bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thalamus sends information about arousal but not valence to the amygdala
Authors: Leppla Chris A , Keyes Laurel R , Glober Gordon , Matthews Gillian A , Batra Kanha , Jay Maya , Feng Yu , Chen Hannah S , Mills Fergil , Delahanty Jeremy , Olson Jacob M , Nieh Edward H , Namburi Praneeth , Wildes Craig , Wichmann Romy , Beyeler Anna , Kimchi Eyal Y , Tye Kay M 
Published: July 2022

AbstractRationaleThe basolateral amygdala (BLA) and medial geniculate nucleus of the thalamus (MGN) have both been shown to be necessary for the formation of associative learning. While the role that the BLA plays in this process has long been emphasized, the MGN has been less well-studied and surrounded by debate regarding whether the relay of sensory information is active or passive.ObjectivesWe seek to understand the role the MGN has within the thalamoamgydala circuit in the formation of associative learning.MethodsHere, we use optogenetics to dissect the MGN-BLA circuit and explore the specific subpopulations for evidence of learning and synthesis of information that could impact downstream BLA encoding. We employ various machine learning techniques to investigate function within neural subpopulations. We introduce a novel method to investigate tonic changes across trial-by-trial structure, which offers an alternative approach to traditional trial-averaging techniques.ResultsWe find that the MGN appears to encode arousal but not valence, unlike the BLA which encodes for both. We find that the MGN and the BLA appear to react differently to expected and unexpected outcomes; the BLA biased responses toward reward prediction error and the MGN focused on anticipated punishment. We uncover evidence of tonic changes by visualizing changes across trials during inter-trial intervals (baseline epochs) for a subset of cells.ConclusionWe conclude that the MGN-BLA projector population acts as both filter and transferer of information by relaying information about the salience of cues to the amygdala, but these signals are not valence-specified.PrefaceIn tribute to Nadia Chaudhri, and her discoveries regarding how contexts can modulate the representation of cues in the amygdala (Sciascia et al., 2015), and other mesolimbic circuit components (Chaudhri et al., 2009, 2008; Valyear et al., 2020), here we explore what information processing precedes entry into the basolateral amygdala (BLA) from the thalamus and develop visualization approaches for exploring across-trial temporal dynamics in addition to within-trial population activity.
The 16S rRNA Gene Is Not a Precise Classifier for Luteibacter Species
Authors: Baltrus David A. , Carter Morgan E. 
Published: July 2022

AbstractLuteibacter species are found throughout agricultural and plant associated microbial communities, and have largely been identified and classified through comparisons of the 16S rRNA genes. Through comparisons of 16S classifications with whole genome phylogenies and ANI, we highlight a somewhat unique situation whereby Luteibacter pinisoli and Luteibacter sp. 9143 would be classified as the same species using 16S rRNA sequences but are clearly differentiated by these other metrics. We present this case as an outlier, but also as an example for the challenges of classification solely using 16S rRNA gene sequences.
Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications
Authors: Roura Adria-Jaume , Szadkowska Paulina , Poleszak Katarzyna , Dabrowski Michal J. , Ellert-Miklaszewska Aleksandra , Wojnicki Kamil , Ciechomska Iwona A. , Stepniak Karolina , Kaminska Bozena , Wojtas Bartosz 
Published: July 2022

AbstractBackgroundGlioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite gross surgery and forceful radio- and chemotherapy, survival of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and the transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new and targetable mechanisms of gliomagenesis.ResultsWe predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in the accessible chromatin in human glioma cells and GBM patient samples. The Cancer Genome Atlas and Glioma Atlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background. In contrast to the majority of tumors, c-Jun expression was higher in GBMs than in normal brain and c-Jun binding sites were found in multiple genes overexpressed in GBMs such as VIM, FOSL2 or UPP1. Binding of c-Jun to the VIM gene promoter is stronger in GBM cells than in cells derived from benign glioma as evidenced by gel shift and supershift assays. Regulatory regions of a majority of the c-Jun targets have distinct DNA methylation in GBMs suggesting the contribution of DNA methylation to the c-Jun-dependent regulation.ConclusionsWe identified distinct TFs-gene networks in GBMs compared to benign gliomas, a predominant role of c-Jun in controlling genes driving gliomagenesis and a modulatory role of DNA methylation.
Corruption of DNA End-Joining in Mammalian Chromosomes by Progerin Expression as Revealed by a Model Cell Culture System
Authors: Joudeh Liza A. , DiCintio Alannah J. , Ries Madeline R. , Gasperson Andrew S. , Griffin Kennedy E. , Robbins Victoria P. , Bonner Makenzie , Nolan Sarah , Black Emma , Waldman Alan S. 
Published: July 2022

ABSTRACTHutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging and a life expectancy of about 14 years. HGPS is commonly caused by a point mutation in the LMNA gene which codes for lamin A, an essential component of the nuclear lamina. The HGPS mutation alters splicing of the LMNA transcript, leading to a truncated, farnesylated form of lamin A termed “progerin.” HGPS is associated with accumulation of genomic DNA double-strand breaks (DSBs), suggesting altered DNA repair. DSB repair normally occurs by either homologous recombination (HR), an accurate, templated form of repair, or by non-homologous end joining (NHEJ), an error-prone non-templated rejoining of DNA ends. Some NHEJ events occur via high-fidelity joining of DNA ends and we refer to such events as precise ligation (PL). Previously, we reported that expression of progerin correlated with increased NHEJ relative to HR. We now report on progerin’s impact on the nature of DNA end-joining. We used a model system involving a DNA end-joining reporter substrate integrated into the genome of cultured thymidine kinase-deficient mouse fibroblasts. Some cells were engineered to express progerin. DSBs were induced in the substrate through expression of endonuclease I-SceI, and DSB repair events were recovered through selection for thymidine kinase function. Progerin expression correlated with a significant shift away from PL and toward error-prone NHEJ. Our work suggests that progerin suppresses interactions between complementary sequences at DNA termini, shifting DSB repair toward low-fidelity DNA end-joining and perhaps contributing to aging through compromised genome stability.
Differential effects of ankle constraints on foot placement control between normal and split belt treadmills
Authors: Hos Mayra , van Iersel Lieke , van Leeuwen Moira , Bruijn Sjoerd M. 
Published: July 2022

AbstractMediolateral ankle moment control contributes to gait stability. Ankle moments can be constrained by walking with a shoe with a ridge underneath the sole, narrowing the mediolateral support surface. In our previous study, such ankle moment constraints resulted in an increased step width and a decrease in the degree of foot placement control, as defined by the percentage of variance in foot placement that can be explained by CoM state. However, since our previous study was performed on a split-belt treadmill and the narrow ridge could fit inside the gap between the belts, it is not evident whether these effects can be attributed to the constrained ankle moment control or to avoidance of this gap. Therefore, we investigated if the effects of ankle moment constraints are dependent on whether participants walk on a normal treadmill or a split-belt treadmill. We included fourteen healthy young adults. Walking with constrained ankle moment control resulted in a wider step width on both treadmills. Yet, the increase in step width was larger on the split-belt treadmill compared to on the normal treadmill. We only found a decreased degree of foot placement control on the split-belt treadmill, whilst the degree of foot placement control increased on the normal treadmill. We conclude that the effects of ankle moment constraints reported in our previous study were confounded by the use of a split-belt treadmill. For future research, we recommend using a normal treadmill whenever possible, because the gap in a split-belt treadmill might affect gait parameters.
ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast
Authors: Akhuli Dipayan , Dhar Anubhav , Viji Aileen Sara , Bhojappa Bindu , Palani Saravanan 
Published: July 2022

AbstractSpecialized epitope tags continue to be an integral component in various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA Toolkit for Imaging and Biochemistry in Yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises of tagging plasmids for labelling a protein-of-interest with the ALFA tag, and detection plasmids encoding a fluorescent protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., cytoskeleton, nucleus, centrosome, divisome and exocyst) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-targeting or effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications.ImportanceIn yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Though proven to be efficient, these tags lack the versatility for usage across different cell biological and biochemical studies of a given protein-of-interest. Therefore, there is an urgent need for a unified platform for visualization, biochemical, and functional analyses of proteins-of-interest in yeast. Herein, we have engineered ALIBY, a plasmid-based toolkit which expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long duration live-cell imaging and biochemical applications in yeast.
Staphylococcus aureusBreast Implant Infection Isolates Display Recalcitrance to Antibiotic Pocket Irrigants
Authors: Duran Ramirez Jesus M. , Gomez Jana , Hanson Blake , Isa Taha , Myckatyn Terence , Walker Jennifer N 
Published: July 2022

AbstractBreast implant-associated infections (BIAIs) are a common complication following breast prostheses placement and account for ∼100,000 infections annually. The frequency, high cost of treatment, and morbidity make BIAIs a significant health burden for women. Thus, effective BIAI prevention strategies are urgently needed. This study tests the efficacy of one infection prevention strategy: the use of a triple antibiotic pocket irrigant (TAPI) againstStaphylococcus aureus, the most common cause of BIAIs. TAPI, which consists of 50,000 U bacitracin, 1 g cefazolin, and 80 mg gentamicin diluted in 500 mL of saline, is used to irrigate the breast implant pocket during surgery. We usedin vitroandin vivoassays to test the efficacy of each antibiotic in TAPI, as well as TAPI at the concentration used during surgery. We found that planktonically grownS. aureusBIAI isolates displayed susceptibility to gentamicin, cefazolin, and TAPI. However, TAPI treatment enhanced biofilm formation of BIAI strains. Furthermore, we compared TAPI treatment of aS. aureusreference strain (JE2) to a BIAI isolate (117) in a mouse BIAI model. TAPI significantly reduced infection of JE2 at 1- and 7-days post infection (dpi). In contrast, BIAI strain 117 displayed high bacterial burdens in tissues and implants, which persisted out to 14-dpi despite TAPI treatment. Lastly, we demonstrated that TAPI was effective againstP. aeruginosareference (PAO1) and BIAI strainsin vitroandin vivo. Together, these data suggestS. aureusBIAI strains employ unique mechanisms to resist antibiotic prophylaxis treatment and promote chronic infection.
Surface integrity analysis of machined surface of Ni-Ti shape memory alloy during wire spark erosion machining
Authors: Singh Thakur , Kumar Jatinder , Misra Joy Prakash 
Published: July 2022

Purpose
The purpose of this paper is to analyze the surface integrity, including recast layer thickness, surface crack density, X-ray diffractions study and microhardness for Ni53.49Ti46.51 shape memory alloy (SMA) during wire-spark erosion machining.

Design/methodology/approach
Four persuasive process parameters, that is, spark on time (SON), spark off time (SOFF), wire feed (WF) and spark gap voltage (SV), have been chosen for the current investigation. Efforts have been done to explore the effects of above said parameters on the machined surface of Ni-Ti SMA by embracing box Behnken design of response surface methodology (RSM). Cutting speed and ten-point mean roughness (Rz) has been taken into account as response variables. Analysis of variance test was also performed for both response parameters with the coefficient of determination (R2) 0.9610 for cutting speed and 0.9252 for ten-point mean Rz.

Findings
The recast layer thickness from 7.83 to 12.13 µm was developed near the machined surface at different parametric settings. The least surface crack density was found at the lowest value of ten-point mean Rz, while most surface crack density was identified at the highest value of cutting speed. The microhardness near the machined surface was increased by approximately 1.8 times bulk-hardness of Ni53.49Ti46.51 SMA.

Originality/value
Some researchers have done a study on average surface roughness, but very few investigators concentrated on ten-point mean Rz. Surface crack density is an essential aspect of machined parts; other researchers have seldom reported it. The novelty of this research work is that the influence of SON, SV, WF and SOFF on cutting speed, Rz, recast layer thickness, micro-hardness and surface crack density proximate the machined surface while machining workpiece material.
Metaverse: welcome to the new fraud marketplace
Authors: Smaili Nadia , de Rancourt-Raymond Audrey 
Published: July 2022

Purpose
The purpose of this study is to examine the risks of the metaverse ecosystem. This study provides an overview of the metaverse and its evolution and discusses the various fraud risks it poses for organizations (including boards of directors, forensic accountants, auditors and accountants). Given the advantages of the metaverse and the growing interest it is attracting from organizations, this paper sheds light on the importance of mitigating its risks.

Design/methodology/approach
Based on a systematic review of the literature on the metaverse and analysis of the fraud triangle, this study examines the different fraud risks it poses. More specifically, this study analyzes 21 articles on the metaverse published between 2021 and 2022 and attempts to answer the following research questions: What are the risks inherent in the metaverse? What are the fraud risks associated with it? What are the opportunities and pressures it brings? What is the rationalization underlying its use? This study conducts the analysis on two levels, that of the individual (user) and that of the organization. This paper summarizes the findings of publications on the metaverse in 2021 and 2022 to discover its various definitions and the opportunities and risks it represents.

Findings
This paper offers an insightful discussion of the advantages and risks the metaverse can bring. Because this analysis shows that any organization could be vulnerable to metaverse risks, this study provides organizations with strategies to deter, detect and prevent fraud and reputational risks. Regulatory bodies, financial authorities, board of directors and fraud investigators should all consider these risks before investing in the metaverse.

Originality/value
This paper adds new insights to the scarce research on the metaverse and cybersecurity by exploring the opportunities and risks it presents. It has several implications for organizations, boards of directors, management and regulatory authorities.
Remote OPAC users’ search query reformulation (SQR) patterns: a transaction log analysis
Authors: Ndumbaro Faraja 
Published: July 2022

PurposeUsers' search logs are implicit feedbacks on how searchers interact with online information retrieval (IR) systems. The purpose of this paper is to analyze search query reformulation (SQR) patterns of University of Dar es Salaam remote OPAC users.Design/methodology/approachQualitative and quantitative analysis of transaction logs were employed to ascertain the characteristics of search queries and the patterns in which remote OPAC users reformulate their search queries. The study covered a period of six months, commencing from January to June 2019.FindingsA total of 30,474 search hits were submitted by remote OPAC users during the period under study. Individuals from academic and research institutions, computing consortia, and telecommunication companies are the main users of the system. Most of the searches originated from North America and Europe, with few searches coming from China and India. Besides improving search results, SQRs are linked with the existence of multiple information demands as manifested by the use of heterogeneous headwords within individual search episodes.Research limitations/implicationsData collected covered only six months. Similarly, it was however not possible to analyze users' search query formulation within specific contexts such as task-based information searching.Practical implicationsA query recommendation system should be integrated into the OPAC functionalities to improve users' search experiences. Alternatively, there should be a migration to a new system that offers more advanced search features and functionalities.Originality/valueThe study has contributed new insights in SQR studies particularly on how non-institutional affiliated users translate their information needs into search queries during information searching processes.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-09-2020-0389
It takes a community to maintain a tree hollow: Food web complexity enhances decomposition and wood mould production
Authors: Wetherbee Ross , Birkemoe Tone , Asplund Johan , Renčo Marek , Sverdrup‐Thygeson Anne 
Published: July 2022

AbstractVeteran trees are keystone structures and play vital roles in ecosystems. Tree hollows, which are filled with a mix of leaves and wood that is transformed by the biotic community into wood mould, represent an important microhabitat. Tree hollow communities consist of three major groups of organisms: microbes, mesofauna (nematodes, mites and springtails) and macrofauna (beetles, millipedes and other insects). Little is known about the interplay between associated biota and their importance for decomposition and wood mould production. The aim of this study was to test how initial food web complexity in artificial tree hollows influences community structure, decomposition, and wood mould production. We used large wooden boxes to imitate natural hollows, and mounted them on 20 veteran oaks in Southern Norway. The food webs were manipulated into three levels: (i) a complex community with macrofauna and mesofauna, (ii) a simple community without macrofauna, and (iii) only the defaunated material. Three boxes (one of each treatment, N = 60 boxes) were mounted on each oak and left in the field from May 2017 to October 2019 (28 months). After the field experiment, macrofauna and mesofauna were collected and identified, mass loss in the boxes was determined, and nitrogen and phosphorus concentrations in the wood mould were measured. We found that the complex community treatment had the greatest diversity of beetles and the highest number of predatory macrofauna. The nematodes within the complex community treatment had greater trophic structuring with K‐selected species associated with stable conditions. The nematodes communities also indicated that the complex community had a balanced decomposition pathway, while the simple community was dominated by fungi and the defaunated community by bacteria. Lastly, we found that the boxes with the complex community treatment had the highest overall rate of mass loss, and greater amounts of wood mould with higher concentrations of nitrogen and phosphorus. Our results indicate that macrofauna in artificial hollows increase trophic structuring, enhance decomposition rates and wood mould production, and mediate the decomposition pathway. These findings highlight the importance of food web complexity for promoting biodiversity and ecosystem functioning in veteran tree hollows.Read the free Plain Language Summary for this article on the Journal blog.
Psychological well‐being and salivary markers of inflammation: The moderating effect of age
Authors: Lee Sung‐Ha , Chey Jeanyung , Ahn Woo‐Young , Woo Choong‐Wan , Youm Yoosik , Kim Hairin , Oh Naeun , Park Hyeyoung , Gim Suhwan , Lee Eunjin , Choi Incheol 
Published: July 2022

AbstractIncreasing evidence suggests a significant impact of higher psychological well‐being (PWB) on health outcomes; however, such associations have been studied exclusively in middle‐aged to older adults. This study examined the aging effect on PWB measures as well as the moderating effect of age on the link between PWB and inflammation, using salivary markers by comparing the younger adults (n = 127; Mage = 22.98 years) versus older adults (n = 75; Mage = 75.60 years). Older adults showed significantly lower levels of PWB, particularly regarding purpose in life and personal growth. Moreover, higher purpose in life was associated with lower salivary IL‐1ß and IL‐6 (b = 0.83, p < .001; b = 0.81, p < .01) only in the older adult group but not in younger adults. These findings highlight the potential buffering effect of the sense of living well on physiological pathways in later life.