bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early life stress exposure increases susceptibility to high fat/high sucrose diet in female mice
Authors: Frick Jenna M. , Eller Olivia C. , Foright Rebecca M. , Levasseur Brittni M. , Yang Xiaofang , Wang Ruipeng , Winter Michelle K. , O’Neil Maura F. , Morris E. Matthew , Thyfault John P. , Christianson Julie A. 
Published: July 2022

AbstractExposure to stress early in life has been associated with adult-onset co-morbidities such as chronic pain, metabolic dysregulation, obesity, and inactivity. We have established an early life stress model using neonatal maternal separation (NMS) in mice, which displays evidence of increased body weight and adiposity, widespread mechanical allodynia, and hypothalamic-pituitary-adrenal axis dysregulation in male mice. Early life stress and consumption of a western style diet contribute to the development of obesity, however, relatively few pre-clinical studies have been performed in female rodents, which are known to be protected against diet induced obesity and metabolic dysfunction. In this study we gave naïve and NMS female mice access to a high-fat/high-sucrose (HFS) diet beginning at 4 weeks of age. Robust increases in body weight and fat were observed in HFS-fed NMS mice during the first 10 weeks on the diet, driven partly by increased food intake. Female NMS mice on a HFS diet showed widespread mechanical hypersensitivity compared to either naïve mice on a HFS diet or NMS mice on a control diet. HFS diet-fed NMS mice also had impaired glucose tolerance and fasting hyperinsulinemia. Strikingly, female NMS mice on a HFS diet showed evidence of hepatic steatosis with increased triglyceride levels and altered glucocorticoid receptor levels and phosphorylation state. They also exhibited increased energy expenditure as observed via indirect calorimetry and expression of pro-inflammatory markers in perigonadal adipose. Altogether, our data suggest that early life stress exposure increased the susceptibility of female mice to develop diet-induced metabolic dysfunction and pain-like behaviors.
Molecular recording of calcium concentration via calcium-dependent protein proximity labeling
Authors: Wren Kim J. , Yong Adeline J. H. , Aisenberg Erin E. , Wang Wei , Dawson Ted M. , Dawson Valina L. , Gao Ruixuan , Bateup Helen S. , Jan Yuh Nung , Ingolia Nicholas T. 
Published: July 2022

AbstractCalcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that combines the power of genetically encoded calcium indicators with protein proximity labeling. The enzyme, Cal-ID, biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity mapping in the brain. Cal-ID produces a biochemical record of calcium signaling and neuronal activity with high spatial resolution and molecular specificity.
Bioenergetic-Related Gene Expression in the Hippocampus Predicts Internalizing vs. Externalizing Behavior in a F2Cross of Selectively-Bred Rats
Authors: Hebda-Bauer Elaine K. , Hagenauer Megan H. , Munro Daniel B. , Blandino Peter , Meng Fan , Arakawa Keiko , Chitre Apurva S. , Ozel A. Bilge , Mohammadi Pejman , Watson Stanley J. , Flagel Shelly B. , Li Jun , Palmer Abraham A. , Akil Huda 
Published: July 2022

AbstractSelectively-bred High Responder (bHR) and Low Responder (bLR) rats model the extreme externalizing and internalizing behavior accompanying many psychiatric disorders. To elucidate gene expression underlying these heritable behavioral differences, bHRs and bLRs (generation 37) were used to produce a F0-F1-F2cross. We measured exploratory locomotion, anxiety-like behavior, and reward cue sensitivity (Pavlovian Conditioned Approach), and performed hippocampal RNA-Seq in male and female F0s (n=24) and F2s (n=250). Behaviors that diverged during selective breeding remained correlated in F2s, implying a shared genetic basis. F0bHR/bLR differential expression was robust, surpassing differences associated with sex, and predicted expression patterns associated with F2 behavior. With bHR-like behavior, gene sets related to growth/proliferation were upregulated, whereas with bLR-like behavior, gene sets related to mitochondrial function, oxidative stress, and microglial activation were upregulated. This differential expression could be successfully predicted based on F0 genotype using cis-expression quantitative trait loci (cis-eQTLs) identified in the F2s. Colocalization of these cis-eQTLs with behavioral Quantitative Trait Loci pinpointed 16 differentially expressed genes that were strong candidates for mediating the influence of genetic variation on behavioral temperament. Our findings implicate hippocampal bioenergetic regulation of oxidative stress, microglial activation, and growth-related processes in shaping behavioral temperament, modulating vulnerability to psychiatric disorders.
No evidence that synonymous mutations in yeast genes are mostly deleterious
Authors: Kruglyak Leonid , Beyer Andreas , Bloom Joshua S. , Grossbach Jan , Lieberman Tami D. , Mancuso Christopher P. , Rich Matthew S. , Sherlock Gavin , van Nimwegen Erik , Kaplan Craig D. 
Published: July 2022

AbstractIn a recent paper1, Shen et al. reported that most mutations in the coding regions of 21 yeast genes were strongly deleterious, and that the distributions of fitness effects were similar for synonymous and nonsynonymous mutations. Taken at face value, these results would conflict with well-established findings from a broad range of fields and approaches. Here, we argue that these results arose from a lack of appropriate controls for the impacts of background genetic effects in edited strains. A re-examination of the data in Shen et al. strongly suggests that it is entirely consistent with the expectation that most nonsynonymous and nearly all synonymous mutations have no detectable effects on fitness. We present analyses which show that the data is inconsistent with the proposed explanation that pervasive fitness effects of synonymous mutations arise from their effects on mRNA levels, that the sequence-based fitness assay overestimates fitness effects compared to the growth-based fitness assay, and that the observed wide fitness distributions for nonsense mutations are consistent with ‘off-target’ effects or other uncontrolled sources of biological variation contributing to measured fitness. We conclude by discussing the essential controls and other experimental design considerations that are required to produce interpretable results regarding the fitness effects of mutations in large-scale screens.
Inhibiting circRNA Cdr1as expression in the ILPFC of adult male C57BL/6J mice impairs fear extinction memory
Authors: Zajaczkowski Esmi Lau , Zhao Qiongyi , Liau Wei-Siang , Gong Hao , Madugalle Sachithrani Umanda , Periyakaruppiah Ambika , Leighton Laura Jane , Musgrove Mason , Ren Haobin , Davies Joshua , Marshall Paul Robert , Bredy Timothy William 
Published: July 2022

AbstractCircular RNAs (circRNAs) comprise a novel class of regulatory RNAs that are abundant in the brain, particularly within synapses. They are highly stable, dynamically regulated, and display a range of functional roles, including as decoys for miRNAs and proteins and, in some cases, translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, relatively few studies have shown a causal link between circRNA function and memory. To address this knowledge gap, we sequenced circRNAs in the synaptosome compartment of the medial prefrontal cortex of fear extinction trained male C57BL/6J mice and found 12837 circRNAs enriched at the synapse, including Cdr1as. Targeted knockdown of Cdr1as in the neural processes of the infralimbic prefrontal cortex of male C57BL/6J mice led to impaired fear extinction memory. Altogether, our findings highlight the importance of localised circRNA activity at the synapse for memory formation and suggest that circRNAs may have a more widespread effect on brain function than previously thought.
synapsis: A Bioconductor package to automate the analysis of meiotic double-strand break repair and crossover formation
Authors: McNeill Lucy , Tsui Vanessa , Crismani Wayne 
Published: July 2022

AbstractSummaryImmunofluorescent staining is commonly used to generate images to characterise cytological phenotypes. The manual quantification of DNA double-strand breaks and their repair intermediates during meiosis using image data requires a series of subjective steps, from image selection to the counting of particular events per nucleus. Here we describe synapsis, a Bioconductor package, which includes a set of functions to automate the process of identifying meiotic nuclei and quantifying key double-strand break formation and repair events in a rapid, scalable and reproducible workflow, and compare it to manual user quantification. The software can be extended for other applications in meiosis research, such as incorporating machine learning approaches to categorise meiotic substages.Availability and implementationsynapsis can be freely downloaded and installed at: http://bioconductor.org/packages/release/bioc/html/synapsis.htmlR functions and further information can be found at https://gitlab.svi.edu.au/drr-public/synapsisContactwcrismani@svi.edu.au
ompC/F mutations drive XDR phenotype and lineage defining super clones of E. coli: Sequential events and consequences
Authors: Devanga Ragupathi Naveen Kumar , Muthuirulandi Sethuvel Dhiviya Prabaa , Vasudevan Karthick , Murugan Dhivya , Neeravi Ayyan Raj , Bakthavatchalam Yamuna Devi , Velmurugan Aravind , Walia Kamini , Veeraraghavan Balaji 
Published: July 2022

AbstractMulti-drug resistant Escherichia coli is an increasing public health problem. Though, PBP3 insertions with blaNDM, blaCMY and blaOXA-48 like is restricted to South-East Asia with few reports from USA. The study suggests ompC/F variants as a core factor to classify ESBL (E), non-ESBL (NE), and ESBL with PBP3 and carbapenemases (EPBP3) clones. EPBP3 results in treatment complication, as most of the time, E. coli with PBP3 insertions co-carries blaNDM (87.5%), blaCMY (96.3%) and blaOXA-48 like (88.8%) implicating it as a predisposing factor for carbapenemase gene acquirement. Cefiderocol and cefepime/zidebactam are the choice against EPBP3 E. coli. Evolutionary BEAST analysis revealed consecutive events of YRIN and YRIK insertions in PBP3 gene leading to a surge in MDR E. coli clones. Further, emergence of the super clones STs 410, 405, 167 and 617 featuring these phenotypes is a major threat for developing and developed countries, which needs close monitoring.ImportanceThe manuscript describes various E. coli resistant genotypes across the globe and their importance in the choice of antimicrobial for treatment. The study identified six clades based on ompC and ompF mutations with a strong correlation to PBP3 insertions co-carried with beta-lactamases including blaNDM. Though, the ompC and ompF mutations were reported to precede the acquisition of carbapenemases in E. coli, clade segregation based on AMR genes as observed in this study reveals the ompC and ompF genes as a potential biomarker for AMR clade identification in E. coli. Currently, cefiderocol and cefepime/zidebactam seems to be the only choice to cover the AMR mechanism mediated by PBP3 insertions. Further, emergence of the super clones STs 410, 405, 167 and 617 featuring these PBP3 phenotypes is a major threat for developing and developed countries, which needs close monitoring.
Enabling intrusion detection systems with dueling double deep Q-learning
Authors: Badr Youakim 
Published: July 2022

PurposeIn this research, the authors demonstrate the advantage of reinforcement learning (RL) based intrusion detection systems (IDS) to solve very complex problems (e.g. selecting input features, considering scarce resources and constrains) that cannot be solved by classical machine learning. The authors include a comparative study to build intrusion detection based on statistical machine learning and representational learning, using knowledge discovery in databases (KDD) Cup99 and Installation Support Center of Expertise (ISCX) 2012.Design/methodology/approachThe methodology applies a data analytics approach, consisting of data exploration and machine learning model training and evaluation. To build a network-based intrusion detection system, the authors apply dueling double deep Q-networks architecture enabled with costly features, k-nearest neighbors (K-NN), support-vector machines (SVM) and convolution neural networks (CNN).FindingsMachine learning-based intrusion detection are trained on historical datasets which lead to model drift and lack of generalization whereas RL is trained with data collected through interactions. RL is bound to learn from its interactions with a stochastic environment in the absence of a training dataset whereas supervised learning simply learns from collected data and require less computational resources.Research limitations/implicationsAll machine learning models have achieved high accuracy values and performance. One potential reason is that both datasets are simulated, and not realistic. It was not clear whether a validation was ever performed to show that data were collected from real network traffics.Practical implicationsThe study provides guidelines to implement IDS with classical supervised learning, deep learning and RL.Originality/valueThe research applied the dueling double deep Q-networks architecture enabled with costly features to build network-based intrusion detection from network traffics. This research presents a comparative study of reinforcement-based instruction detection with counterparts built with statistical and representational machine learning.
An assessment of indoor environmental quality in COVID-19 affected houses: a case study in Banda Aceh, Indonesia
Authors: Sari Laina Hilma , Kayan Brit Anak , Zahriah Zahriah 
Published: July 2022

PurposeDuring the COVID-19 pandemic in 2020–2021 in Indonesia, the indoor environmental quality (IEQ) of local houses occupied by infected occupants was adversely affected. This paper aims to appraise the IEQ of the affected Banda Aceh houses with insights into enabling them to be resilient against the negative impacts of the pandemic.Design/methodology/approachQuantitative field measurement in the case study of five concrete houses located in urban areas which are affected by IEQ factors: (1) indoor air quality (IAQ), (2) thermal comfort and (3) visual comfort, compared against the Indonesian National standard (SNI). The case study involved measurement of the first two factors over 24 h, while the third factor was measured during sun hours. Considering the limitations of the measuring tools for logging available data in this research, air quality is measured from 8 am to 10 pm.FindingsThermal comfort in the affected houses is generally regarded as warm, optimal and cool comfort, indicated by the effective temperatures of between 20.5 and 27.1°C. Frequently closed windows, limited land area and access had caused a lack of air circulation, with air velocity of dominantly 0 m/s in the houses. The illuminance of natural light received in three houses was insufficient – less than 120 lux as compared with the other two. This study found an uptrend of higher air temperature and relative humidity in the affected houses resulting in poorer IAQ; conversely, the higher the air velocity in the houses, the fewer the indoor air pollutants such as formaldehyde (HCHO), total volatile organic compounds (TVOC) and carbon dioxide (CO2).Originality/valueThis study is a pioneer in evaluating IEQ in houses occupied by COVID-19 patients in Indonesia, especially in dwelling cases in Aceh Province. It also encompasses environmental and societal challenges to sustaining resilient buildings in pandemic hit regions.
Enhancing the resilience of road networks to flooding
Authors: Xu Wenping , Zhang Yuan , Proverbs David. , Zhong Zhi 
Published: July 2022

PurposeThis paper aims to clarify the resistance degree of group road logistics to flood disaster resilience. The paper measures the resilience of group road logistics by establishing network structure model. The purpose of this study is to improve the resilience of road log.Design/methodology/approachThis paper adopts Delphi method to collect data, interviews mainly flood management experts and supply chain risk management experts, and then analyzes the data through the network structure model combined with interpretative structure model (ISM) and analytical network process (ANP).FindingsThe results show that flood frequency and drainage systems are the main factors affecting the resilience of road transport logistics in urban areas. These research results provide useful guidance for the effective planning and design of urban road construction and infrastructure.Research limitations/implicationsHowever, the main factors affecting the resilience of road transport logistics are likely to change with the development of factors such as climate, economy and environment. Therefore, in future work, the authors' research will focus on the further application of this evaluation method.Practical implicationsThe results show that the impact of flooding on the four dimensions of road logistics resilience varies. This shows that in deciding what intervention measures are to be taken to improve the resilience of the road network to flooding, various measures need to be considered.Social implicationsThis paper provides a more scientific analysis of the risk management ability of the road network in the face of floods. In addition, it also provides a useful reference for urban road planners.Originality/valueThis paper addresses a clear need to study how to build models to improve the resilience of road logistics in flood risk.
Post-implementation challenges of ERP system in pharmaceutical companies
Authors: Singh Shikha , Singh Smriti , Misra Subhas C. 
Published: July 2022

PurposeMany organizations failed to generate profits after investing considerable money and time in Enterprise Resource Planning (ERP) systems. This study, therefore, sought to identify the challenges encountered by pharmaceutical firms during the post-implementation of ERP systems.Design/methodology/approachA case-based study followed by general survey-based research was carried out in pharmaceutical firms to determine the critical post-implementation challenges of ERP systems. DANP (DEMATEL-based ANP) and Wilcoxon Signed Rank test were used to find the causal/critical challenges and rank them.FindingsAfter analyzing a pharmaceutical case company and conducting a general survey among pharmaceutical companies, statistical analysis was performed to identify the most significant challenges, namely, “Inefficient troubleshooting mechanism”, “Lack of training during post-implementation stage” and “Difficulty in identifying invalid data when entered into the ERP system”. Furthermore, organization-wide challenges are considered to be the most important.Practical implicationsThe paper identifies the challenges faced during the post-implementation phase of ERP systems. This work brings out the issues with ERP systems' performance after their implementation, which is related to the quality of the ERP systems. This work will support the risk identification and mitigation during ERP implementation to eradicate the problems after its implementation. This work may trigger the ERP system developers to improve its features and performance for better manufacturing and supply chain management system in pharmaceutical firms.Originality/valueThis study is uniquely conducted in pharmaceutical firms to study the benefits and challenges of adopted ERP systems. A pilot case study served as the foundation for the generalizability of other pharmaceutical firms' findings through a non-parametric test.
Tribological behavior of dimples textured rolling element bearings under stepped load and starved lubrication
Authors: Long Risheng , Ma Qiang , Jin Zhihao , Zhang Yimin , Han Hui , Sun Shaoni , Du Xuanying 
Published: July 2022

Purpose
The purpose of this paper is to report the tribological behavior of dimples textured rolling element bearings (REBs) under variable load and starved lubrication.

Design/methodology/approach
The pattern parameters include line-diameter of dimples (200 µm, 250 µm, 300 µm), depth of dimples (10 µm, 20 µm, 30 µm). Dimple patterns were prepared on the raceways of the shaft washers of cylindrical roller thrust bearings (CRTBs). A vertical wear test rig was used to obtain their coefficients of friction (COFs) under stepped load (1200–6000 N, with a manually increase of 1200 N every 3600 s) and starved lubrication. The wear losses and worn surfaces were characterized. The tribological performance between stepped load and fixed load (4000 N) was compared. The influence mechanism of dimples on the friction and wear properties of CRTBs under stepped load and starved lubrication was also discussed.

Findings
Compared with the data of smooth ones, the average COFs of the dimples textured bearings are almost all reduced under stepped load and starved lubrication, while their mass losses almost all get higher. The depth−diameter ratio and the effective volume coefficient of dimples are the important factors. In this work, compared with the smooth group, when the line-diameter of dimple is 250 µm and the depth is 20 µm, i.e. the depth−diameter ratio is 0.08, its average COF is reduced by 46.8% and its mass loss is reduced by about 7%, showing wonderful friction-reducing effect and good wear resistance.

Originality/value
This work can provide a reference for the raceway design of REBs.
A study on the mediating effects of anxiety and happiness for workplace loneliness and behavioral outcomes of Korean police officers
Authors: Chung Yang Woon , Dong Xue Tong , Yun Jeong Kwon 
Published: July 2022

PurposeWorkplace loneliness has become a concern in diverse work settings. However, workplace loneliness research is in its early stages of development and not much is known about the effects of it on organizations and its members, especially in police organizations. The purpose of this study is to investigate the relationships between workplace loneliness, anxiety, happiness, task performance, and organizational citizenship behavior (OCB). Data from police officers in Korea were used to test these relationships.Design/methodology/approachUsing a three-wave time-lagged procedure, the study sample consisted of 227 police officers in South Korea from one regional police headquarters (Yongin Dongbu Police Station) and four substations in the Yongin region. The study tested parallel mediation of anxiety and happiness in the relationships between workplace loneliness and workplace outcomes using the PROCESS macro (Model 4) for SPSS 26.FindingsThe regression analyses with bootstrapping results indicated that police officers' anxiety and happiness served as mediating mechanisms linking workplace loneliness with task performance and OCB.Originality/valueThe police force is a very significant facet within society. However, research has not yet investigated loneliness in the police context. Thus, the study investigated the proximal and distal effects of workplace loneliness by associating workplace loneliness with task performance and OCB via anxiety and happiness.