone PDF hL(x) to the twist-2 transversity PDF h1(x). These BC-type sum rules can also be derived for the corresponding quasi-PDFs. We perform a perturbative check of the BC-type sum rules in the quark target model and the Yukawa model, by going beyond the ultraviolet (UV) divergent terms. We employ dimensional regularization (DR) and cutoff schemes to regulate UV divergences, and show that the BC-type sum rules hold for DR, while they are generally violated when using a cutoff. This violation can be traced back to the breaking of rotational invariance. We find corresponding results for the sum rule relating the mass of the target to the twist-3 PDF e(x). Moreover, we supplement our analytical results with numerical calculations.
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How bad is crime for business? Evidence from consumer behaviorUnderstanding how consumers respond to crime offers evidence of how safety perception impacts individuals daily choices and has important implications for economic development of communities. This paper investigates the impact of local crime on subsequent consumer visits to food and entertainment retails using a novel longitudinal dataset with point-specific crime and consumer visit data. We leverage the richness of our data to account for unobserved heterogeneity and time variant confounders through temporal and geographical variation. Our results show that consumers respond more strongly to property and street crimes. The response concentrates on the venue visit decision rather than the intensity of consumption (i.e. duration) in the venue.
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The geographical dispersion of inventor networks in peripheral economiesIn this paper we explore patenting activity in two peripheral economies (Portugal and Greece), to analyze the dispersion of inventor networks. Inventor networks are key conduits through which knowledge flows. Therefore, they can be critical in the catch-up process of peripheral economies – economies that belong to the group of rich countries but have weaker innovation systems. As global value chains fragment into geographically dispersed activities, opportunities arise for peripheral economies to participate in global innovation processes. However, different types of innovation activities have distinct network properties. More codifiable innovative activities can be carried out through collaboration by internationally dispersed teams. On the other hand, activities that are more dependent on tacit knowledge are likely to require the co-location of knowledge workers. This implies that innovation that relies mostly on tacit knowledge will provide limited connectivity benefits for peripheral economies’ innovation systems. We hypothesize that, while this is generally true, “leading” innovative multinational enterprises may possess more sophisticated capabilities for transnational collaboration than less innovative firms. Therefore, innovation in activities involving tacit knowledge may show different network characteristics depending on who performs them: leading firms or “laggards”. Our results, based on data from Portugal and Greece are consistent with our hypotheses.
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Modeling of Dynamic Mechanical Response of Li-Ion cells with Homogenized Electrolyte-Solid InteractionsSeveral recent studies have revealed substantial strain-rate dependence of lithium-ion batteries subjected to dynamic mechanical loadings. This behavior has been shown to be strongly dependent on the cell type, geometry, and setting. While still far from being fully understood, this dependence is believed to be connected to the solid-liquid interactions between the porous solid materials inside the electrodes and separators and the liquid electrolyte. This understanding has been supported by tests on dry cells revealing a significantly simpler behavior, being determined primarily by the constitutive material properties as compared to wet cells. This paper provides a modeling approach for the fluid-solid interaction inside battery cells by utilizing a pore fluid movement feature originally developed for geo-materials. By applying this module to the dry cell structure, the essentials of the peculiar load displacement patterns observed with active cells could be reproduced for two types of cells, a prismatic and a pouch cell. It is believed that this procedure, elucidating the underlying physics, and yet being simple, effective, and less time consuming than potential alternative techniques, will be exceedingly useful for evaluating crash behavior of electric vehicles. It allows making realistic calculations feasible based on experiments performed only on dry cells quasi-statically.
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Effects of Intimate Partner Violence During COVID-19 and Pandemic-Related Stress on the Mental and Physical Health of Women VeteransBackground: Little is known about women veterans’ intimate partner violence (IPV) experiences during the COVID-19 pandemic or the impacts of pandemic-related stress on their mental and physical health. Objectives: To identify IPV experiences among women veterans prior to and during the pandemic, pandemic-related stressors, and examine their respective contributions to mental and physical health. Design: National sample of women veterans drawn from a larger web-based longitudinal study. Relationships between recent IPV and pandemic-related stressors were tested with linear regressions, controlling for pre-pandemic IPV and mental and physical health symptoms, demographic, and military-related covariates. Participants: One hundred forty-two women veterans (Mage=58.8 years). Main Measures: We assessed IPV (CTS-2), PTSD (PCL-5), depression (CESD), anxiety (DASS-A), physical health (PHQ-15), and physical health–related quality of life (SF-12) prior to the pandemic (June 2016–December 2016/January 2017) and during the pandemic study period (March 2020–December 2020/January 2021). We assessed pandemic-related stressors (EPII) during the pandemic study period. Key Results: Over a third (38.7%) of participants experienced IPV during the pandemic study period (psychological: 35.9%, physical: 9.9%, sexual: 4.2%). Overall rates, frequency, and severity of IPV experience did not significantly differ between the pre-pandemic and pandemic study periods. Few participants tested positive for COVID-19 (4.2%); however, most participants reported experiencing pandemic-related stressors across life domains (e.g., social activities: 88%, physical health: 80.3%, emotional health: 68.3%). IPV during the pandemic and pandemic-related stressors were both associated with greater PTSD and depressive symptoms. Pandemic-related stressors were associated with worse anxiety and physical health symptoms. Neither IPV during the pandemic nor pandemic-related stressors were associated with physical health–related quality of life. Conclusions: IPV experiences during the pandemic were common among women veterans, as were pandemic-related stressors. Although IPV did not increase in the context of COVID-19, IPV experiences during the pandemic and pandemic-related stressors were linked with poorer mental and physical health.
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First Measurement of High-Energy Reactor Antineutrinos at Daya BayThis Letter reports the first measurement of high-energy reactor antineutrinos at Daya Bay, with nearly 9000 inverse beta decay candidates in the prompt energy region of 8–12 MeV observed over 1958 days of data collection. A multivariate analysis is used to separate 2500 signal events from background statistically. The hypothesis of no reactor antineutrinos with neutrino energy above 10 MeV is rejected with a significance of 6.2 standard deviations. A 29% antineutrino flux deficit in the prompt energy region of 8–11 MeV is observed compared to a recent model prediction. We provide the unfolded antineutrino spectrum above 7 MeV as a data-based reference for other experiments. This result provides the first direct observation of the production of antineutrinos from several high-Qβ isotopes in commercial reactors.
