bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR
Authors: Hinkel Lauren A. , Willsey Graham G. , Lenahan Sean M. , Eckstrom Korin , Schutz Kristin C. , Wargo Matthew J. 
Published: November 2021

ABSTRACTGlutamine amidotransferase-1 domain-containing AraC-family transcriptional regulators (GATRs) are present in the genomes of many bacteria, including all Pseudomonas species. The involvement of several characterized GATRs in amine-containing compound metabolism has been determined, but the full scope of GATR ligands and regulatory networks are still unknown. Here, we characterize Pseudomonas putida’s detection of the animal-derived amine compound, creatine, a compound particularly enriched in muscle and ciliated cells by a creatine-specific GATR, PP_3665, here named CahR (Creatine amidohydrolase Regulator). cahR is necessary for transcription of the gene encoding creatinase (PP_3667/creA) in the presence of creatine and is critical for P. putida’s ability to utilize creatine as a sole source of nitrogen. The CahR/creatine regulon is small and electrophoretic mobility shift demonstrates strong and specific CahR binding only at the creA promoter, supporting the conclusion that much of the regulon is dependent on downstream metabolites. Phylogenetic analysis of creA orthologs associated with cahR orthologs highlights a strain distribution and organization supporting likely horizontal gene transfer, particularly evident within the genus Acinetobacter. This study identifies and characterizes the GATR that transcriptionally controls P. putida metabolism of creatine, broadening the scope of known GATR ligands and suggesting GATR diversification during evolution of metabolism for aliphatic nitrogen compounds.
Detection of velogenic avian paramyxoviruses in rock doves in New York City, New York
Authors: Francisco Isabel , Bailey Shatoni , Bautista Teresa , Diallo Djenabou , Gonzalez Jesus , Gonzalez Joel , Roubidoux Ericka Kirkpatrick , Ajayi Paul K. , Albrecht Randy A. , McMahon Rita , Krammer Florian , Marizzi Christine 
Published: November 2021

AbstractAvian paramyxovirus 1 (APMV-1), also known as Newcastle disease virus (NDV), causes severe and economically important disease in poultry around the globe. Although a limited amount of APMV-1 strains in urban areas have been characterized, the role of the urban wild bird population as an APMV-1 reservoir is unclear. Since urban birds may have an important role for long-term circulation of the virus, fecal and swab samples were collected by community scientists from wild birds in New York City (NYC), New York, United States. These samples were screened for APMV-1 and genotypically characterized by sequencing of the complete genome. A total of 885 samples were collected from NYC parks and from a local wildlife rehabilitation clinic from October 2020 through June 2021. Eight birds (1.1 %) screened positive for the APMV-1 nucleoprotein gene by conventional reverse transcription polymerase chain reaction (RT-PCR), and two live viruses were isolated via egg culture. The F protein cleavage site, an indicator of pathogenicity, was present in the two samples fully sequenced by next generation sequencing, and positioned 112R R K K R F117. Phylogenetic analysis of the F gene coding sequence classified both isolates into genotype VI, a diverse and predominant genotype responsible for NDV outbreaks in pigeon and dove species worldwide.ImportanceHere we describe the first large-scale effort to screen for APMV-1 in New York City’s wild bird population as part of the New York City Virus Hunters program, a community science initiative. We have characterized two isolates of NDV, with phylogenetic analyses suggesting diversity in established and circulating strains of pigeon paramyxoviruses. Our isolates are also domestic reference strains for future APMV-1 vaccine developments. Future surveillance in this region may contribute to our understanding of NDV’s evolution and genetic diversity, as well as inform poultry husbandry and vaccination practices in New York State.
Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function
Authors: Popović Branka , Nicolet Benoît P. , Guislain Aurélie , Engels Sander , Jurgens Anouk P. , Paravinja Natali , Freen-van Heeren Julian J. , van Alphen Floris P.J. , van den Biggelaar Maartje , Salerno Fiamma , Wolkers Monika C. 
Published: November 2021

AbstractPotent T cell responses against infections and malignancies depend on the release of effector molecules, such as pro-inflammatory cytokines. Because effector molecules can be toxic, their production is tightly regulated through post-transcriptional events at 3’ Untranslated Regions (3’UTRs). RNA binding proteins (RBPs) were shown to be key regulators herein. With an RNA aptamer-based capture assay from human T cells, we identified >130 RBPs interacting with theIFNG, TNFandIL23’UTRs in human T cells. T cell activation altered RBP-RNA interactions, revealing that RBP-target mRNA interactions rapidly respond to stimulation. Furthermore, we uncovered the intricate and time-dependent regulation of cytokine production by RBPs: whereas HuR supports early cytokine production, ZFP36L1, ATXN2L and ZC3HAV1 dampen and shorten the production duration, each at different time points. Strikingly, even though ZFP36L1 deletion did not phenotypically rescue T cell dysfunction in tumors, the increased production of cytokines and cytotoxic molecules resulted in superior anti-tumoral T cell responsesin vivo. Our findings thus show that identifying RBP-RNA interactions reveals key modulators of T cell responses in health and disease.
A systematic literature review on supply chain approaches
Authors: Sadeghi Asl Ramin , Bagherzadeh Khajeh Majid , Pasban Mohammad , Rostamzadeh Reza 
Published: November 2021

PurposeThe purpose of this paper is to present green supply chain, resilient supply chain, agile supply chain, cold supply chain and lean supply chain (GRACL SC) procedures based on a detailed perspective, analyzing subjects in the past 19 years with a systematic literature review (SLR) of the papers reported from 2000 to 2019, and offering information and guidelines for further studies.Design/methodology/approachThis research is based on 17 keywords in the title and topic of the articles and collects data from Web of Science (WOS) databases and objectively chooses 1,190 articles and performs meta-data analyses. Tables and statistical reports are based on the following three filters: publication year, authors and document type. At least, 39 publications from the ISI WOS has been examined for presenting information of categorization of the conducted research with regard to the content analysis, comprising the conceptual development and obstacles, cooperation with the supply chain elements, as well as mathematical and other optimization models.FindingsFinally, this study answered three main questions in the research and demonstrates that the majority studies in the green supply chain (GSC) and a minimum number of studies on the cold supply chain have been conducted and 27 factors are chosen to achieve the 2000 to 2019 GRACL SCM model which robust and fit for Iranian food industries. The model shows that the agile, resilient and lean supply chain have direct effect on GSC and it can be said that all 27 groups which are selected for the final model of this research can be the main groups in the supply chain.Originality/valueThis paper was actually conducted by authors who reported it. To prevent plagiarized, redoubled efforts have been made and actually this paper is based on SLR methodology and the results are real and the researcher discusses the results appropriately. This investigation can have a positive impact within the field of expanding supply chain flexibility and lessening squander within the Iranian generation framework.
Volumetric adaptive slicing of manifold mesh for rapid prototyping based on relative volume error
Authors: Chen Qianyong , Xu Jinghua , Zhang Shuyou 
Published: November 2021

Purpose
Compared with cusp height and area deviation ratio, volume error (VE) caused by the layer height could represent the stair-case effect more comprehensively. The proposed relative volume error (RVE)-based adaptive slicing method takes VE rather than cusp height as slicing criteria, which can improve part surface quality for functionalized additive manufacturing.

Design/methodology/approach
This paper proposes a volumetric adaptive slicing method of manifold mesh for rapid prototyping based on RVE. The pre-height sequences of manifold mesh are first preset to reduce the SE by dividing the whole layer sequence into several parts. A breadth-first search-based algorithm has been developed to generate a solid voxelization to get VE. A new parameter RVE is proposed to evaluate the VE caused by the sequence of the layer positions. The RVE slicing is conducted by iteratively adjusting the layer height sequences under different constraint conditions.

Findings
Three manifold models are used to verify the proposed method. Compared with uniform slicing with 0.2 mm layer height, cusp height-based method and area deviation-based method, the standard deviations of RVE of all three models are improved under the proposed method. The surface roughness measured by the confocal laser scanning microscope proves that the proposed RVE method can greatly improve part surface quality by minimizing RVE.

Originality/value
This paper proposes an RVE-based method to balance the surface quality and print time. RVE could be calculated by voxelized parts with required accuracy at a very fast speed by parallel.
A systematic review and meta‐analysis of the efficacy of processing stages and interventions for controllingCampylobactercontamination during broiler chicken processing
Authors: Dogan Onay B. , Aditya Anand , Ortuzar Juan , Clarke Jennifer , Wang Bing 
Published: November 2021

AbstractSystematic review and meta‐analysis were conducted to quantify the effects of processing stages and interventions on the prevalence and concentration ofCampylobacteron broiler carcasses. To comprehensively capture relevant evidence, six databases were searched using the keywords “Campylobacter” and “broiler chicken.” The literature search yielded 10,450 unique citations, and after applying predetermined inclusion and exclusion criteria, 72 and 53 relevant citations were included in meta‐analyses for processing stages and interventions, respectively. As the two primary outcomes, log reduction and prevalence changes were estimated for each stage or intervention using a random‐effects meta‐analysis approach whenever possible. The outcome‐level quality assessment was conducted following the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. The analysis revealed that scalding and chilling majorly reduces the prevalence and concentration ofCampylobacter. Immersion chilling reduces the concentration regardless of chemical additives, but its effect on prevalence is not conclusive. The effects of carcass washing applications remain uncertain due to the inconsistency and imprecision of both outcomes. Defeathering and evisceration were identified as stages that can increase both prevalence and concentration. Both chemical and physical processing interventions provide limited efficacy in concentration and prevalence reduction. Major limitations of the review were inconsistency and imprecision at the outcome level and reporting issues and data gaps at the study level. The results are expected to inform quantitative microbial risk assessment model development and support evidence‐based decision‐making.
Policosanol alleviates hepatic lipid accumulation by regulating bile acids metabolism in C57BL6/mice through AMPK–FXR–TGR5 cross‐talk
Authors: Zhai Zhenya , Niu Kai‐Min , Liu Huiping , Lin Chong , Tu Yue , Liu Yichun , Cai Lichuang , Ouyang Kexian , Liu Jianping 
Published: November 2021

AbstractPolicosanol exhibits a lipid accumulation alleviating effect, but the underlying mechanisms remains unclear. Bile acids are a significant factor in regulating cholesterol and lipid metabolism homeostasis in mammals. This study was aimed to elucidate the alleviating effect and underlying mechanisms of policosanol on hepatic lipid accumulation through bile acid (BA) metabolism. Policosanol supplementation significantly reduced hepatic triglycerides (19.29%), cholesterol (30.38%) in high fat diet (HFD) induced obese mice (P < 0.05). Furthermore, compared with the control group, HFD decreased the levels of total BAs (TBAs, 37.67%) and cholic acid (CA, 62.74%) in the serum of mice (P < 0.05). Meanwhile, compared to HFD group, policosanol also increased the level of secondary BAs (SBAs) and muricholic acids (MCAs, P < 0.05). qRT‐PCR combined with protein level analysis revealed that policosanol significantly decreased sterol regulatory element‐binding protein (SREBP‐1c) and CD36, and increased the expression level of cytochrome P450 family 7 subfamily A member 1 (CYP7A1) and cytochrome P450 Family 27 Subfamily A Member 1 (CYP27A1, P < 0.05). Additionally, in the liver, policosanol was found downregulated the expression of farnesoid X receptor (FXR)‐small heterodimer partner (SHP), and activate the Takeda G‐coupled protein receptor 5 (TGR5)‐adenosine‐monophosphate‐activated protein kinase (APMK) signaling pathway (P < 0.05). Peroxisome proliferator activated receptor (PPAR)‐α, hormone sensitive lipase (HSL), and carnitine palmitoyltransferase (CPT)‐1α also significantly increased in HP group (P < 0.05). The aforementioned results reveal that the potential mechanism of policosanol in alleviating liver lipid accumulation is to promote BA synthesis and lipolysis through regulating the cross‐talk of the AMPK–FXR–TGR5. New insight for the application of policosanol as an anti‐fatty liver functional food ingredient or supplement is also provided.Practical ApplicationPolicosanol is an important active component of cereals and insect waxes (15–80%). However, almost no policosanol in refined foods such as clear corn germ oil and wheat flour. This study showed that oral administration of policosanol can significantly reduce triglyceride and cholesterol levels in the liver through affecting AMPK–TGR5–FXR cross‐talk, whereas no significant toxicological effect is reported in human and mouse models. This study may provide theoretical support for the theory of dietary structure and the development of dietary supplements to improve lipid metabolism targeting the “bile acid–AMPK–TGR5” pathway.
Hexokinases II‐mediated glycolysis governs susceptibility to crizotinib in ALK‐positive non‐small cell lung cancer
Authors: Lin Caiyu , Chen Hengyi , Han Rui , Li Li , Lu Conghua , Hao Shuai , Wang Yubo , He Yong 
Published: November 2021

AbstractBackgroundActivation of ALK leads to a high level of aerobic glycolysis related to crizotinib insensitivity in anaplastic lymphoma kinase‐positive non‐small cell lung cancer (ALK+ NSCLC). The strategy and mechanism of glycolysis inhibition in sensitizing ALK+ NSCLC cells to crizotinib requires further investigation.MethodsThe levels of glycolysis in H3122 and H2228 cells were evaluated through detection of glucose consumption and lactate production. MTT assay was used to explore the effects of glycolytic inhibitors on crizotinib sensitivity, and the potential mechanism of action were detected by colony formation, Ki67 incorporation assay, transwell assay, small interfering RNA technology and western blot analysis.ResultsALK+ NSCLC cells exhibited significantly higher levels of glycolysis compared to ALK− NSCLC cells. Long‐term exposure to crizotinib could decrease the sensitivity of ALK+ NSCLC cells to crizotinib via increasing the levels of glycolysis related to hexokinases II (HK2). Crizotinib in combination with glycolysis inhibitor 2‐deoxy‐D‐glucose (2DG) synergistically inhibited proliferation, glycolysis, colony formation and invasion ability of ALK+ NSCLC cells. 2DG sensitization crizotinib might be associated with the inhibition of HK2‐mediated glycolysis and P‐ALK/AKT/mTOR signaling pathway in H3122 and H2228 cells.ConclusionsThese results indicate that HK2‐mediated glycolysis plays a crucial role in the increased tolerance of ALK+ NSCLC cells to crizotinib. 2DG may sensitize ALK+ NSCLC to crizotinib via suppression of HK2‐mediated glycolysis and the AKT/mTOR signaling pathway.
pyRSD‐CoEv: A python package for selective sweep detection and co‐evolutionary gene cluster identification
Authors: Zhu Xingxing , Zhang Haoyu , Tang Qianzi 
Published: November 2021

SummaryGenes undergo distinct selective sweeps, and also interact and coevolve, forming the bases of complex phenotypic traits. Therefore, the identification of genes that coevolve or are under artificial selective sweeps is of great importance. However, previous computational methods have been designed for either populations of closely related breeds or individuals of distinct species. Approaches intended specifically for closely related individuals without replicate (i.e. each breed/strain is represented by only one individual) are long overdue. We present a free, powerful, open source package, pyRSD‐CoEv, that allows the identification of genes undergoing coevolution and/or selection‐based sweeps. pyRSD‐CoEv includes two main analysis workflows for genomic variant data: (i) the identification of selective sweeps using relative homozygous single nucleotide variant density (RSD); and (ii) the identification of coevolutionary gene clusters based on correlated evolutionary rates. The python package pyRSD‐CoEv is written using python 3.7 and is freely available from the github website at https://github.com/QianZiTang/pyRSD‐CoEv. It runs on Linux.
Women's and men's experiences in group therapy for substance use disorders: A qualitative analysis
Authors: Sugarman Dawn E. , Meyer Laurel E. , Reilly Meghan E. , Greenfield Shelly F. 
Published: November 2021

AbstractBackground and ObjectivesThis thematic analysis of qualitative interviews from participants in Stage II randomized controlled trial examined women's and men's experiences in group therapy for substance use disorders (SUDs).MethodsInterviews were conducted with 77 women and 38 men after completion of either the gender‐specific Women's Recovery Group (WRG) or mixed‐gender Group Drug Counseling (GDC). Interviews were coded for themes using a deductive approach with a coding scheme modified from the Stage I trial. Satisfaction was measured quantitatively posttreatment.ResultsParticipants had high satisfaction scores with no significant differences between groups. Women in GDC rated group gender composition as less helpful than those in WRG. In the GDC group, women more frequently discussed the theme of self‐perception (e.g., feelings of comfort, safety, shame) compared with men. Men overwhelmingly expressed the benefits of having women in the group, whereas women expressed advantages and disadvantages of mixed‐gender groups and preference for single‐gender groups. Guilt and shame were discussed by women and men; however, only women discussed stigma and its important role in their addiction and recovery.Discussion and ConclusionMen more frequently endorsed the helpfulness of mixed‐gender groups than did women while women appreciated the enhanced support in single‐gender SUD groups. Issues of stigma are especially salient for women.Scientific SignificanceMen and women express differences in their experiences of SUD group therapy. Only women endorse stigma as an obstacle to their treatment and recovery. Tailoring treatment to meet women's and men's needs may enhance engagement, retention, and clinical outcomes.
Associations between poor gross and fine motor skills in pre‐school and peer victimization concurrently and longitudinally with follow‐up in school age – results from a population‐based study
Authors: Øksendal Elise , Brandlistuen Ragnhild Eek , Holte Arne , Wang Mari Vaage 
Published: November 2021

BackgroundChildren with poor motor skills are at increased risk of peer victimization. However, it is unclear whether poor gross and fine motor skills are differently linked to peer victimization among pre‐school and schoolchildren.AimsTo investigate associations between poor gross and fine motor skills measured in pre‐school and the associations to peer victimization measured concurrently and in school age.SampleData from the Norwegian Mother, Father and Child Cohort Study (MoBa), and the Medical Birth Registry of Norway were used. Participants with complete questionnaires at 3, 5, and 8 years (n = 23 215) were included.MethodsA longitudinal design and an autoregressive cross‐lagged model were used to investigate if poor gross and fine motor skills at 3 and 5 years predicted peer victimization at 5 and 8 years. Because emotional difficulties are associated with both motor skills and peer victimization, the results were adjusted for emotional difficulties.ResultsOnly poor fine motor skills at 3 years had a significant association to peer victimization at 5 years. Poor gross motor skills at 5 years had a stronger association to peer victimization measured concurrently compared to poor fine motor skills, and only poor fine motor skills at 5 years was significantly linked to peer victimization at 8 years. No gender difference was found between these paths.ConclusionsTeachers and parents should be aware that motor skills predict peer victimization, and that poor gross and fine motor skills have different associations to peer victimization measured at different ages.
Development co‐operation by European regions: Introducing the subnational donor governance dataset
Authors: Reinsberg Bernhard , Dellepiane Sebastian 
Published: November 2021

SummaryMotivationInterest in the international development co‐operation activities of subnational governments like Catalonia, Flanders, and Scotland has grown in recent years. Beyond these well‐known cases, however, we currently lack systematic evidence on the scope of the phenomenon.PurposeThis article introduces a new dataset of 195 European regions to provide systematic information on which regions engage in international development co‐operation. The dataset includes information on institutional structures and governance modalities, aid motivations, aid modalities, and aid policies.Methods and approachTo demonstrate the utility of our dataset, we provide descriptive insights into the phenomenon of subnational development co‐operation while at the same time suggesting questions for future research that can be addressed with the help of the dataset.FindingsWe find that subnational development co‐operation extends far beyond some well‐cited cases, given that around 70 regions have some institutional structure for development co‐operation. With relatively small budgets, regional aid delivery primarily relies on non‐governmental organizations (NGOs) and supports a variety of purposes in the sustainable development agenda, including human rights, environmental affairs, fair trade, sustainable consumption, and development education at home.Policy implicationsBeing the first of its kind, the dataset advances our understanding of subnational governments as autonomous providers of development aid and their potential role in helping advance the Sustainable Development Goals in the multi‐level global development governance architecture.