bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclease genes occupy boundaries of genetic exchange between bacteriophages
Authors: Barth Zachary K , Dunham Drew T , Seed Kimberley D 
Published: March 2023

ABSTRACTHoming endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4’s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.
Syndromic surveillance as a predictive tool for health-related school absences in COVID-19 Sentinel Schools in Catalonia, Spain
Authors: Ganem Fabiana , Alonso Lucia , Colom-Cadena Andreu , Bordas Anna , Folch Cinta , Soriano-Arandes Antoni , Casabona Jordi 
Published: March 2023

ABSTRACTMonitoring influenza-like illness through syndromic surveillance could be an important strategy in the COVID-19 emergence scenario. The study aims to implement syndromic surveillance for children aged 6-11 years in COVID-19 sentinel schools in Catalonia. Data collection was made by self-applied survey to collect daily health status and symptoms. We proceed logistic mixed models and a Latent Class Analysis to investigate associations with syndromes and school absence. Were enrolled 135 students (2163 person-days) that filled 1536 surveys and 60 participants reported illness (29.52 by 100 person/day) and registered 189 absence events, 62 of them (32.8%) related to health reasons. Subgroups of influenza-like illness were founded such as a significantly and positively association with school absences. The findings of this study can be applied to the detection of health events, and association with school absences, offering an opportunity for quick action, or simply for monitoring and understanding the students’ health situation.ARTICLE SUMMARY LINEThis study confirms the relevance of syndromic surveillance in students from 6 to 11 years of age as a strategy to timely detect events that can cause school absence, either to support public health actions by applying analytical models that improve their potential in providing systematized information, or to monitor and understand the health situation of students, thus offering an opportunity for rapid action.
MAPTallele and haplotype frequencies in Nigerian Africans: population distribution and association with Parkinson’s disease risk and age at onset
Authors: Okunoye Olaitan , Ojo Oluwadamilola , Abiodun Oladunni , Abubakar Sani , Achoru Charles , Adeniji Olaleye , Agabi Osigwe , Agulanna Uchechi , Akinyemi Rufus , Ali Mohammed , Ani-Osheku Ifeyinwa , Arigbodi Owotemu , Bello Abiodun , Erameh Cyril , Farombi Temitope , Fawale Michael , Imarhiagbe Frank , Iwuozo Emmanuel , Komolafe Morenikeji , Nwani Paul , Nwazor Ernest , Nyandaiti Yakub , Obiabo Yahaya , Odeniyi Olanike , Odiase Francis , Ojini Francis , Onwuegbuzie Gerald , Osaigbovo Godwin , Osemwegie Nosakhare , Oshinaike Olajumoke , Otubogun Folajimi , Oyakhire Shyngle , Ozomma Simon , Samuel Sarah , Taiwo Funmilola , Wahab Kolawole , Zubair Yusuf , Hernandez Dena , Bandres-Ciga Sara , Blauwendraat Cornelis , Singleton Andrew , Houlden Henry , Hardy John , Rizig Mie , Okubadejo Njideka 
Published: March 2023

AbstractBackgroundThe microtubule-associated protein tau (MAPT) gene is critical because of its putative role in the causal pathway of neurodegenerative diseases including Parkinson’s disease (PD). However, there is a lack of clarity regarding the link between the main H1 haplotype and risk of PD. Inconsistencies in reported association may be driven by genetic variability in the populations studied to date. Data onMAPThaplotype frequencies in the general population and association studies exploring the role ofMAPThaplotypes in conferring PD risk in black Africans are lacking.ObjectivesTo determine the frequencies ofMAPThaplotypes and explore the role of the H1 haplotype as a risk factor for PD risk and age at onset in Nigerian Africans.MethodsThe haplotype and genotype frequencies ofMAPTrs1052553 were analysed using PCR-based KASP™ in 907 individuals with PD and 1,022 age-matched neurologically normal controls from the Nigeria Parkinson’s Disease Research (NPDR) network cohort. Clinical data related to PD included age at study, age at onset, and disease duration.ResultsThe frequency of the mainMAPTH1 haplotype in this cohort was 98.7% in individuals with PD, and 99.1% in healthy controls (p=0.19). The H2 haplotype was present in 41/1929 (2.1%) of the cohort (PD - 1.3%; Controls - 0.9%; p=0.24). The most frequentMAPTgenotype was H1H1 (PD - 97.5%, controls - 98.2%). The H1 haplotype was not associated with PD risk after accounting for gender and age at onset (Odds ratio for H1/H1 vs H1/H2 and H2/H2: 0.68 (95% CI:0.39-1.28); p=0.23).ConclusionsOur findings support previous studies that report a low frequency of theMAPTH2 haplotype in black ancestry Africans, but document its occurrence in the Nigerian population (2.1%). In this cohort of black Africans with PD, theMAPTH1 haplotype was not associated with an increased risk or age at onset of PD.
Associations of polygenic inheritance of physical activity with aerobic fitness, cardiometabolic risk factors and diseases: the HUNT Study
Authors: Tynkkynen Niko Paavo , Törmäkangas Timo , Palviainen Teemu , Hyvärinen Matti , Klevjer Marie , Joensuu Laura , Kujala Urho , Kaprio Jaakko , Bye Anja , Sillanpää Elina 
Published: March 2023

ABSTRACTBackgroundPhysical activity (PA), aerobic fitness, and cardiometabolic diseases (CMD) are highly heritable multifactorial phenotypes. Shared genetic factors may underlie the associations between higher levels of PA and better aerobic fitness and a lower risk for cardiometabolic CMDs. Our aim was first to validate PA genotype against self-reported leisure-time PA (LTPA) and second to study how PA genotype associates with aerobic fitness and CMD risk factors. Finally, we investigated if PA genotype predicts CMD endpoints. We expected that these analyses would provide evidence for pleiotropic effects (same gene variants explaining both phenotypes) of PA and CMDs.Methods and findingsPolygenic risk score (PRS) for PA was constructed in the Trøndelag Health Study (N=47,148) using UK Biobank single nucleotide polymorphism-specific weights (N=400,124). The results showed that genotypes predisposing to higher PA were associated with greater self-reported PA (Beta [B]=0.282 MET-h·wk-1per SD of PRS for PA, 95% confidence interval [CI]=0.211, 0.354) but not with aerobic fitness. These genotypes were also associated with healthier profile in CMD risk factors (waist circumference [B=-0.003 cm, 95% CI=-0.004, -0.002], body mass index [B=-0.002 kg·(m2)-1, 95% CI=-0.004, -0.001], high-density lipoprotein cholesterol [B=0.004 mmol·L-1, 95% CI=0.002, 0.006]) and lower incidence of hypertensive diseases (HR=0.97, 95% CI=0.951, 0.990), stroke (HR=0.94, 95% CI=0.903, 0.978) and type 2 diabetes (HR=0.94, 95% CI=0.902, 0.970). When accounting for self-reported PA, the associations between PA genotypes and CMD risk factors remained statistically significant.ConclusionsGenotypes predisposing to higher PA were associated with higher amount of PA. However, in general the predictive value of the PRS for PA in predicting self-reported PA was low, possibly because of the acknowledged inconsistencies in assessing PA in cohort studies. Genotypes predisposing to higher PA were also associated with better cardiometabolic health and lower incidence of CMDs, and the observed associations were independent of self-reported PA. These results support earlier findings suggesting small pleiotropic effects between PA and CMDs and provide new evidence about associations with polygenic inheritance of PA and intermediate CMD risk factors. The observed association were however small, and results do not suggest clinical relevance in health promotion.
Neurophysiological and computational mechanisms of non-associative and associative memories during complex human behavior
Authors: Xiao Yuchen , López Paula Sánchez , Wu Ruijie , Srinivasan Ravi , Wei Peng-Hu , Shan Yong-Zhi , Weisholtz Daniel , Cosgrove Garth Rees , Madsen Joseph R , Stone Scellig , Zhao Guo-Guang , Kreiman Gabriel 
Published: March 2023

AbstractThe ability to transiently remember what happened where and when is a cornerstone of cognitive function. Forming and recalling working memories depends on detecting novelty, building associations to prior knowledge, and dynamically retrieving context-relevant information. Previous studies have scrutinized the neural machinery for individual components of recognition or associative memory under laboratory conditions, such as recalling elements from arbitrary lists of words or pictures. In this study, we implemented a well-known card- matching game that integrates multiple components of memory formation together in a naturalistic setting to investigate the dynamic neural processes underlying complex natural human memory. We recorded intracranial field potentials from 1,750 depth or subdural electrodes implanted in 20 patients with pharmacologically-intractable epilepsy while they were performing the task. We leveraged generalized linear models to simultaneously assess the relative contribution of neural responses to distinct task components. Neural activity in the gamma frequency band signaled novelty and graded degrees of familiarity, represented the strength and outcome of associative recall, and finally reflected visual feedback on a trial-by-trial basis. We introduce an attractor-based neural network model that provides a plausible first-order approximation to capture the behavioral and neurophysiological observations. The large-scale data and models enable dissociating and at the same time dynamically tracing the different cognitive components during fast, complex, and natural human memory behaviors.
Direct Thalamic Inputs to Hippocampal CA1 Transmit a Signal That Suppresses Ongoing Contextual Fear Memory Retrieval
Authors: Ratigan Heather C. , Krishnan Seetha , Smith Shai , Sheffield Mark E. J. 
Published: March 2023

SUMMARYMemory retrieval of fearful experiences is essential for survival but can be maladaptive if not appropriately suppressed. Fear memories can be acquired through contextual fear conditioning (CFC) which relies on the hippocampus. The thalamic subregion Nucleus Reuniens (NR) is necessary for contextual fear extinction and strongly projects to hippocampal subregion CA1. However, the NR-CA1 pathway has not been investigated during behavior, leaving unknown its role in contextual fear memory retrieval. We implement a novel head-restrained virtual reality CFC paradigm and show that inactivation of the NR-CA1 pathway prolongs fearful freezing epochs, induces fear generalization, and delays extinction. We usein vivosub-cellular imaging to specifically record NR-axons innervating CA1 before and after CFC. We find NR-axons become selectively tuned to freezing only after CFC, and this activity is well-predicted by an encoding model. We conclude that the NR-CA1 pathway actively suppresses fear responses by disrupting ongoing hippocampal-dependent contextual fear memory retrieval.
Accountability, emergency and liberty during COVID-19 in the UK 2020–22
Authors: Ferry Laurence , Midgley Henry , Green Stuart 
Published: March 2023

PurposeThe study explains why Parliamentarians in the United Kingdom (UK) focused on accountability through data during the COVID-19 pandemic, as well as on how data could be used to improve the government’s response to the pandemic.Design/methodology/approachUnderstanding the implications of accountability for COVID-19 is crucial to understanding how governments should respond to future pandemics. This article provides an account of what a select committee in the UK thought were the essential elements of these accountability relationships. To do so, the authors use a neo-Roman concept of liberty to show how Parliamentary oversight of the pandemic for accountability was crucial to maintaining the liberty of citizens during the crisis and to identify what lessons need to be learnt for future crises.FindingsThe study shows that Parliamentarians were concerned that the UK government was not meeting its obligations to report openly about the COVID-19 pandemic to them. It shows that the government did make progress in reporting during the pandemic but further advancements need to be made in future for restrictions to be compatible with the protection of liberty.Research limitations/implicationsThe study extends the concept of neo-Roman liberty showing how it is relevant in an emergency situation and provides an account of why accountability is necessary for the preservation of liberty when the government uses emergency powers.Practical implicationsGovernments and Parliaments need to think about how they preserve liberty during crises through enhanced accountability mechanisms and the publication of data.Originality/valueThe study extends previous work on liberty and calculation, providing a theorisation of the role of numbers in the protection of liberty.
Political connections and financial performance: the moderating role of director efficacy
Authors: Niazi Murtaza Masud , Othman Zaleha , Chandren Sitraselvi 
Published: March 2023

Purpose
Firm performance has become a thriving research field. However, a review of previous studies shows that the answers to several fundamental questions remain vague and require further investigation. Thus, the purpose of this study is twofold. The first is to determine the extent of the involvement of political connections (PCs) in Pakistani-listed companies, and the second is to examine the association between PCs and firm financial performance with director efficacy’s moderating role.

Design/methodology/approach
A data set of 221 non-financial companies listed on the Pakistan Stock Exchange for 10 years (2008–2017) was analysed using panel-corrected standard error regression. Additionally, the authors address endogeneity issue by using Hackman two-stage estimation and lagged variables regression.

Findings
The study found that PCs negatively affected the firm’s financial performance, and director efficacy as a moderator strengthened this relationship. The result is consistent with the political economy theory that argues that an unstable political system and a weak judicial system will strongly affect investors and their rights.

Practical implications
The impact of political influence on the corporate sector remains a concern for policymakers, regulators, investors, financial experts, auditors and academic researchers. This study’s findings are that an effective board of directors can strengthen the company’s best practices by controlling political connectedness to protect all the interested parties, particularly investors, and restore their confidence. Therefore, the results of this study can assist all stakeholders when a PCs exists to make the right decisions.

Originality/value
The study extends the literature in terms of theoretical contribution that uses an integrative approach to combine political economy theory, agency theory and resource dependence theory to address the moderating role of director efficacy with an association between PCs and firm financial performance. To the best of the authors’ knowledge, no extant research has investigated the association between PCs and firm financial performance using five aspects of PCs, along with moderator director efficacy.
Reciprocal action learning: manager and employee development
Authors: Lyons Paul , Bandura Randall 
Published: March 2023

Purpose
The purpose of this paper is the presentation of a learning model for a manager and employee working collaboratively to make advances in knowledge, skills, work performance and in the quality of their relationship. The model is called reciprocal action learning.

Design/methodology/approach
The approach was to examine concepts and research that could be linked to reciprocal learning. Desired, ultimately, was creation of a proposal that put forth an explanation of manager–employee learning and a means for placing the effort into practice. Theories and concepts are identified in support of the learning approach and its functioning. Action or experiential learning was identified as the vehicle for implementation.

Findings
Substantive, supportive information was identified in the expression of a practical action plan for a manager to use to spring reciprocal learning to life.

Practical implications
The action plan set forth can serve as a model or template for a manager, particularly those managers with little experience in guiding employee learning. Initial use of the concepts and action plan could be regarded as an experiment and could set the stage for additional, more informed efforts at reciprocal learning.

Originality/value
While much empirical and other research addresses employee learning and management/manager learning, there is very little research or material available regarding how a manager and an employee can directly learn together in working on an issue (problem, change, improvement, etc.) in a collaborative fashion that embraces equality.
Are more courses of immunochemotherapy beneficial for the short‐term outcome of locally advanced esophageal squamous cell carcinoma?
Authors: Huang Yuanheng , Su Xiaodong , Guo Qiyu , Luo Guangyu , He Haoqiang , Cai Peiqiang , Cai Muyan , Yue Haodong , Wang Zhiqiang , Yang Guozhen , Lin Peng , Zhang Xu 
Published: March 2023

AbstractBackgroundImmune checkpoint inhibitor (ICI) monotherapy and neoadjuvant immunochemotherapy have shown promising results in esophageal carcinoma. However, it is still unclear whether more courses of immunochemotherapy are therapeutically better. We aimed to investigate the safety and efficacy of three courses of neoadjuvant treatment for patients with locally advanced esophageal squamous cell carcinoma (ESCC).MethodsPatients with locally advanced ESCC received three courses of camrelizumab plus nab‐paclitaxel and capecitabine before undergoing surgery. Additionally, patients received safety, computed tomography (CT), and endoscopy (with endoscopic ultrasonography and mucosal biopsy) assessments before and in the second and third courses of treatment. We used the CT and endoscopic assessment results from the second and third courses for comparison.ResultsFrom May 2020 to December 2021, 47 patients were enrolled at Sun Yat‐sen University Cancer Center. In our study, 43 patients completed three courses of preoperative chemotherapy combined with anti‐Programmed cell death‐1 (PD‐1) therapy and radical surgical resection. The toxicity of the third course of immunochemotherapy was mild and well tolerated without increased treatment‐related adverse events (TRAEs) and mortality compared with that of the second course of treatment. In terms of efficacy, an additional course of treatment after the second course of treatment was effective, with increased CT and endoscopy T (clinical T stage) downstaging rates by 16.3% and 25.9%, N (clincial N stage) downstaging rates by 7.0% and 11.1%, and objective response rates (ORRs) by 13.6% and 22.0%, respectively.ConclusionsRegardless of downstaging or ORR, three courses of immunochemotherapy appear to be superior to two courses of treatment without increasing TRAEs.
Training of novice surgeons using dynamic computer assisted dental implant surgery: An exploratory randomized trial
Authors: Kunakornsawat Wirawat , Serichetaphongse Pravej , Arunjaroensuk Sirida , Kaboosaya Boosana , Mattheos Nikos , Pimkhaokham Atiphan 
Published: March 2023

AbstractBackgroundDynamic Computer Assisted Implant Surgery (CAIS) systems have been shown to improve accuracy of implant placement, thus training in the use of such systems is becoming increasingly important. There is a scarcity of research on how to implement dynamic CAIS training in the settings of postgraduate university education.PurposeTo determine the effectiveness of two modes of CAIS training programs on motor skill acquisition of novice surgeons.Materials and methodsThirty‐six postgraduate students without experience in dynamic CAIS systems were randomly assigned to a distributed training program (3 training sessions over 3 days) or a massed training (3 training sessions over the same day). A post‐test involving the placement of one implant was conducted for both groups, 7 days after completion of the training. Surgical time and implant accuracy were recorded and analyzed, using independent t‐tests, with 0.05 significant level.ResultsBoth groups reached the accuracy benchmarks expected by current standards in the use of CAIS. No significant differences with regards to accuracy were found between the groups, but a trend was documented favoring performance of distributed (mean difference—0.4, 95% confidence interval—0.7–0.1) in the accuracy at platform level. Distributed training students performed faster than massed for the third trial (mean difference—95.0, 95% confidence interval—178.8 to −11.2).ConclusionsNovice students reached the accuracy benchmarks with the use of CAIS through both a massed and a distributed training program, while there was a strong but marginally not significant trend for higher accuracy in the distributed group. Students who received the training in the distributed format over the process of different days, performed faster. Trial registered in Thai Clinical Trials Registry: https://www.thaiclinicaltrials.org/show/TCTR20230109002. This clinical trial was not registered prior to participant recruitment and randomization.
Pentanucleotide repeat‐related disorders: Genetics and bioinformatic discovery and detection
Authors: Silveira Isabel , Bennett Mark F. 
Published: March 2023

AbstractIn recent years, a large group of familial epilepsies and hereditary ataxias have emerged, caused by an extraordinary type of a novel pentanucleotide repeat expansion that has arisen in a preexisting nonpathogenic repeat tract. Remarkably, these insertions have occurred in noncoding regions of genes expressed in the cerebellum, but with highly diverse functions. These conditions, clinically very heterogeneous, may remain underdiagnosed in patients with atypical phenotypes and age at onset. They share, however, many genetic and phenotypic features, and discovery or detection of their pathogenic pentanucleotide repeats for diagnostic purposes can be achieved using recent bioinformatic methods. Here, we focus on the latest advances regarding the peculiar group of pentanucleotide repeat‐related disorders beyond epilepsies.