bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic control of a sex-specific piRNA program
Authors: Chen Peiwei , Aravin Alexei A. 
Published: October 2022

AbstractSexually dimorphic traits in morphologies are widely studied, but those in essential molecular pathways remain largely unexplored. Previous work showed substantial sex differences inDrosophilagonadal piRNAs, which guide PIWI proteins to silence selfish genetic elements thereby safeguarding fertility. However, the genetic control mechanisms of piRNA sexual dimorphism remain unknown. Here, we showed that most sex differences in the piRNA program originate from the germline rather than gonadal somatic cells. Building on this, we dissected the contribution of sex chromosome and cellular sexual identity towards the sex-specific germline piRNA program. We found that the presence of the Y chromosome is sufficient to recapitulate some aspects of the male piRNA program in a female cellular environment. Meanwhile, sexual identity controls the sexually divergent piRNA production from X-linked and autosomal loci, revealing a crucial input from sex determination into piRNA biogenesis. Sexual identity regulates piRNA biogenesis through Sxl and this effect is mediated in part through chromatin proteins Phf7 and Kipferl. Together, our work delineated the genetic control of a sex-specific piRNA program, where sex chromosome and sexual identity collectively sculpt an essential molecular trait.
One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression inSaccharomyces cerevisiae
Authors: Hammer Staci E. , Polymenis Michael 
Published: October 2022

ABSTRACTEnzymes of one-carbon metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of one-carbon metabolism. Here, we report that the levels of theS. cerevisiaeenzymes Ade17p and Cho2p, involved in thede novosynthesis of purines and phosphatidylcholine, respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies one-carbon units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize phosphatidylcholinede novoincho2Δcells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome,cho2Δcells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that one-carbon metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
Ecological effects of genome size in yellow starthistle (Centaurea solstitialis) vary between invaded and native ranges
Authors: Cang F. Alice , Dlugosch Katrina M. 
Published: October 2022

AbstractInvasive species have become a pervasive threat on every continent and across a broad array of environments. Several traits predicted to promote invasion success, such as small seed size, rapid vegetative growth and short time to reproduction, are correlated with smaller genome sizes in a number of systems. To understand the influence of genome size on plant invasion dynamics, we compared genome sizes and traits inCentaurea solstitialis(YST) genotypes from the Californian invasion to those from their native source region in Spain. We conducted a common garden experiment and genome size survey to ask: (1) Is the invasion associated with genome size reduction? (2) To what extent can differences in genome size explain previously observed increases in plant size and reproduction in YST invasions? (3) Finally, we tested for expected evolutionary patterns in genome size across populations, including evidence of selection favouring reduced genome sizes at higher elevations, and evidence of stochastic processes leading to increases in genome sizes where effective population sizes are smaller. We found a reduction in corrected genome size in the invaded range, as well as significant interaction effects of range x elevation on genome size, and range x genome size on flowering time variation. Specifically, larger genomes tended to flower later and genome size decreased with increasing elevation in the invasion only. These emergent relationships in invading YST suggest potential selection for smaller genomes following introduction of YST to its invaded range. We also found a significant effect of measurement date on genome size estimation by flow cytometry, and this effect was more pronounced among native range genotypes.
Maximization of Energy Recovery from Starch Processing Wastewater by Thermophilic Dark Fermentation Coupled with Microbial fuel Cell Technology
Authors: Kumar Mohit , Pandit Soumya , Patel Vinay , Das Debabrata 
Published: October 2022

AbstractUtilization of organic wastewater for hydrogen production has dual advantages of clean energy generation and bioremediation which is sustainable for a longer period. To maximize the energy recovery from starch rich wastewater, a two stage system comprising of thermophilic dark fermentation coupled with microbial fuel cell was employed. A single parameter optimization strategy was implemented for the operation of the batch system. The maximum cumulative hydrogen production obtained was 2.56 L L−1with a 48 % reduction in COD under the optimal conditions of 35 g L−1initial substrate concentration (COD), temperature 60oC, and pH 6.5. The H2yield and H2production rate were 6.8 mol H2/kg CODreducedand 731.3 mL L−1h−1respectively. The effect of the organic loading rate (OLR) on H2production rate was studied in a continuous stirred tank reactor (CSTR). A maximum hydrogen production rate of 913 mL L−1h−1was observed at an OLR of 5.6 g L− 1h−1. Effluent recycle played an important role in the improvement of H2production. A maximum H2production rate of 1224 mL L−1h−1was observed at a recycle ratio of 0.6. Power density of 4.2 W m−3was observed with MFC using the dark fermentative spent media neutralized with carbonate buffer at an optimal pH of 7. A total COD reduction of 86% was observed.
Subcortical Auditory Model including Efferent Dynamic Gain Control with Inputs from Cochlear Nucleus and Inferior Colliculus
Authors: Farhadi Afagh , Jennings Skyler G. , Strickland Elizabeth A. , Carney Laurel H. 
Published: October 2022

AbstractWe developed an auditory model with a time-varying, gain-control signal based on the physiology of the efferent system and the sub-cortical neural pathways. The medial olivocochlear (MOC) efferent stage of the model receives excitatory projections from both fluctuation-sensitive model neurons of the inferior colliculus (IC) and wide-dynamic-range model neurons of the cochlear nucleus. The response of the model MOC stage dynamically controls cochlear gain via simulated outer hair cells. In response to amplitude-modulated (AM) noise, firing rates of most IC neurons with band-enhanced modulation transfer functions in awake rabbits increase over a time course consistent with the dynamics of the MOC efferent feedback. These changes in the rates of IC neurons in awake rabbits were employed to adjust the parameters of the efferent stage of the proposed model. Responses of the proposed model to AM noise were able to simulate the increasing IC rate over time, while the model without the efferent system did not show this trend. The proposed model with efferent gain control provides a powerful tool for testing hypotheses, shedding insight on mechanisms in hearing, specifically those involving the efferent system.
Phosphate Starvation Signaling Increases Mitochondrial Membrane Potential through Respiration-independent Mechanisms
Authors: Ouyang Yeyun , Cunningham Corey N. , Berg Jordan A. , Toshniwal Ashish G. , Hughes Casey E. , Van Vranken Jonathan G. , Jeong Mi-Young , Cluntun Ahmad A. , Lam Geanette , Winter Jacob M. , Akdoǧan Emel , Dove Katja K. , Gygi Steven P. , Dunn Cory D , Winge Dennis R , Rutter Jared 
Published: October 2022

AbstractMitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of the mitochondrial membrane potential is also observed in primary and immortalized mammalian cells as well as inDrosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial functions even with defective mitochondria.
Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID-19
Authors: Aguilar Ricardo , López-Verges Sandra , Quintana Anarellys , Morris Johanna , Lopez Lineth , Cooke Ana , Quiel Dimas , Buitron Natalie , Pérez Yaseikiry , Lobo Lesbia , Ballesteros Maura , Pitti Yaneth , Diaz Yamilka , Saenz Lisseth , Franco Danilo , Castillo Daniel , Valdespino Elimelec , Blanco Isabel , Romero Emilio , Cubilla-Batista Idalina , Villarreal Alcibiades 
Published: October 2022

AbstractAt the beginning of the SARS-CoV-2 pandemic, transfusion of COVID-19 convalescent plasma (CCP) was considered as one of the possibilities to help severe patients to overcome COVID-19 disease. The use of CCP has been controversial as its effectiveness depends on many variables from the plasma donor and the COVID-19 patient, for example, time of convalescence or symptoms onset. This was a feasibility study assessing the safety of multiple doses of CCP in mechanically ventilated intubated patients with respiratory failure due to COVID-19. Thirty (30) patients with severe respiratory failure, in ICU, with invasive mechanical ventilation received up to 5 doses of 300 to 600 ml of CP on alternate days (0,2,4,6 and 8) until extubation, futility, or death. Nineteen patients received five doses, seven received four, and four had 2 or 3 doses. On day 28 of follow-up, 57% of patients recovered and were at home and the long-term mortality observed was 27%. The ten severe adverse events reported in the study were unrelated to CCP transfusion. This study suggests that transfusion of multiple doses of convalescent plasma (CP) is safe. This strategy may represent an option to use in new studies, given the potential benefit of CCP transfusions in the early stage of infection in unvaccinated populations and in settings where monoclonal antibodies or antivirals are contraindicated or not available.Summary boxTransfusion of multiple doses (up to 5 doses) of 300-600 ml of convalescent plasma from COVID-19 recovered patients is safe as it does not induce more severe effects than a single dose.Independent of the number of transfused doses, most patients had detectable levels of total and neutralizing antibodies in plasma.Future studies are needed to determine if multiple transfusion doses are more efficient in preventing severity than a single dose.
The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya
Authors: Githinji George , Lambisia Arnold W. , Omah Ifeanyi , O’Toole Aine , Mohamed Khadija Said , de Laurent Zaydah R. , Makori Timothy O. , Mwanga Mike , Mburu Maureen W. , Morobe John M. , Ong’era Edidah M. , Ndwiga Leonard , Gathii Kimita , Thiongo Kelvin , Omuoyo Don Williams O. , Chepkorir Edith , Musyoki Jennifer , Kingwara Leonard , Matoke Damaris , Oyola Samuel O. , Onyango Clayton , Waitumbi John , Bulimo Wallace , Khamadi Samoel , Kiiru John N. O. , Kinyanjui Samson , Cotten Matthew , Tsofa Benjamin , Ochola-Oyier Isabella , Rambaut Andrew , Nokes D. James , Bejon Philip , Agoti Charles 
Published: October 2022

AbstractThe emergence and establishment of SARS-CoV-2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS-CoV-2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wild-type virus. We estimate that more than 1000 SARS-CoV-2 introductions occurred in the two-year epidemic period (March 2020 – September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy.
Programmatic Effectiveness of a Pediatric Typhoid Conjugate Vaccine Campaign in Navi Mumbai, India
Authors: Hoffman Seth A. , LeBoa Christopher , Date Kashmira , Haldar Pradeep , Harvey Pauline , Shimpi Rahul , An Qian , Zhang Chenhua , Jayaprasad Niniya , Horng Lily , Fagerli Kirsten , Borhade Priyanka , Chakraborty Debjit , Bahl Sunil , Katkar Arun , Kunwar Abhishek , Yewale Vijay , Andrews Jason R. , Bhatnagar Pankaj , Dutta Shanta , Luby Stephen P. 
Published: October 2022

ABSTRACTBackgroundThe WHO recommends vaccines for prevention and control of typhoid fever, especially where antimicrobial-resistant typhoid circulates. In 2018 the Navi Mumbai Municipal Corporation (NMMC), implemented a TCV campaign. The campaign targeted all children aged 9-months through 14-years within NMMC boundaries (∼320,000 children) over 2 vaccination phases. The phase 1 campaign occurred from July 14-August 25, 2018 (71% coverage, ∼113,420 children). We evaluated the campaign’s programmatic effectiveness in reducing typhoid cases at the community level.MethodsWe established prospective, blood culture-based surveillance at 6 hospitals in Navi Mumbai, offering blood cultures to children presenting with fever for at least 3 days. We employed a cluster-randomized test-negative design to estimate the effectiveness of the vaccination campaign on pediatric typhoid cases. We matched culture-confirmed typhoid cases with up to 3 culture-negative controls by age and date of blood culture and assessed community vaccine campaign phase as an exposure using conditional logistic regression.ResultsBetween September 1, 2018–March 31, 2021, we identified 81 typhoid cases and matched these with 238 controls. Cases were 0.44 times as likely to live in vaccine campaign communities (campaign effectiveness, 56%, 95%CI: 25%-74%, p=0.002). Cases ≥ 5-years-old were 0.37 times as likely (95% CI: 0.19-0.70; p-value = 0.002) and cases during the first year of surveillance were 0.30 times as likely (95% CI: 0.14-0.64; p-value = 0.002) to live in vaccine campaign communities.ConclusionsOur findings support the use of TCV mass vaccination campaigns as effective population-based tools to combat typhoid fever.SummaryIn 2018, the Navi Mumbai Municipal Corporation conducted a typhoid conjugate vaccine campaign in half of its communities. Utilizing a test-negative design, we estimate that this campaign reduced typhoid risk by 56% (25-74%) in vaccinated communities compared to non-campaign communities.
Parkinson’s disease impairs cortical sensori-motor decision-making cascades
Authors: Tomassini A. , Cope T. E. , Zhang J. , Rowe J. B. 
Published: October 2022

AbstractThe transformation from perception to action requires a set of decisions about the nature of the percept, identification and selection of response options, and execution of the appropriate motor response. The unfolding of such decisions is mediated by distributed representations of the decision variables - evidence and intentions – that are represented through oscillatory activity across the cortex. Here we combine magneto-electroencephalography and linear ballistic accumulator models of decision-making to reveal the impact of Parkinson’s disease during the selection and execution of action. We used a visuomotor task in which we independently manipulated uncertainty in sensory and action domains. A generative accumulator model was optimized to single-trial neurophysiological correlates of human behaviour, mapping the cortical oscillatory signatures of decision-making, and relating these to separate processes accumulating sensory evidence and selecting a motor action. We confirmed the role of widespread beta oscillatory activity in shaping the feed-forward cascade of evidence accumulation from resolution of sensory inputs to selection of appropriate responses. By contrasting the spatiotemporal dynamics of evidence accumulation in age-matched healthy controls and people with Parkinson’s disease, we identified disruption of the beta-mediated cascade of evidence accumulation as the hallmark of atypical decision-making in Parkinson’s disease. In frontal cortical regions, there was inefficient processing and transfer of perceptual information. Our findings emphasize the intimate connection between abnormal visuomotor function and pathological oscillatory activity in neurodegenerative disease. We propose that disruption of the oscillatory mechanisms governing fast and precise information exchanges between the sensory and motor systems contributes to behavioural changes in people with Parkinson’s disease.
Impact of COVID-19 related maternal stress on fetal brain development: A Multimodal MRI study
Authors: Rajagopalan Vidya , Reynolds William T. , Zepeda Jeremy , Lopez Jeraldine , Ponrartana Skorn , Wood John , Ceschin Rafael , Panigrahy Ashok 
Published: October 2022

AbstractBackgroundDisruptions in perinatal care and support due to the COVID-19 pandemic was an unprecedented but significant stressor among pregnant women. Various neurostructural differences have been re-ported among fetuses and infants born during the pandemic compared to pre-pandemic counterparts. The relationship between maternal stress due to pandemic related disruptions and fetal brain is yet unexamined.MethodsPregnant participants with healthy pregnancies were prospectively recruited in 2020-2022 in the greater Los Angeles Area. Participants completed multiple self-report assessments for experiences of pandemic related disruptions, perceived stress, and coping behaviors and underwent fetal MRI. Maternal perceived stress exposures were correlated with quantitative multimodal MRI measures of fetal brain development using ltivariate models.ResultsFetal brain stem volume increased with increased maternal perception of pandemic related stress positively correlated with normalized fetal brainstem volume (suggesting accelerated brainstem maturation). In contrast, increased maternal perception of pandemic related stress correlated with reduced global fetal brain temporal functional variance (suggesting reduced functional connectivity).ConclusionsWe report alterations in fetal brainstem structure and global functional fetal brain activity associated with increased maternal stress due to pandemic related disruptions, suggesting altered fetal programming. Long term follow-up studies are required to better understand the sequalae of these early multi-modal brain disruptions among infants born during the COVID-19 pandemic.
Identification of dendritic cell-T cell interactions driving immune responses to food
Authors: Canesso Maria C.C. , Castro Tiago B.R. , Nakandakari-Higa Sandra , Lockhart Ainsley , Esterházy Daria , Reis Bernardo S. , Victora Gabriel D. , Mucida Daniel 
Published: October 2022

AbstractThe intestinal immune system must concomitantly tolerate food and commensals and protect against pathogens. Dendritic cells (DCs) orchestrate these immune responses by presenting luminal antigens and inducing functional differentiation of CD4+T cells into regulatory (pTreg) or pro-inflammatory (Th) subsets. However, the exact nature of the DCs inducing tolerance or inflammation to dietary antigens has been difficult to define. Using an intestine-adapted Labeling Immune Partnerships by SorTagging Intercellular Contacts (LIPSTIC) combined with single-cell transcriptomics, we characterized DCs presenting dietary antigens in the context of tolerance or infection. At steady-state, migratory cDC1 and cDC2 DCs, but not resident DCs, were found to present dietary antigen to cognate CD4+T cells. Whereas cDC2s promoted T cell activation, only cDC1s induced their differentiation into pTregs. Infection with the helminthStrongyloides venezuelensisabrogated cDC1 presentation of dietary antigens, preventing pTreg and oral tolerance induction. In contrast,Heligmosomoides polygyrusinfection only partially affected cDC1s, allowing oral tolerance to be maintained. An expanded population of cDC2s that induced type-2 immunity during both helminth infections did not present dietary antigens, demonstrating that compartmentalized presentation of luminal antigens can prevent food-specific Th2 responses during inflammatory conditions. Our data uncover novel cellular mechanisms by which tolerance to food is induced and can be disrupted during infections.