bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dairying enabled Early Bronze Age Yamnaya steppe expansions
Authors: Wilkin Shevan , Ventresca Miller Alicia , Fernandes Ricardo , Spengler Robert , Taylor William T.-T. , Brown Dorcas R. , Reich David , Kennett Douglas J. , Culleton Brendan J. , Kunz Laura , Fortes Claudia , Kitova Aleksandra , Kuznetsov Pavel , Epimakhov Andrey , Zaibert Victor F. , Outram Alan K. , Kitov Egor , Khokhlov Aleksandr , Anthony David , Boivin Nicole 
Published: September 2021

AbstractDuring the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic–Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains1,2 and Mongolia3. Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport4–6 and regular dietary dependence on meat and milk5, hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic–Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.
Structural basis of human transcription–DNA repair coupling
Authors: Kokic Goran , Wagner Felix R. , Chernev Aleksandar , Urlaub Henning , Cramer Patrick 
Published: September 2021

AbstractTranscription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published3,4 data, the structures provide a model for transcription–repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, ECTCR, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.
Underwater noise mitigation in the Santa Barbara Channel through incentive-based vessel speed reduction
Authors: ZoBell Vanessa M. , Frasier Kaitlin E. , Morten Jessica A. , Hastings Sean P. , Peavey Reeves Lindsey E. , Wiggins Sean M. , Hildebrand John A. 
Published: September 2021

AbstractCommercial shipping is the dominant source of low-frequency noise in the ocean. It has been shown that the noise radiated by an individual vessel depends upon the vessel’s speed. This study quantified the reduction in source levels (SLs) and sound exposure levels (SELs) for ships participating in two variations of a vessel speed reduction (VSR) program. SLs and SELs of individual ships participating in the program between 2014 and 2017 were statistically lower than non-participating ships (p < 0.001). In the 2018 fleet-based program, there were statistical differences between the SLs and SELs of fleets that participated with varying degrees of cooperation. Significant reductions in SL and SEL relied on cooperation of 25% or more in slowing vessel speed. This analysis highlights how slowing vessel speed to 10 knots or less is an effective method in reducing underwater noise emitted from commercial ships.
Predicting the gender of individuals with tinnitus based on daily life data of the TrackYourTinnitus mHealth platform
Authors: Allgaier Johannes , Schlee Winfried , Langguth Berthold , Probst Thomas , Pryss Rüdiger 
Published: September 2021

AbstractTinnitus is an auditory phantom perception in the absence of an external sound stimulation. People with tinnitus often report severe constraints in their daily life. Interestingly, indications exist on gender differences between women and men both in the symptom profile as well as in the response to specific tinnitus treatments. In this paper, data of the TrackYourTinnitus platform (TYT) were analyzed to investigate whether the gender of users can be predicted. In general, the TYT mobile Health crowdsensing platform was developed to demystify the daily and momentary variations of tinnitus symptoms over time. The goal of the presented investigation is a better understanding of gender-related differences in the symptom profiles of users from TYT. Based on two questionnaires of TYT, four machine learning based classifiers were trained and analyzed. With respect to the provided daily answers, the gender of TYT users can be predicted with an accuracy of 81.7%. In this context, worries, difficulties in concentration, and irritability towards the family are the three most important characteristics for predicting the gender. Note that in contrast to existing studies on TYT, daily answers to the worst symptom question were firstly investigated in more detail. It was found that results of this question significantly contribute to the prediction of the gender of TYT users. Overall, our findings indicate gender-related differences in tinnitus and tinnitus-related symptoms. Based on evidence that gender impacts the development of tinnitus, the gathered insights can be considered relevant and justify further investigations in this direction.
Secondary predation constrains DNA-based diet reconstruction in two threatened shark species
Authors: de Bruyn Mark , Barbato Matteo , DiBattista Joseph D. , Broadhurst Matt K. 
Published: September 2021

AbstractIncreasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the ‘Russian-doll’ approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small,S. mokkaranfed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, whileC. limbatusmostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator’s stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focussing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.
The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei
Authors: Bakari-Soale Majeed , Ikenga Nonso Josephat , Scheibe Marion , Butter Falk , Jones Nicola G. , Kramer Susanne , Engstler Markus 
Published: September 2021

AbstractThe biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.
CRISPR/Cas9 small promoter deletion in H19 lncRNA is associated with altered cell morphology and proliferation
Authors: da Silva Santos Renan , Pinheiro Daniel Pascoalino , Teixeira Louhanna Pinheiro Rodrigues , Sales Sarah Leyenne Alves , dos Santos Luciano Maria Claudia , de Lima Melo Mayara Magna , Pinheiro Ronald Feitosa , Tavares Kaio César Simiano , Furtado Gilvan Pessoa , Pessoa Claudia , Furtado Cristiana Libardi Miranda 
Published: September 2021

AbstractThe imprinted H19 long non-coding RNA, a knowing oncofetal gene, presents a controversial role during the carcinogenesis process since its tumor suppressor or oncogenic activity is not completely elucidated. Since H19 lncRNA is involved in many biological pathways related to tumorigenesis, we sought to develop a non-cancer lineage with CRISPR-Cas9-mediated H19 knockdown (H19-) and observe the changes in a cellular context. To edit the promoter region of H19, two RNA guides were designed, and the murine C2C12 myoblast cells were transfected. H19 deletion was determined by DNA sequencing and gene expression by qPCR. We observed a small deletion (~ 60 bp) in the promoter region that presented four predicted transcription binding sites. The deletion reduced H19 expression (30%) and resulted in increased proliferative activity, altered morphological patterns including cell size and intracellular granularity, without changes in viability. The increased proliferation rate in the H19- cell seems to facilitate chromosomal abnormalities. The H19- myoblast presented characteristics similar to cancer cells, therefore the H19 lncRNA may be an important gene during the initiation of the tumorigenic process. Due to CRISPR/Cas9 permanent edition, the C2C12 H19- knockdown cells allows functional studies of H19 roles in tumorigenesis, prognosis, metastases, as well as drug resistance and targeted therapy.
Plateaus, rebounds and the effects of individual behaviours in epidemics
Authors: Berestycki Henri , Desjardins Benoît , Heintz Bruno , Oury Jean-Marc 
Published: September 2021

AbstractPlateaus and rebounds of various epidemiological indicators are widely reported in Covid-19 pandemics studies but have not been explained so far. Here, we address this problem and explain the appearance of these patterns. We start with an empirical study of an original dataset obtained from highly precise measurements of SARS-CoV-2 concentration in wastewater over nine months in several treatment plants around the Thau lagoon in France. Among various features, we observe that the concentration displays plateaus at different dates in various locations but at the same level. In order to understand these facts, we introduce a new mathematical model that takes into account the heterogeneity and the natural variability of individual behaviours. Our model shows that the distribution of risky behaviours appears as the key ingredient for understanding the observed temporal patterns of epidemics.
Short-term facilitation of breathing upon cessation of hypoxic challenge is impaired in male but not female endothelial NOS knock-out mice
Authors: Getsy Paulina M. , Sundararajan Sripriya , May Walter J. , von Schill Graham C. , McLaughlin Dylan K. , Palmer Lisa A. , Lewis Stephen J. 
Published: September 2021

AbstractDecreases in arterial blood oxygen stimulate increases in minute ventilation via activation of peripheral and central respiratory structures. This study evaluates the role of endothelial nitric oxide synthase (eNOS) in the expression of the ventilatory responses during and following a hypoxic gas challenge (HXC, 10% O2, 90% N2) in freely moving male and female wild-type (WT) C57BL6 and eNOS knock-out (eNOS–/–) mice. Exposure to HXC caused an array of responses (of similar magnitude and duration) in both male and female WT mice such as, rapid increases in frequency of breathing, tidal volume, minute ventilation and peak inspiratory and expiratory flows, that were subject to pronounced roll-off. The responses to HXC in male eNOS–/– mice were similar to male WT mice. In contrast, several of the ventilatory responses in female eNOS–/– mice (e.g., frequency of breathing, and expiratory drive) were greater compared to female WT mice. Upon return to room-air, male and female WT mice showed similar excitatory ventilatory responses (i.e., short-term potentiation phase). These responses were markedly reduced in male eNOS–/– mice, whereas female eNOS–/– mice displayed robust post-HXC responses that were similar to those in female WT mice. Our data demonstrates that eNOS plays important roles in (1) ventilatory responses to HXC in female compared to male C57BL6 mice; and (2) expression of post-HXC responses in male, but not female C57BL6 mice. These data support existing evidence that sex, and the functional roles of specific proteins (e.g., eNOS) have profound influences on ventilatory processes, including the responses to HXC.
Standard hospital blanket warming cabinets can be utilized for complete moist heat SARS-CoV2 inactivation of contaminated N95 masks for re-use
Authors: Kumar Anand , Kasloff Samantha B. , Cutts Todd , Leung Anders , Sharma Naresh , Vazquez-Grande Gloria , Drew Tracy , Laframboise Denis , Orofino Olivero , Tanelli Joe , Krishnan Jay 
Published: September 2021

AbstractShortages of personal protective equipment for use during the SARS-CoV-2 pandemic continue to be an issue among health-care workers globally. Extended and repeated use of N95 filtering facepiece respirators without adequate decontamination is of particular concern. Although several methods to decontaminate and re-use these masks have been proposed, logistic or practical issues limit adoption of these techniques. In this study, we propose and validate the use of the application of moist heat (70 °C with humidity augmented by an open pan of water) applied by commonly available hospital (blanket) warming cabinets to decontaminate N95 masks. This report shows that a variety of N95 masks can be repeatedly decontaminated of SARS-CoV-2 over 6 h moist heat exposure without compromise of their filtering function as assessed by standard fit and sodium chloride aerosol filtration efficiency testing. This approached can easily adapted to provide point-of-care N95 mask decontamination allowing for increased practical utility of mask recycling in the health care setting.
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes
Authors: Karunakaran Kalyani B. , Amemori Satoko , Balakrishnan N. , Ganapathiraju Madhavi K. , Amemori Ken-ichi 
Published: September 2021

AbstractMechanisms underlying anxiety disorders remain elusive despite the discovery of several associated genes. We constructed the protein–protein interaction networks (interactomes) of six anxiety disorders and noted enrichment for striatal expression among common genes in the interactomes. Five of these interactomes shared distinctive overlaps with the interactomes of genes that were differentially expressed in two striatal compartments (striosomes and matrix). Generalized anxiety disorder and social anxiety disorder interactomes showed exclusive and statistically significant overlaps with the striosome and matrix interactomes, respectively. Systematic gene expression analysis with the anxiety disorder interactomes constrained to contain only those genes that were shared with striatal compartment interactomes revealed a bifurcation among the disorders, which was influenced by the anterior cingulate cortex, nucleus accumbens, amygdala and hippocampus, and the dopaminergic signaling pathway. Our results indicate that the functionally distinct striatal pathways constituted by the striosome and the matrix may influence the etiological differentiation of various anxiety disorders.
Limit of detection in different matrices of 19 commercially available rapid antigen tests for the detection of SARS-CoV-2
Authors: Cubas-Atienzar Ana I. , Kontogianni Konstantina , Edwards Thomas , Wooding Dominic , Buist Kate , Thompson Caitlin R. , Williams Christopher T. , Patterson Edward I. , Hughes Grant L. , Baldwin Lisa , Escadafal Camille , Sacks Jilian A. , Adams Emily R. 
Published: September 2021

AbstractIn the context of the coronavirus disease 2019 (COVID-19) pandemic there has been an increase of the use of antigen-detection rapid diagnostic tests (Ag-RDT). The performance of Ag-RDT vary greatly between manufacturers and evaluating their analytical limit of detection (LOD) has become high priority. Here we describe a manufacturer-independent evaluation of the LOD of 19 marketed Ag-RDT using live SARS-CoV-2 spiked in different matrices: direct culture supernatant, a dry swab, and a swab in Amies. Additionally, the LOD using dry swab was investigated after 7 days’ storage at − 80 °C of the SARS-CoV-2 serial dilutions. An LOD of ≈ 5.0 × 102 pfu/ml (1.0 × 106 genome copies/ml) in culture media is defined as acceptable by the World Health Organization. Fourteen of 19 Ag-RDTs (ActiveXpress, Espline, Excalibur, Innova, Joysbio, Mologic, NowCheck, Orient, PanBio, RespiStrip, Roche, Standard-F, Standard-Q and Sure-Status) exceeded this performance criteria using direct culture supernatant applied to the Ag-RDT. Six Ag-RDT were not compatible with Amies media and a decreased sensitivity of 2 to 20-fold was observed for eleven tests on the stored dilutions at − 80 °C for 7 days. Here, we provide analytical sensitivity data to guide appropriate test and sample type selection for use and for future Ag-RDT evaluations.
Versatile cell-based assay for measuring DNA alkylation damage and its repair
Authors: Li Yong , Mao Peng , Basenko Evelina Y. , Lewis Zachary , Smerdon Michael J. , Czaja Wioletta 
Published: September 2021

AbstractDNA alkylation damage induced by environmental carcinogens, chemotherapy drugs, or endogenous metabolites plays a central role in mutagenesis, carcinogenesis, and cancer therapy. Base excision repair (BER) is a conserved, front line DNA repair pathway that removes alkylation damage from DNA. The capacity of BER to repair DNA alkylation varies markedly between different cell types and tissues, which correlates with cancer risk and cellular responses to alkylation chemotherapy. The ability to measure cellular rates of alkylation damage repair by the BER pathway is critically important for better understanding of the fundamental processes involved in carcinogenesis, and also to advance development of new therapeutic strategies. Methods for assessing the rates of alkylation damage and repair, especially in human cells, are limited, prone to significant variability due to the unstable nature of some of the alkyl adducts, and often rely on indirect measurements of BER activity. Here, we report a highly reproducible and quantitative, cell-based assay, named alk-BER (alkylation Base Excision Repair) for measuring rates of BER following alkylation DNA damage. The alk-BER assay involves specific detection of methyl DNA adducts (7-methyl guanine and 3-methyl adenine) directly in genomic DNA. The assay has been developed and adapted to measure the activity of BER in fungal model systems and human cell lines. Considering the specificity and conserved nature of BER enzymes, the assay can be adapted to virtually any type of cultured cells. Alk-BER offers a cost efficient and reliable method that can effectively complement existing approaches to advance integrative research on mechanisms of alkylation DNA damage and repair.
Research on routing and scheduling algorithms for the simultaneous transmission of diverse data streaming services on the industrial internet
Authors: Song Yan , Guo Chenyang , Xu Panfeng , Li Lina , Zhang Rui 
Published: September 2021

AbstractOPC UA PubSub Over TSN is the core of the Industrial Internet and guarantees flexible interaction features for multiple parties in real-time for industrial communication. To achieve the transmission of time-triggered traffic in PubSub NetworkMessage, routing and scheduling data need to be analyzed. Traditional routing and scheduling methods have disadvantages such as low calculation efficiency, slow convergence speed, and poor reliability. Therefore, a routing and scheduling method for OPC UA PubSub NetworkMessage time-triggered traffic based on an improved ant colony algorithm is proposed. First, we analyze the network topology model, traffic model, and traffic transmission constraints of TSN; then, we apply the K-means clustering algorithm, the KSP algorithm based on the shortest path idea, and an improved ant colony algorithm for traffic classification, routing, and scheduling calculation. Experimental results show that this method can effectively reduce the delay increase caused by link congestion, improve the ability to schedule time-triggered traffic, and accelerate the convergence rate of iteration.