bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allosteric communication induced by GTP binding sets off a closed-to-open transition in a bacterial dynamin-like protein
Authors: Schumann Wibke , Strodel Birgit 
Published: January 2023

AbstractDynamin superfamily proteins are mechanochemical GTPases that operate in highly oligomeric and highly cooperative superstructures to deform lipid membranes. It is known from the structures of a bacterial dynamin-like protein (BDLP) that binding of GTP and association of BDLP with lipids causes a transition from closed to open hinge 1 that affects oligomerization. We trace this radical, large-scale conformational change at the atomic level with unbiased, replica exchange, and umbrella sampling molecular dynamics simulations. We decipher how GTP loading from the GTPase domain to the distal stalk end is mediated by an allosteric network of salt bridges that act in response to GTP binding and subsequent conformational changes in GTPase domain motifs. Two previously undiscovered motifs have been identified whose movements free the paddle from the GTPase domain, allowing large-scale domain rearrangements. In addition, a novel wide-open state of BDLP reminiscent of human dynamin 1 is discovered. Our results explain several aspects of the BDLP cycle and have broad implications for other members of the dynamin family.
Human tissues exhibit diverse composition of translation machinery
Authors: Anisimova Aleksandra S. , Kolyupanova Natalia M. , Makarova Nadezhda E. , Egorov Artyom A. , Kulakovskiy Ivan V. , Dmitriev Sergey E. 
Published: January 2023

AbstractWhile protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g. PABP and eRF3 paralogs, eIF2B subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified testis and brain as organs with the most diverged expression of translation-associated genes.
Schizophrenia, inflammation and temporal change in brain morphology: an omnigenic Mendelian randomization study
Authors: Ren Hongyan , Liu Yunjia , Zhang Yamin , Wang Qiang , Deng Wei , Ma Xiaohong , Zhao Liansheng , Li Xiaojing , Sham Pak , Li Tao 
Published: January 2023

AbstractThe last decades of research in schizophrenia witnessed a shift of etiological speculation from neurotransmitters to inflammation. However, identifying definite inflammatory effectors of schizophrenia remains elusive due to confounding factors such as medication and metabolic status. To tackle this issue, we carried out omnigenic-based Mendelian randomization (MR) analysis to explore the inflammatory responses of schizophrenia and the brain morphological consequences caused by these SCZ-triggering inflammation responses. Our results identified seven SCZ-triggering inflammation markers, with P values surviving the Bonferroni multiple comparisons (B_NGF, P = 1.45 × 10−8; GROA (CXCL1) P = 1.15 × 10−4; IL8, P = 3.64 × 10−7; MCSF, P = 9.30 × 10−4; MCP3 (CCL7), P = 1.3 × 10−6; TNF_β, P = 3.63 × 10−4; CRP, P = 1.71 × 10−32). Further, three of them, GROA (CXCL1), IL8 and CRP, could lead to significant linear change rate of brain morphologies, especially white matter in both cerebral and cerebellum. Our study is the first to use an omnigenic conceptual framework to capture the immune pathology of schizophrenia. Although future studies adopting a different methodology are needed to validate our results, our study provides another piece of evidence that extensive and low-grade neuroinflammation exists in schizophrenia and that some of these inflammation markers could be potential targets for the precise diagnosis and treatment of schizophrenia.
Dopamine enhances population coding of fear in prefrontal cortex
Authors: Lesas Jeremy , Pierre Feugas , Herry Cyril , Dejean Cyril 
Published: January 2023

AbstractFear acquisition is a survival strategy enabling the prediction of potential threat on the basis of reliable environmental cues identified through associative learning. In this study we investigated the role of dorsomedial prefrontal cortex (dmPFC) – ventral tegmental area (VTA) coordination in fear acquisition. Despite the implication of a VTA-dmPFC circuit in fear acquisition, the mechanism by which the two structures interact and, most particularly, the manner in which dmPFC neuronal dynamics are impacted by DA remain largely unexplored. The present paper addresses this question by means of behavioral, optogenetic, and electrophysiological experiments. We first characterize the dynamics of VTA neurons and their relation with dmPFC during fear acquisition to then manipulate this dopaminergic inputs to dmPFC and address its role in fear memory expression and its dmPFC neuronal correlates. Our data first unravel that VTA neurons develop a conditioned stimulus coding activity through consecutive pairings with the unconditioned aversive stimulus and maintain this predictive activity overnight. Shutting down these VTA inputs to dmPFC resulted in a reduction in fear behavior and changes in population coding. These alteration were specific to spontaneous expression of fear and the population coding supporting that behavior. Our data show that dopamine role is to increase the accuracy of fear coding in dmPFC.
An investigation of the impact of community controls on commonly reported epidemiological estimates in tuberculosis (TB) household contact study
Authors: Shi Haodong , Li Tenglong 
Published: January 2023

AbstractBackgroundTuberculosis (TB) has long been a major public health problem worldwide. In particular, during the period of the raging covid-19 epidemic, the situation of tuberculosis prevention and control has been critical. However, current TB household contact study describes the general risk of TB in target population and are unable to characterize the individual risk following exposure to active TB cases.MethodWe designed a dynamic simulation program for TB transmission to generate simulated datasets based on historical data on TB infection in four regions of Brazil, conducted a household contact study of household contacts with active TB (n=1711), and added matched (n=1362) and unmatched (n=1276) community control households to generate different datasets, respectively. We estimated the Second attack rate (SAR), Odds ratio, relative risk for each dataset.ResultEnrolling community controls extends the classical model of infectious disease SAR to TB in a household contact setting. Allowing us to separate the risk of household exposure from the risk of TB infection in the community, thus obtaining separate estimates of SAR and risk of contact with active TB cases. But over-matching for community control can lead to a reduction in the amount of data and even mask certain risk factors.
Oomycete effector AVRblb2 targets cyclic nucleotide-gated channels through calcium sensors to suppress pattern-triggered immunity
Authors: Lee Soeui , Lee Hye-Young , Kang Hui Jeong , Seo Ye-Eun , Lee Joo Hyun , Choi Doil 
Published: January 2023

SUMMARYTransient, rapid increase of cytosolic Ca2+upon pathogen infection is essential for plant pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). Several cyclic nucleotide-gated channels (CNGCs) have been implicated; however, their regulatory mechanisms remain elusive. Here, thePhytophthora infestansRXLR effector AVRblb2 family targeted NbCNGC18–20 at the plasma membrane, inhibiting Ca2+influx and PTI. AVRblb2 required calmodulin (CaM) and calmodulin-like (CML) proteins as co-factors to interact withN. benthamianaCNGCs (NbCNGCs), forming the AVRblb2-CaM/CML-NbCNGCs complex. After recognizing PAMPs, NbCNGC18 formed active heteromeric channels with other CNGCs, potentially providing selectivity for diverse signals to fine-tune cytosolic Ca2+levels and responses. AVRblb2 suppressed the Ca2+influx and oxidative burst induced by NbCNGC18 heteromeric complexes. Silencing CNGC18, CNGC20, and CNGC25 compromised the effect of AVRblb2 onP. infestansvirulence, confirming that AVRblb2 contributed to virulence by targeting CNGCs. Our findings delineated the regulatory mechanism and role of effector-targeted Ca2+channels in plant innate immunity.
Assessing the effectiveness of portable HEPA air cleaners for reducing particulate matter exposure in King County, Washington homeless shelters during the COVID-19 pandemic: implications for community congregate settings
Authors: Huang Ching-Hsuan , Bui Thu , Hwang Daniel , Shirai Jeffry , Austin Elena , Cohen Martin , Gould Timothy , Larson Timothy , Novosselov Igor , Tan Shirlee , Seto Edmund 
Published: January 2023

AbstractOver four thousand portable air cleaners (PACs) with high-efficiency particulate air (HEPA) filters were distributed by Public Health - Seattle & King County to homeless shelters during the COVID-19 pandemic. This study aimed to evaluate the real-world effectiveness of these HEPA PACs in reducing indoor particles and understand the factors that affect their use in homeless shelters. Four rooms across three homeless shelters with varying geographic locations and operating conditions were enrolled in this study. At each shelter, multiple PACs were deployed based on the room volume and PAC’s clean air delivery rate rating. The energy consumption of these PACs was measured using energy data loggers at 1-min intervals to allow tracking of their use and fan speed for three two-week sampling rounds, separated by single-week gaps, between February and April 2022. Total optical particle number concentration (OPNC) was measured at 2-min intervals at multiple indoor locations and an outdoor ambient location. The empirical indoor and outdoor total OPNC were compared for each site. Additionally, linear mixed-effects regression models (LMERs) were used to assess the relationship between PAC use time and indoor/outdoor total OPNC ratios (I/OOPNC). Based on the LMER models, one percent increase in the hourly, daily and total time PACs were used significantly reduced I/OOPNCby 0.34 [95% CI: 0.28, 0.40], 0.51 [95% CI: 0.20, 0.78], 2.52 [95% CI: 1.50, 3.28], respectively, indicating that keeping PACs on resulted in significantly lower I/OOPNCor relatively lower indoor total OPNC than outdoors. The survey suggested that keeping PACs on and running was the main challenge when operating them in shelters. These findings suggested that HEPA PACs were an effective short-term strategy to reduce indoor particle levels in community congregate living settings during non-wildfire seasons and the need for formulating practical guidance for using them in such an environment.
Field assessment of the burden and determinants of malaria transmission to inform tailoring of interventions (microstratification) in Ibadan and Kano metropolis: Study protocol
Authors: Ozodiegwu Ifeoma D. , Ogunwale Akintayo O. , Surakat Olabanji , Akinyemi Joshua O. , Bamgboye Eniola , Fagbamigbe Adeniyi F. , Bello Musa Muhammad , Adamu Al-Mukhtar Y. , Uhomobhi Perpetua , Ademu Cyril , Okoronkwo Chukwu , Adeleke Monsuru , Ajayi IkeOluwapo 
Published: January 2023

AbstractIntroductionRapid urbanization in Nigerian cities may likely result in small-scale variation in malaria transmission with a higher malaria burden in informal settlements and slums. However, data is unavailable to quantify city-level variations in transmission risk and to inform selection of appropriate interventions. We are conducting field studies to understand how malaria risk varies at the smallest administrative units (wards) in two major Nigerian cities – Ibadan and Kano – to inform tailoring of interventions for cities in Nigeria’s National Malaria Strategic Plan.Methods and AnalysisThis is a mixed-method research design involving qualitative and quantitative research methods. We will carry out formative qualitative studies to inform sampling strategies for formal settlements, informal settlements and slums and the design of survey questionnaires. Cross-sectional surveys will be conducted in the wet and dry seasons across wards in the study cities and within different settlement types at the household and health facility levels to map all-age and under-five malaria prevalence and evaluate related risk factors. A 12-month longitudinal study among children under the age of 10 years will provide information on malaria seasonality in the two cities and related factors. Entomological surveys will be used to undertaken for eight months (four months in each season) per city to assess local transmission risk in both cities. Descriptive and regression analysis will be applied to study data to assess malaria prevalence, seasonality and related factors. Mathematical models of malaria transmission for each study ward will be developed based on study data to inform assessment of the impact of various intervention scenarios specified by the NMEP on malaria transmission.Ethics and DisseminationThis protocol has been approved by Nigeria’s National Health Research Committee and relevant institutional Ethical Review Committees. Study results will be disseminated to key stakeholders and study communities.Strength and LimitationsStrengthsCross-sectional and longitudinal study sampling procedures and questionnaire design are enhanced by a strong formative research foundationStudy design and site selection are informed by modeling and local knowledgeThe combination of human and vector studies will provide detailed information on malaria transmission risk and associated driversLimitationsCross-sectional study may not be powered to measure all-age prevalence as sample size estimation is based on prevalence among children under the age of five yearsStudy findings may not adequately measure transmission burden and risk factors in unsampled wards
Comparison of external treatment of Acupuncture and moxibustion and intervention of Chinese and Western Medicine on postoperative pain of hemorrhoids: A systematic review and meta-analysis
Authors: Zou XinYan , Liu QiaoQiao , Gao LongXia , Zhao HanQing 
Published: January 2023

AbstractObjectiveTo evaluate the clinical efficacy and safety of acupuncture and moxibustion in the treatment of postoperative pain of hemorrhoids compared with traditional Chinese medicine and western medicine.MethodsThe CNKI, pubMed, Cochrane Library, Science Direct, Wan Fang, VIP, CBM, WOS, Bailian Yun Library and other databases were systematically retrieved from 2017 to October 2022 for clinical randomized controlled trials of acupuncture versus traditional Chinese and Western medicine for postoperative pain in hemorrhoids. The two evaluators independently retrieved, sifted through literature and extracted data for inclusion in a randomized controlled trial of acupuncture for the treatment of hemorrhoid pain that matched the study. Literature quality assessment was performed using RevMan5.4 for meta-analysis.ResultsA total of 540 related literature articles were retrieved, of which 139 were from CNKI, 104 from Wan Fang, 104 from VIP26, 7 from PubMed, 9 from Cochrane, 35 from WOS, 173 from China Biomedical Literature Database, 1 from Science Direct and 46 from the Bailian Yun Library, Screening resulted in inclusion of 10 RCTs including 870 patients. Meta analysis showed that there was no significant difference in the degree of pain in 2 hours [MD=0.01, 95%CI (−0.23, 0.24), P ≤ 0.95]. And it showed that the total effective rate of the two groups was [RR=1.14, 95%CI (1.06, 1.24), P ≤ 0.0001], intervention for 2days pain degree was [MD=-0.41, 95%CI (−0.69, 0.13), P ≤ 0.004], the incidence of adverse reaction was [RR=0.15, 95%CI (0.03, 0.79), P=0.03], the difference was statistically significant (P<0.05).ConclusionDrug treatment is effective quickly, analgesia effect is better than acupuncture in early treatment, but the effect is not lasting. Acupuncture treatment is slow to start but the effects of acupuncture will gradually become apparent at a later stage. However, due to the low quality of inclusion, multicenter, large sample size and double-blind randomized controlled trials are still needed.
Level of partograph utilization and its predictors among obstetrics care givers in Ilu Aba Bor Zone, Southwest Ethiopia: a cross-sectional study
Authors: Tesfaye Getamesay Aynalem , Chanie Fentaneh Teshome , Gemechu Ebissa Negera 
Published: January 2023

AbstractBackgroundWorldwide, several thousands of mothers die per a year due to pregnancy and birth related complications. Most of maternal deaths can be minimized using partograph routinely. In spite of the priceless importance of partograph in reducing maternal death, its level of utilization and associated factors has been little known among obstetrics care providers in Ilu Aba Bor Zone.ObjectiveThis study aimed at assessing the level of partograph utilization and associated factors among obstetric care givers in Ilu Aba Bor Zone, South West Ethiopia.MethodsAn institution-based cross-sectional study design was employed. A structured self-administered and pretested questionnaire adapted from available literatures were used. In addition to descriptive statistics, logistic regression analysis was applied to assess association.ResultsThe level of partograph utilization among obstetrics care providers in the study area was 32.8%. Receiving on-job training on partograph (AOR (Adjusted Odds Ratio) = 2.21, 95%CI (Confidence Interval) = 1.19, 4.11), working in a hospital compared to working in a health center (AOR = 2.43, 95%CI = 1.01, 5.82), having BSc (Bachelor of Science) and above educational status in contrast to having Diploma (AOR = 3.12, 95%CI = 1.59, 6.12), and having partograph in a health facility (AOR= 4.19, 95%CI = 2.12, 8.29) were positively associated with partograph use.ConclusionPartograph utilization level was much lower than World Health Organization recommendation. On-job training on partograph, work place, educational status, and partograph availability were predictors of level of partograph utilization among the obstetric care givers.
Evidence for vocal signatures and voice-prints in a wild parrot
Authors: Smeele Simeon Q. , Senar Juan Carlos , Aplin Lucy M. , McElreath Mary Brooke 
Published: January 2023

AbstractIn humans, identity is partly encoded in a voice-print that is carried across multiple vocalisations. Other species also signal vocal identity in calls, such as shown in the contact call of parrots. However, it remains unclear to what extent other call types in parrots are individually distinct, and whether there is an analogous voice-print across calls. Here we test if an individual signature is present in other call types, how stable this signature is, and if parrots exhibit voice-prints across call types. We recorded 5599 vocalisations from 229 individually-marked monk parakeets (Myiopsitta monachus) over a two year period in Barcelona, Spain. We examined five distinct call types, finding evidence for an individual signature in three. We further show that in the contact call, while birds are individually distinct, the calls are more variable than previously assumed, changing over short time scales (seconds to minutes). Finally, we provide evidence for voice-prints across multiple call types, with a discriminant function being able to predict caller identity across call types. This suggests that monk parakeets may be able to use vocal cues to recognise conspecifics, even across vocalisation types and without necessarily needing active vocal signatures of identity.
Experiential diversity training and science learning for college students alongside peers with intellectual and developmental disabilities
Authors: Rubenzer Kaelin N. , Pierce Jonathan T. 
Published: January 2023

ABSTRACTDiversity, equity and inclusion (DEI) training can benefit STEM students. However, typical college settings often limit college students’ exposure to adult peers with intellectual and developmental disabilities (IDDs), a historically marginalized group. To lower this barrier, we developed a continuing education program, Lifelong Learning with Friends (LLWF), aimed at adults with IDDs on a large university campus, which provides diversity training to college students. In this program, undergraduate and graduate students from scientific and education disciplines are recruited to volunteer as peers and helpers. LLWF has reached hundreds of students with and without IDDs each year and more than 1,500 over the past 12 years. In our program, college students gain DEI training through learning sophisticated academic topics, including sciences, alongside adults with IDDs. Almost half (42%) of surveyed LLWF college volunteers did not have prior exposure to people with IDDs. Following program participation, we found that, irrespective of prior exposure, nearly all (98%) of volunteers had elevated their expectations of people with IDDs and reported increased interest in IDDs-focused research, education, social interaction, and advocacy. Additionally, college volunteers reported that they improved their science communication by seeing how science could be taught to a broad audience that includes adults with IDDs. We therefore suggest that other universities may consider our LLWF model to enhance DEI training by expanding opportunities for neurotypical students to befriend and learn science alongside adults with IDDs.
A robust closed-tube method for resolvingtp53M214Kgenotypes
Authors: Silvius Katherine M. , Kendall Genevieve C. 
Published: January 2023

AbstractThetp53M214Kzebrafish mutant developed by Berghmans et al 20051is a versatile platform with which to model a diverse spectrum of human diseases. However, currently available genotyping methods for this mutant require lengthy processes such as restriction digests and outsourced Sanger sequencing. To address this deficiency, we leveraged high-resolution melting analysis (HRMA) technology in conjunction with a parallel, in-tandem wildtype spike-in approach to develop a robust genotyping protocol capable of discriminatingtp53M214Kzygosity. Here, we describe our method in detail. We anticipate that our genotyping protocol will benefit researchers utilizing thetp53M214Kzebrafish mutant by offering reliable results with a faster turnaround time than conventional approaches.