bluuebunny/crossref_metadata_2025_split huggingface dataset:
Force and theα-C-terminal domains bias RNA polymerase recycling
Authors: Qian Jin , Wang Bing , Artsimovitch Irina , Dunlap David , Finzi Laura 
Published: November 2023

AbstractAfter RNA polymerase (RNAP) reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA before restarting RNA synthesis from the previous or a different promoter. We monitored such secondary transcription using magnetic tweezers to determine the effect of low forces, protein roadblocks, and transcription factors. Up to 60% of RNAPs diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained bound to these sliding RNAPs, enabling recognition of secondary promoters and additional rounds of transcription, and the addition of elongation factor NusG, which competes withσ70for binding to RNAP, limited additional rounds of transcription. Surprisingly, RNAP blocked by a DNA-boundlacrepressor could slowly re-initiate transcription at the block-age and was not affected by NusG, suggesting aσ-independent pathway. Force biased the frequency of encounters between convergent or divergent promoters such that transcription was repetitive only from the promoter opposing the direction of force. Sliding RNAP recognized and could subsequently re-initiate from promoters in either orientation. However, deletions of theα-C-terminal domains severely limited the ability of RNAP to turn around.
Effects of Reproductive Experience on Cost-Benefit Decision Making in Females and Males
Authors: Faraji Mojdeh , Viera-Resto Omar A. , Setlow Barry , Bizon Jennifer L. 
Published: November 2023

AbstractAlmost all individuals undergo reproductive and/or parenting experience at some point in their lives, and pregnancy and childbirth in particular are associated with alterations in the prevalence of several psychiatric disorders. Research in rodents shows that maternal experience affects spatial learning and other aspects of hippocampal function. In contrast, there has been little work in animal models concerning how reproductive experience affects cost-benefit decision making, despite the relevance of this aspect of cognition for psychiatric disorders. To begin to address this issue, reproductively experienced (RE) and reproductively naïve (RN) female and male Long-Evans rats were tested across multiple tasks that assess different forms of cost-benefit decision making. In a risky decision-making task, in which rats chose between a small, safe food reward and a large food reward accompanied by variable probabilities of punishment, RE and RN males did not differ, whereas RE females chose the large risky reward significantly more frequently than RN females (greater risk taking). In an intertemporal choice task, in which rats chose between a small, immediate food reward and a large food reward delivered after a variable delay period, RE males chose the large reward more frequently than RN males, whereas RE females chose the large reward less frequently than RN females. Together, these results show distinct effects of reproductive experience on different forms of cost-benefit decision making in rats of both sexes, and highlight reproductive status as a variable that could influence aspects of cognition relevant for psychiatric disorders.
Post-translational regulation of Platelet-derived growth factor receptor β is critical for fracture repair in aged mice
Authors: Tao Jianguo , Lipe Brea , Boyce Brendan F. , Xing Lianping , Zhang Hengwei 
Published: November 2023

AbstractIncreased protein ubiquitination was observed in fracture callus and particularly in aged mice. Treatment of proteasome inhibitor enhanced fracture repair in young and mice by increasing the number of mesenchymal progenitor cells (MPCs). However, the protein targets of proteasome inhibitor are still not known. Ub-proteomics identifies the top ub-proteins in MPCs and osteoblasts. Among them, PDGFRβ plays important roles both in osteogenesis and angiogenesis, which were reduced in callus of aged mice. We examine the dramatic decrease of PDGFRβ protein level, increased Ub-PDGFRβ, but mild decrease of mRNA in callus of aged mice, suggesting dys-regulated protein modification is the major cause of decreased PDGFRβ level. Decreased PDGFRβ results in the failure of PDGF-BB enhanced MPCs proliferation and fracture repair in aged mice. Co-treatment with proteasome inhibitor rescues the ability of PDGF-BB on MPC proliferation and fracture repair. Our findings not only discover the protein target of proteasome inhibitor in MPCs, but importantly connect the compromised effect of PDGF treatment on diseases with PDGFRβ proteasomal degradation. We open a new avenue for the treatment of fracture repair in elderly with the combination of PDGF-BB and proteasome inhibitor.
Multimodal single cell-resolved spatial proteomics reveals pancreatic tumor heterogeneity
Authors: Xu Yanfen , Wang Xi , Li Yuan , Mao Yiheng , Su Yiran , Yang Yun , Gao Weina , Fu Changying , Chen Wendong , Ye Xueting , Liang Fuchao , Bai Panzhu , Sun Ying , Xu Ruilian , Tian Ruijun 
Published: November 2023

AbstractDespite the advances in antibody-guided cell typing and mass spectrometry-based proteomics, their integration is hindered by challenges for processing rare cells in the heterogeneous tissue context. Here, we introduce Spatial and Cell-type Proteomics (SCPro), which combines multiplexed imaging and flow cytometry with ion exchange-based protein aggregation capture technology to characterize spatial proteome heterogeneity with single cell resolution. The SCPro was employed to explore the pancreatic tumor microenvironment and revealed the spatial alternations of over 5,000 proteins by automatically dissecting up to 100 single cells guided by multi-color imaging of centimeter-scale formalin-fixed, paraffin-embedded tissue slide. To enhance cell-type resolution, we characterized the proteome of 14 different cell types by sorting up to 1,000 cells from the same tumor, which allows us to deconvolute the spatial distribution of immune cell subtypes and leads to the discovery of a novel subtype of regulatory T cells. Together, the SCPro provides a multimodal spatial proteomics approach for profiling tissue proteome heterogeneity.
Acoustic inspired brain-to-sentence decoder for logosyllabic language
Authors: Feng Chen , Cao Lu , Wu Di , Zhang En , Wang Ting , Jiang Xiaowei , Zhou Chenhao , Chen Jinbo , Wu Hui , Lin Siyu , Hou Qiming , Lin Chin-Teng , Zhu Junming , Yang Jie , Sawan Mohamad , Zhang Yue 
Published: November 2023

AbstractMany severe neurological diseases, such as stroke and amyotrophic lateral sclerosis, can impair or destroy the ability of verbal communication. Recent advances in brain-computer interfaces (BCIs) have shown promise in restoring communication by decoding neural signals related to speech or motor activities into text. Existing research on speech neuroprosthesis has predominantly focused on alphabetic languages, leaving a significant gap of logosyllabic languages such as Mandarin Chinese which are spoken by more than 15% of the world population. Logosyllabic languages pose unique challenges to brain-to-text decoding due to extended character sets (e.g., 50,000+ for Mandarin Chinese) and complex mapping between characters and pronunciation. To address these challenges, we established a speech BCI designed for Mandarin, decoding speech-related stereoelectroencephalography (sEEG) signals into coherent sentences. We leverage the unique acoustic features of Mandarin Chinese syllables, constructing prediction models for syllable components (initials, tones, and finals), and employ a language model to resolve pronunciation to character ambiguities according to the semantic context. This method leads to a high-performance decoder with a median character accuracy of 71.00% over the full character set, demonstrating huge potentials for clinical application. To our knowledge, we are the first to report brain-to-sentence decoding for logosyllabic languages over full character set with a large intracranial electroencephalography dataset.
Stomatal maturomics: identifying genes regulating guard cell maturation and function formation from single-cell transcriptomes
Authors: Peng Yuming , Liu Yi , Wang Yifan , Qin Yue , Ma Shisong 
Published: November 2023

AbstractStomata play critical roles in gas exchange and immunity to pathogens. While many genes regulating early stomatal development up to the production of young guard cells (GCs) have been described in Arabidopsis, much less is known about how young GCs develop into mature functional stomata. Here we performed a maturomics study on stomata, with “maturomics” defined as omics analysis of the maturation process of a tissue or organ. We developed an integrative scheme to analyze three public stomata-related single-cell RNA-seq datasets and identified a list of 586 genes that were specifically up-regulated in all three datasets during stomata maturation and function formation. The list, termed sc_586, is enriched with known regulators of stomatal maturation and functions. We selected two candidate G2-like TFs genes,MYS1andMYS2, from the list to investigate their roles in stomata. Our results showed that these two genes redundantly regulate the size and hoop rigidity of mature GCs, and their double mutations caused mature GCs to have severe defects in regulating their stomatal apertures. Our analysis thus provides a valuable gene list for studying GC maturation and function formation.
Micrococcal nuclease regulates biofilm formation and dispersal in methicillin-resistantStaphylococcus aureusUSA300
Authors: Kaplan Jeffrey B. , Florjanczyk Aleksandr P. , Ochiai Maria , Jones Caleb D. , Horswill Alexander R. 
Published: November 2023

ABSTRACTBiofilm formation is an important virulence factor for methicillin-resistantStaphylococcus aureus(MRSA). The extracellular matrix of MRSA biofilms contains significant amounts of double-stranded DNA. MRSA cells also secrete micrococcal nuclease (Nuc1) which degrades double-stranded DNA. In this study we used anuc1mutant strain to investigate the role of Nuc1 in MRSA biofilm formation and dispersal. Biofilm was quantitated in microplates using a crystal violet binding assay. Extracellular DNA (eDNA) was isolated from colony biofilms and analyzed by agarose gel electrophoresis. In some experiments, broth or agar was supplemented with sub-MIC amoxicillin to induce biofilm formation. Biofilm erosion was quantitated by culturing biofilms on rods, transferring the rods to fresh broth, and enumerating CFUs that detached from the rods. Biofilm sloughing was investigated by culturing biofilms in glass tubes perfused with broth and measuring the sizes of the detached cell aggregates. We found that anuc1mutant strain produced significantly more biofilm and more eDNA than a wild-type strain in both the absence and presence of sub-MIC amoxicillin.nuc1mutant biofilms grown on rods detached significantly less than wild-type biofilms. Detachment was restored by exogenous DNase or a wild-typenuc1gene on a plasmid. In the sloughing assay,nuc1mutant biofilms released cell aggregates that were significantly larger than those released by wild-type biofilms. Our results suggest that Nuc1 modulates biofilm formation, biofilm detachment, and the sizes of detached cell aggregates. These processes may play a role in the spread and subsequent survival of MRSA biofilms during biofilm-related infections.
Performance of the 0/2‐hour high‐sensitivity cardiac troponin T diagnostic protocol in a multisite United States cohort
Authors: Supples Michael W. , Snavely Anna C. , Ashburn Nicklaus P. , Allen Brandon R. , Christenson Robert H. , Nowak Richard , Wilkerson R. Gentry , Mumma Bryn E. , Madsen Troy , Stopyra Jason P. , Mahler Simon A. 
Published: November 2023

AbstractBackgroundThe diagnostic performance of the high‐sensitivity troponin T (hs‐cTnT) 0/2‐h algorithm is unclear among U.S. emergency department (ED) patients with acute chest pain.MethodsA preplanned subgroup analysis of the STOP‐CP cohort study was conducted. Participants with 0‐ and 2‐h hs‐cTnT measures prospectively enrolled at eight U.S. EDs from January 2017 to September 2018 were stratified into rule‐out, observation, and rule‐in zones using the hs‐cTnT 0/2‐h algorithm alone and combined with the history, electrocardiogram, age, and risk factor (HEAR) score. The primary outcome was adjudicated 30‐day cardiac death or myocardial infarction (CDMI). The sensitivity and negative predictive value (NPV) of the 0/2‐h rule‐out zone and specificity and positive predictive value (PPV) of the rule‐in zone for 30‐day CDMI were calculated.ResultsOf the 1307 patients accrued, 53.6% (700/1307) were male and 58.6% (762/1307) were White, with a mean ± SD age of 57.5 ± 12.7 years. At 30 days, CDMI occurred in 12.9% (168/1307) of participants. The 0/2‐h algorithm ruled out 61.4% (802/1307) of patients. Among rule‐out patients, 1.9% (15/802) experienced 30‐day CDMI, resulting in a sensitivity of 91.1% (95% confidence interval [CI] 85.7%–94.9%) and NPV of 98.1% (95% CI 96.9%–98.9%). The 0/2‐h algorithm ruled in 12.4% (162/1307) patients of whom 61.7% (100/162) experienced 30‐day CDMI. The rule‐in zone specificity was 94.6% (95% CI 93.1%–95.8%) and PPV was 61.7% (95% CI 53.8%–69.2%) for 30‐day CDMI. The 0/2‐h algorithm combined with HEAR score ruled out 30.7% (401/1307) of patients with a sensitivity and NPV for 30‐day CDMI of 98.2% (95% CI 94.9%–99.6%) and 99.3% (95% CI 97.8%–99.8%), respectively.ConclusionsThe hs‐cTnT 0/2‐h algorithm ruled out most patients. With NPV of <99% for 30‐day CDMI, the hs‐cTnT 0/2‐h algorithm, many emergency physicians may not consider it safe to use for U.S. ED patients. When combined with a low‐risk HEAR score, NPV was >99% for 30‐day CDMI at the cost of reduced efficacy.
A rare homozygous variant in TERT gene causing variable bone marrow failure, fragility fractures, rib anomalies and extremely short telomere lengths with high serum IgE
Authors: Elbadry Mahmoud I. , Tawfeek Ahmed , Hirano Tomonori , El‐Mokhtar Mohamed A. , Kenawey Mohamed , Helmy Ahmed M. , Ogawa Seishi , Mughal M. Zulf , Nannya Yasuhito 
Published: November 2023

SummaryBy whole exome sequencing, we identified a homozygous c.2086 C→T (p.R696C) TERT mutation in patients who present with a spectrum of variable bone marrow failure (BMF), raccoon eyes, dystrophic nails, rib anomalies, fragility fractures (FFs), high IgE level, extremely short telomere lengths (TLs), and skewed numbers of cytotoxic T cells with B and NK cytopenia. Haploinsufficiency in the other family members resulted in short TL and osteopenia. These patients also had the lowest bone mineral density Z‐score compared to other BMF‐patients. Danazol/zoledronic acid improved the outcomes of BMF and FFs. This causative TERT variant has been observed in one family afflicted with dyskeratosis congenita (DC), and thus, we also define a second report and new phenotype related to the variant which should be suspected in severe cases of DC with co‐existent BMF, FFs, high IgE level and rib anomalies.
High fat diet‐induced maternal obesity in mice impairs peripartum maternal behaviour
Authors: Brown Rosemary Shanon Eileen , Jacobs Ireland M. , Khant Aung Zin , Knowles Pene J. , Grattan David R. , Ladyman Sharon R. 
Published: November 2023

AbstractObesity during pregnancy represents a significant health issue and can lead to increased complications during pregnancy and impairments with breastfeeding, along with long‐term negative health consequences for both mother and offspring. In rodent models, diet‐induced obesity (DIO) during pregnancy leads to poor outcomes for offspring. Using a DIO mouse model, consisting of feeding mice a high fat diet for 8 weeks before mating, we recapitulate the effect of high pup mortality within the first 3 days postpartum. To examine the activity of the dam around the time of birth, late pregnant control and DIO dams were recorded in their home cages and the behaviour of the dam immediately before and after birth was analysed. Prior to giving birth, DIO dams spent less time engaging in nesting behaviour, while after birth, DIO dams spent less time in the nest with their pups compared to control dams, indicating reduced pup‐engagement in the early postpartum period. We have previously reported that lactogenic hormone action, mediated by the prolactin receptor, in the medial preoptic area of the hypothalamus (MPOA) is critical for the onset of normal postpartum maternal behaviour. We hypothesized that DIO dams may have lower lactogenic hormone activity during late pregnancy, which would contribute to impaired onset of normal postpartum maternal behaviour. Day 16 lactogenic activity, transport of prolactin into the brain, and plasma prolactin concentrations around birth were all similar in control and DIO dams. Moreover, endogenous pSTAT5, a marker of prolactin receptor activity, in the MPOA was unaffected by DIO. Overall, these data indicate that lactogenic activity in late pregnancy of DIO dams is not different to controls and is unlikely to play a major role in impaired onset of normal postpartum maternal behaviour.
The effects of post‐COVID‐19 fatigue in nurses on organizational outcomes
Authors: Çiriş Yıldız Cennet , Yildirim Dilek , Kara Sercan , Karagöz Esra 
Published: November 2023

AbstractThis study was conducted to determine the effects of fatigue in nurses with confirmed COVID‐19 infection on organizational outcomes. The study was carried out with the participation of 200 nurses who had tested positive for COVID‐19 in the last eighteen months and had COVID‐19‐related fatigue complaints. Data were collected between October 2022 and February 2023 using a questionnaire consisting of the Chalder Fatigue Scale, the Work Alienation Scale, the Turnover Intention Scale, and the Employee Performance Scale. Fatigue was the most common symptom of COVID‐19 in this study, as in other results. The number of being infected with COVID‐19 and education levels were found to be significant predictors of post‐COVID‐19 fatigue. Post‐COVID‐19 fatigue had an effect on turnover intention and alienation to work, but it did not affect employee performance. In this study, the effects of post‐COVID‐19 fatigue on organizational outcomes such as employee performance, turnover intention, and work alienation were determined. Therefore, regardless of its source, fatigue should be dealt with managerially, and preventive policies and procedures should be developed.
The Effects of Group Composition and Dynamics on Collective Performance
Authors: Almaatouq Abdullah , Alsobay Mohammed , Yin Ming , Watts Duncan J. 
Published: November 2023

AbstractAs organizations gravitate to group‐based structures, the problem of improving performance through judicious selection of group members has preoccupied scientists and managers alike. However, which individual attributes best predict group performance remains poorly understood. Here, we describe a preregistered experiment in which we simultaneously manipulated four widely studied attributes of group compositions: skill level, skill diversity, social perceptiveness, and cognitive style diversity. We find that while the average skill level of group members, skill diversity, and social perceptiveness are significant predictors of group performance, skill level dominates all other factors combined. Additionally, we explore the relationship between patterns of collaborative behavior and performance outcomes and find that any potential gains in solution quality from additional communication between the group members are outweighed by the overhead time cost, leading to lower overall efficiency. However, groups exhibiting more “turn‐taking” behavior are considerably faster and thus more efficient. Finally, contrary to our expectation, we find that group compositional factors (i.e., skill level and social perceptiveness) are not associated with the amount of communication between group members nor turn‐taking dynamics.
Soil Formation on Sugar Industry Waste in the Central Chernozemic Zone
Authors: Zamotaev I. V. , Gracheva R. G. , Konoplianikova Yu. V. , Dolgikh A. V. , Karelin D. V. , Belonovskaya E. A. , Dobryansky A. S. , Mikheev P. V. 
Published: November 2023

Abstract
Soils formed in treatment facilities of sugar beet factories in the forest-steppe zone of Kursk oblast were studied. Technogenic factors of soil formation associated with the industrial sugar beet activity and post-technogenic processes during the abandonment of treatment facilities are considered. The alternation of settling ponds and the earth walls separating them are the main factors determining “cellular” pattern of the soil cover. The mode of inflow and discharge and the composition of wastewater, as well as the duration of the abandonment of settling ponds determine the specifics of soils forming in the bottoms of the ponds. Mucky–humus quasi-gley stratified soils (Calcaric Gleysol) are formed in operating settling ponds under the periodic impact of sewage mixed with other wastes. When calcareous sewage sludge (press mud) is previously removed from abandoned ponds, dark-humus quasi-gley soils (Gleyic Cambisol) are formed in 30 years in the presence of perched water table, and quasi-gley zooturbated Chernozems are developed in 40 years under the conditions of periodic moistening. Soil formation in settling ponds with preserved sewage sludge and abandoned 20 years ago is noticeably intensive only in the upper 10–15 cm, and properties of the stratified sediment are preserved below. Dark-humus technogenic artistratified soils (Spolic Technosols) are identified there. Typical dark-humus soils (Eutric Cambisols (Organotransportic) are formed on earth walls in about 50–60 years, and incompletely developed strongly alkaline technogenic pelozems (Spolic Technosols (Transportic)) are formed on earth walls covered with calcareous sewage sludge; these soils consist of the virtually unchanged mixed material of technogenic sediments. All soils are alkaline and strongly alkaline and rich in organic matter, carbonates, phosphates, nutrients and some heavy metals from wastewater. According to the combination of properties, the soils of the sugar industry treatment facilities have no direct natural analogues in the central chernozemic region and are a vivid example of soils forming under extreme conditions of resource excess.