Biology subjects

Pekar, J.

Publications and source records attributed to Pekar, J..

6 recordsLinked to original sources

bioRxiv2026

Retest Reliability of Task-related fMRI BOLD Signals during Sequential Decision Making

IntroductionFunctional magnetic resonance imaging (fMRI) is widely used to study neural processes of behavior, but evaluations of test-retest reliability (TRR) of task-related blood-oxygen-level-dependent (BOLD) responses are scarce for many cognitive tasks. Such information is particularly important for longitudinal and intervention research. The ability to learn associations between choices and outcomes across decision stages is crucial for daily behavior. We assessed the measurement reliability of behavioral performance and fMRI BOLD signals during value-based sequential decision making to evaluate the TRR of task-relevant regions for future research on non-invasive brain stimulations. MethodsTwenty healthy adults (22 to 40 years) completed two task-fMRI sessions, at least 2 weeks apart. During scanning, participants performed two variants of a three-stage Markov decision task with conditions varied in temporal contingency (immediate vs. delayed) and magnitude of choice outcomes (high vs. low). Both sessions were conducted under sham tDCS via a focal 3 x 1 montage targeting left dorsolateral prefrontal cortex (DLPFC). TRR was assessed using intraclass correlation coefficients (ICC) with a two-way mixed-effects consistency model for decision performance and task-related fMRI signals at voxel level and summarized in key regions defined by the extended Human Connectome Project atlas (HCPex). ResultsDecision performance was lower with delayed than immediate outcomes (p < 0.001). Higher outcome magnitude improved performance (p < 0.001). Decision performance increased across learning bins (p < 0.001). The behavioral TRR was in the moderate to good level (ICC(3,1) = 0.744 for accuracy; ICC(3,1) = 0.788 for reaction time). At the whole-brain level, contrasting brain activities in delayed with immediate condition revealed suprathreshold cluster peaks in several frontal-parietal (e.g., orbitofrontal, bilateral dorsolateral prefrontal, and medial parietal cortices) and striatal regions (e.g., bilateral putamen). Voxel-wise ICCs revealed variable but often moderate-to-good TRR across task-relevant regions, with stronger reliability in several striatal, orbitofrontal, and left dorsolateral prefrontal parcels, and more variable reliability across anterior cingulate and medial prefrontal parcels. ConclusionThese results from a 2-session tDCS sham-sham stimulation study establish the validity of using the three-stage Markov decision task in future studies about intervention effects on the frontal-parietal-striatal network.

neuroscience↗

bioRxiv2026

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age ([~]1,700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged [~]11,500-3,700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new insights to the genomic evolution and potential host adaptation of sheeppox virus. TeaserAncient viral genomes from manuscripts and teeth illuminate the evolutionary history of sheeppox virus.

genetics↗

bioRxiv2023

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

genomics↗

bioRxiv2021

A remote lecture series roadmap to equity, diversity, and inclusion in STEM

Disparities for women and minorities in science, technology, engineering, and math (STEM) careers have continued even amidst mounting evidence for the superior performance of diverse workforces. In response, we launched the Diversity and Science Lecture series, a cross-institutional platform where junior life scientists present their research and comment on equity, diversity, and inclusion in STEM. We characterize speaker representation from 79 profiles and investigate topic noteworthiness via quantitative content analysis of talk transcripts. Nearly every speaker discussed interpersonal support, and three-fifths of speakers commented on race or ethnicity. Other topics, such as sexual and gender minority identity, were less frequently addressed but highly salient to the speakers who mentioned them. We found that significantly co-occurring topics reflected not only conceptual similarity, such as terms for racial identities, but also intersectional significance, such as identifying as a Latina/Hispanic woman or Asian immigrant, and interactions between priorities and identities, including the heightened value of friendship to the LGBTQ community, which we reproduce using transcripts from an independent seminar series. Our approach to scholar profiles and talk transcripts serves as an example for transmuting hundreds of hours of scholarly discourse into rich datasets that can power computational audits of speaker diversity and illuminate speakers personal and professional priorities.

scientific communication and education↗

bioRxiv2020

Timing the SARS-CoV-2 Index Case in Hubei Province

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

evolutionary biology↗

bioRxiv2020

The emergence of SARS-CoV-2 in Europe and the US

Accurate understanding of the global spread of emerging viruses is critically important for public health response and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and the United States (US). Our results refute prior findings erroneously linking cases in January 2020 with outbreaks that occurred weeks later. Instead, rapid interventions successfully prevented onward transmission of those early cases in Germany and Washington State. Other, later introductions of the virus from China to both Italy and Washington State founded the earliest sustained European and US transmission networks. Our analyses reveal an extended period of missed opportunity when intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established in the US and Europe.

genetics↗