bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially varying effects of measured confounding variables on disease risk
Authors: Wu Chih-Chieh , Chu Yun-Hsuan , Shete Sanjay , Chen Chien-Hsiun 
Published: November 2021

Abstract
Background
The presence of considerable spatial variability in incidence intensity suggests that risk factors are unevenly distributed in space and influence the geographical disease incidence distribution and pattern. As most human common diseases that challenge investigators are complex traits and as more factors associated with increased risk are discovered, statistical spatial models are needed that investigate geographical variability in the association between disease incidence and confounding variables and evaluate spatially varying effects on disease risk related to known or suspected risk factors. Information on geography that we focus on is geographical disease clusters of peak incidence and paucity of incidence.

Methods
We proposed and illustrated a statistical spatial model that incorporates information on known or hypothesized risk factors, previously detected geographical disease clusters of peak incidence and paucity of incidence, and their interactions as covariates into the framework of interaction regression models. The spatial scan statistic and the generalized map-based pattern recognition procedure that we recently developed were both considered for geographical disease cluster detection. The Freeman-Tukey transformation was applied to improve normality of distribution and approximately stabilize the variance in the model. We exemplified the proposed method by analyzing data on the spatial occurrence of sudden infant death syndrome (SIDS) with confounding variables of race and gender in North Carolina.

Results
The analysis revealed the presence of spatial variability in the association between SIDS incidence and race. We differentiated spatial effects of race on SIDS incidence among previously detected geographical disease clusters of peak incidence and incidence paucity and areas outside the geographical disease clusters, determined by the spatial scan statistic and the generalized map-based pattern recognition procedure. Our analysis showed the absence of spatial association between SIDS incidence and gender.

Conclusion
The application to the SIDS incidence data demonstrates the ability of our proposed model to estimate spatially varying associations between disease incidence and confounding variables and distinguish spatially related risk factors from spatially constant ones, providing valuable inference for targeted environmental and epidemiological surveillance and management, risk stratification, and thorough etiologic studies of disease.
Moderately trained male football players, compared to sedentary male adults, exhibit anatomical but not functional cardiac remodelling, a cross-sectional study
Authors: Engvall Jan E. , Aneq Meriam Åström , Nylander Eva , Brudin Lars , Maret Eva 
Published: November 2021

Abstract
Background
Elite athletes have been the subject of great interest, but athletes at an intermediate level of physical activity have received less attention in respect to the presence of cardiac enlargement and/or hypertrophy. We hypothesized that playing football, often defined as demanding less endurance components than running or cycling, would still induce remodelling similar to sports with a dominating endurance component.

Methods
23 male football players, age 25+/− 3.9 yrs. underwent exercise testing, 2D- and 3D- echocardiography and cardiac magnetic resonance (CMR). The results were compared with a control group of engineering students of similar age. The athletes exercised 12 h/week and the control subjects 1 h/week, p < 0.001.

Results
The football players achieved a significantly higher maximal load at the exercise test (380 W vs 300 W, p < 0.001) as well as higher calculated maximal oxygen consumption, (49.7 vs 37.4 mL x kg− 1 x min− 1, p < 0.001) compared to the sedentary group. All left ventricular (LV) volumes assessed by 3DEcho and CMR, as well as CMR left atrial (LA) volume were significantly higher in the athletes (3D-LVEDV 200 vs 154 mL, CMR-LVEDV 229 vs 185 mL, CMR-LA volume 100 vs 89 mL, p < 0.001, p = 0.002 and p = 0.009 respectively). LVEF and RVEF, LV strain by CMR or by echo did not differentiate athletes from sedentary participants. Right ventricular (RV) longitudinal strain, LA and right atrial (RA) strain by CMR all showed similar results in the two groups.

Conclusion
Moderately trained intermediate level football players showed anatomical but not functional cardiac remodelling compared to sedentary males.
Melatonin enhances SIRT1 to ameliorate mitochondrial membrane damage by activating PDK1/Akt in granulosa cells of PCOS
Authors: Zheng Bo , Meng Junan , Zhu Yuan , Ding Min , Zhang Yuting , Zhou Jianjun 
Published: November 2021

AbstractMitochondrial injury in granulosa cells (GCs) is associated with the pathophysiological mechanism of polycystic ovary syndrome (PCOS). Melatonin reduces the mitochondrial injury by enhancing SIRT1 (NAD-dependent deacetylase sirtuin-1), while the mechanism remains unclear. Mitochondrial membrane potential is a universal selective indicator of mitochondrial function. In this study, mitochondrial swelling and membrane defect mitochondria in granulosa cells were observed from PCOS patients and DHT-induced PCOS-like mice, and the cytochrome C level in the cytoplasm and the expression of BAX (BCL2-associated X protein) in mitochondria were significantly increased in GCs, with p-Akt decreased, showing mitochondrial membrane was damaged in GCs of PCOS. Melatonin treatment decreased mitochondrial permeability transition pore (mPTP) opening and increased the JC-1 (5,5′,6,6′-tetrachloro1,1′,3,3′-tetramethylbenzimidazolylcarbocyanine iodide) aggregate/monomer ratio in the live KGN cells treated with DHT, indicating melatonin mediates mPTP to increase mitochondrial membrane potential. Furthermore, we found melatonin decreased the levels of cytochrome C and BAX in DHT-induced PCOS mice. PDK1/Akt played an essential role in improving the mitochondrial membrane function, and melatonin treatment increased p-PDK 1 and p-Akt in vivo and in vitro. The SIRT1 was also increased with melatonin treatment, while knocking down SIRT1 mRNA inhibiting the protective effect of melatonin to activate PDK1/Akt. In conclusion, melatonin enhances SIRT1 to ameliorate mitochondrial membrane damage by activating PDK1/Akt in granulosa cells of PCOS.
Improving peer review of systematic reviews by involving librarians and information specialists: protocol for a randomized controlled trial
Authors: Rethlefsen Melissa L. , Schroter Sara , Bouter Lex M. , Moher David , Ayala Ana Patricia , Kirkham Jamie J. , Zeegers Maurice P. 
Published: November 2021

Abstract
Background
Problems continue to exist with the reporting quality and risk of bias in search methods and strategies in systematic reviews and related review types. Peer reviewers who are not familiar with what is required to transparently and fully report a search may not be prepared to review the search components of systematic reviews, nor may they know what is likely to introduce bias into a search. Librarians and information specialists, who have expertise in searching, may offer specialized knowledge that would help improve systematic review search reporting and lessen risk of bias, but they are underutilized as methodological peer reviewers.

Methods
This study will evaluate the effect of adding librarians and information specialists as methodological peer reviewers on the quality of search reporting and risk of bias in systematic review searches. The study will be a pragmatic randomized controlled trial using 150 systematic review manuscripts submitted to BMJ and BMJ Open as the unit of randomization. Manuscripts that report on completed systematic reviews and related review types and have been sent for peer review are eligible. For each manuscript randomized to the intervention, a librarian/information specialist will be invited as an additional peer reviewer using standard practices for each journal. First revision manuscripts will be assessed in duplicate for reporting quality and risk of bias, using adherence to 4 items from PRISMA-S and assessors’ judgements on 4 signaling questions from ROBIS Domain 2, respectively. Identifying information from the manuscripts will be removed prior to assessment.

Discussion
The primary outcomes for this study are quality of reporting as indicated by differences in the proportion of adequately reported searches in first revision manuscripts between intervention and control groups and risk of bias as indicated by differences in the proportions of first revision manuscripts with high, low, and unclear bias. If the intervention demonstrates an effect on search reporting or bias, this may indicate a need for journal editors to work with librarians and information specialists as methodological peer reviewers.

Trial registration
Open Science Framework. Registered on June 17, 2021, at 10.17605/OSF.IO/W4CK2.
“I took it off most of the time 'cause I felt comfortable”: unmasking, trusted others, and lessons learned from a coronavirus disease 2019 reinfection: a case report
Authors: Dariotis Jacinda K. , Sloane Stephanie M. , Smith Rebecca Lee 
Published: November 2021

Abstract
Background
Severe acute respiratory syndrome coronavirus 2 reinfection prevalence is unknown. It is essential to understand reinfection symptoms and, importantly, the lived experience.

Case presentation
Case study design is the best method for understanding this contemporary pandemic and rare occurrence of reinfections. A 19-year-old White Non-Hispanic woman presented with presumed severe acute respiratory syndrome coronavirus 2 reinfection 6 weeks after initially mild symptomatic infection and consistent repeat negative results. Real-time reverse-transcription polymerase chain reaction from saliva was used for detection. Twice-weekly saliva samples were collected (a) before initial infection, (b) resumed on day 10 after initial infection until reinfection was detected, and (c) resumed on day 10 post-reinfection. A 1.5-hour virtual interview was conducted, transcribed, and independently analyzed by two researchers. Four themes emerged: (1) perceived invincibility or inevitability and subsequent immunity increases risk of transmission via inconsistent preventive behaviors; (2) normalcy desires, trusted others, and implicit social pressures to not wear masks and distance increase one’s coronavirus disease 2019 risk; (3) physical symptoms are more severe with reinfection compared with first infection; and (4) mental health sequelae (trauma and stigma) are more severe and enduring than physical health outcomes.

Conclusions
Unmasked social interactions contradicting public health recommendations were rationalized by social circle members with heavy reliance on feeling asymptomatic, lacking a positive test (testing negative or not testing), or attributing symptoms to allergies. Stigma of testing positive and consequences of not conforming to social group behaviors is overwhelming and creates pressure to take risks. This case study provides insights and lessons learned relevant for public health messaging and continued preventive behaviors.
Exosome-associated host–pathogen interaction: a potential effect of biofilm formation
Authors: Lahiri Dibyajit , Nag Moupriya , Dey Ankita , Sarkar Tanmay , Pattnaik Smaranika , Ghosh Sougata , Edinur Hisham Atan , Pati Siddhartha , Kari Zulhisyam Abdul , Ray Rina Rani 
Published: November 2021

AbstractExosomes being non-ionized micro-vesicles with a size range of 30–100 nm possess the ability to bring about intracellular communication and intercellular transport of various types of cellular components like miRNA, mRNA, DNA, and proteins. This is achieved through the targeted transmission of various inclusions to nearby or distant tissues. This is associated with the effective communication of information to bring about changes in physiological properties and functional attributes. The extracellular vesicles (EVs), produced by fungi, parasites, and bacteria, are responsible to bring about modulation/alteration of the immune responses exerted by the host body. The lipids, nucleic acids, proteins, and glycans of EVs derived from the pathogens act as the ligands of different families of pattern recognition receptors of the host body. The bacterial membrane vesicles (BMVs) are responsible for the transfer of small RNA species, along with other types of noncoding RNA thereby playing a key role in the regulation of the host immune system. Apart from immunomodulation, the BMVs are also responsible for bacterial colonization in the host tissue, biofilm formation, and survival therein showing antibiotic resistance, leading to pathogenesis and virulence. This mini-review would focus on the role of exosomes in the development of biofilm and consequent immunological responses within the host body along with an analysis of the mechanism associated with the development of resistance.
A comprehensive overview of the genetic diversity in Thylamys elegans (Didelphimorphia: Didelphidae): establishing the phylogeographic determinants
Authors: Boric-Bargetto Dusan , Zúñiga-Reinoso Álvaro , Inostroza-Michel Oscar , Rodríguez-Serrano Enrique , González-Acuña Daniel , Palma R. Eduardo , Hernández Cristián E. 
Published: November 2021

Abstract
Background
For the genus Thylamys, the rivers have been reported as barriers to dispersal, limiting current and historical distribution of its lineages. We hypothesized that the Maipo river has affected the genetic structure of northern and southern lineages of Thylamys elegans, recovering a phylogenetic relationships with reciprocally monophyletic sister groups on opposite river banks. We evaluated the role of other rivers in the Mediterranean zone of Chile as historical and recent modulators of the biogeographic processes of this species.

Methods
We applied a phylogeographic approach, using the cytochrome-b mitochondrial gene for 93 individuals of T. elegans, from 37 localities in a latitudinal gradient between 21°25’ and 35˚56’S, encompassing a geographic area between the Atacama Desert and most of the Mediterranean Chilean zone.

Results
The phylogenetics results recovered six lineages within T. elegans: Thylamys elegans elegans, Thylamys elegans coquimbensis, the Loa lineage and three other lineages not described previously (Aconcagua, South 1 and South 2). We suggest that following rivers play a role like primary barrier: the Maipo river in the genetic differentiation of northern and southern ancestral lineages, and the Mataquito river and its tributary Teno river for the South 1 and South 2 lineages. On the other hand, the Quilimarí river preserve the genetic divergence in T. e. coquimbensis and Aconcagua lineage and the Aconcagua river in Aconcagua lineage and T. e. elegans acting like secondary barriers.

Conclusions
We concluded that the genetic diversity and biogeographic history of T. elegans was shaped by mountain glaciers, changes in river water levels during the Pleistocene glaciations and hyperaridity, promoting the differentiation and persistance of the T. elegans lineages.
Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases
Authors: Gilchrist Cameron L. M. , Chooi Yit-Heng 
Published: November 2021

Abstract
Background
Fungi are prolific producers of secondary metabolites (SMs), which are bioactive small molecules with important applications in medicine, agriculture and other industries. The backbones of a large proportion of fungal SMs are generated through the action of large, multi-domain megasynth(et)ases such as polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The structure of these backbones is determined by the domain architecture of the corresponding megasynth(et)ase, and thus accurate annotation and classification of these architectures is an important step in linking SMs to their biosynthetic origins in the genome.

Results
Here we report synthaser, a Python package leveraging the NCBI’s conserved domain search tool for remote prediction and classification of fungal megasynth(et)ase domain architectures. Synthaser is capable of batch sequence analysis, and produces rich textual output and interactive visualisations which allow for quick assessment of the megasynth(et)ase diversity of a fungal genome. Synthaser uses a hierarchical rule-based classification system, which can be extensively customised by the user through a web application (http://gamcil.github.io/synthaser). We show that synthaser provides more accurate domain architecture predictions than comparable tools which rely on curated profile hidden Markov model (pHMM)-based approaches; the utilisation of the NCBI conserved domain database also allows for significantly greater flexibility compared to pHMM approaches. In addition, we demonstrate how synthaser can be applied to large scale genome mining pipelines through the construction of an Aspergillus PKS similarity network.

Conclusions
Synthaser is an easy to use tool that represents a significant upgrade to previous domain architecture analysis tools. It is freely available under a MIT license from PyPI (https://pypi.org/project/synthaser) and GitHub (https://github.com/gamcil/synthaser).
Management control systems in response to social and environmental risk in large Nordic companies
Authors: Semenova Natalia 
Published: November 2021

AbstractThis empirical study investigates the relationships between management control systems and social and environmental risks. Building on Simons’ Levers of Control conceptual framework, this study proposes that companies facing social and environmental risks will enhance the quality of their management control systems by integrating social and environmental elements into management control systems in order to manage the related risks. The study uses a longitudinal dataset of the 1179 largest listed Nordic companies for the period 2014–2018. The multivariate regression confirms a negative relationship between the social and environmental integration and social and environmental risks. The results indicate that the social and environmental integrated performance measurement system and strategy implementation are not congruent with the social and environmental risks that the companies face. Nordic companies have not adopted the social and environmental integrated measurement system and strategy in response to social and environmental risks. When the number of social and environmental incidents increase and companies meet high levels of social and environmental risks, their management control systems do not match the related risks. Such social and environmental integration should be improved in order to prevent wider negative implications of the incidents on the natural environment and society in large.
AddaVax Formulated with PolyI:C as a Potential Adjuvant of MDCK-based Influenza Vaccine Enhances Local, Cellular, and Antibody Protective Immune Response in Mice
Authors: Nian Xuanxuan , Zhang Jiayou , Deng Tao , Liu Jing , Gong Zheng , Lv Chuanshuo , Yao Luyao , Li Junying , Huang Shihe , Yang Xiaoming 
Published: November 2021

AbstractPoor immune responses to inactivated influenza vaccine can be improved by effective and safe adjuvants to increase antibody titers and cellular protective response. In our study, AddaVax and PolyI:C combined adjuvant (AP adjuvant) were used for influenza vaccine development. After immunizing BALB/c mice and Wistar rats intramuscularly, Split inactivated H3N2 vaccine adjuvanted with AP elicited higher serum hemagglutination-inhibition antibodies and IgG titers. We demonstrated that AP induced a transient innate immune cytokines production at the injection site, induced H3N2 uptake by DCs, increased recruitment of monocytes and DCs in LNs, and promoted H3N2 vaccine migration; AP facilitated vaccines to induce a vigorous adaptive immune response. Besides, AP showed good safety as shown by lymph nodes (LNs) size, spleens index of BALB/c mice, and weight changes and C-reaction protein level of BALB/c mice and Wistar rats after repeated administration of high-dose vaccine with or without adjuvant. These findings indicate that AP is a potential novel adjuvant and can be used as a safe and effective adjuvant for MDCK-based influenza inactivated vaccine to induce cellular and antibody protective response.
Thermal–metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high-elevation hypoxia
Authors: Bodensteiner Brooke L. , Gangloff Eric J. , Kouyoumdjian Laura , Muñoz Martha M. , Aubret Fabien 
Published: November 2021

ABSTRACT
In response to a warming climate, many montane species are shifting upslope to track the emergence of preferred temperatures. Characterizing patterns of variation in metabolic, physiological and thermal traits along an elevational gradient, and the plastic potential of these traits, is necessary to understand current and future responses to abiotic constraints at high elevations, including limited oxygen availability. We performed a transplant experiment with the upslope-colonizing common wall lizard (Podarcis muralis) in which we measured nine aspects of thermal physiology and aerobic capacity in lizards from replicate low- (400 m above sea level, ASL) and high-elevation (1700 m ASL) populations. We first measured traits at their elevation of origin and then transplanted half of each group to extreme high elevation (2900 m ASL; above the current elevational range limit of this species), where oxygen availability is reduced by ∼25% relative to sea level. After 3 weeks of acclimation, we again measured these traits in both the transplanted and control groups. The multivariate thermal–metabolic phenotypes of lizards originating from different elevations differed clearly when measured at the elevation of origin. For example, high-elevation lizards are more heat tolerant than their low-elevation counterparts (counter-gradient variation). Yet, these phenotypes converged after exposure to reduced oxygen availability at extreme high elevation, suggesting limited plastic responses under this novel constraint. Our results suggest that high-elevation populations are well suited to their oxygen environments, but that plasticity in the thermal–metabolic phenotype does not pre-adapt these populations to colonize more hypoxic environments at higher elevations.
Uniportal Thoracoscopic Single-Direction Basal Subsegmentectomy (Left S10a+ci): Trans-Inferior-Pulmonary-Ligament Approach
Authors: Liu Chengwu , Wang Wenping , Mei Jiandong , Zhu Yunke , Pu Qiang , Liu Lunxu 
Published: November 2021

AbstractThoracoscopic segmentectomy and subsegmentectomy have been widely accepted for the treatment of peripheral small lung cancers. Thoracoscopic basal subsegmentectomy, especially when performed through a uniportal procedure, is extremely technically challenging, and therefore there are seldom reports of its technical details. In this article, we present a uniportal thoracoscopic left S10a+ci subsegmentectomy following the single-direction strategy through the inferior pulmonary ligament approach.