bluuebunny/crossref_metadata_2025 huggingface dataset:
How does the artificial intelligence-based image-assisted technique help physicians in diagnosis of pulmonary adenocarcinoma? A randomized controlled experiment of multicenter physicians in China
Authors: Li Jiaoyang , Zhou Lingxiao , Zhan Yi , Xu Haifeng , Zhang Cheng , Shan Fei , Liu Lei
Published: October 2022

Objective

Although artificial intelligence (AI) has achieved high levels of accuracy in the diagnosis of various diseases, its impact on physicians’ decision-making performance in clinical practice is uncertain. This study aims to assess the impact of AI on the diagnostic performance of physicians with differing levels of self-efficacy under working conditions involving different time pressures.

Materials and methods

A 2 (independent diagnosis vs AI-assisted diagnosis) × 2 (no time pressure vs 2-minute time limit) randomized controlled experiment of multicenter physicians was conducted. Participants diagnosed 10 pulmonary adenocarcinoma cases and their diagnostic accuracy, sensitivity, and specificity were evaluated. Data analysis was performed using multilevel logistic regression.

Results

One hundred and four radiologists from 102 hospitals completed the experiment. The results reveal (1) AI greatly increases physicians’ diagnostic accuracy, either with or without time pressure; (2) when no time pressure, AI significantly improves physicians’ diagnostic sensitivity but no significant change in specificity, while under time pressure, physicians’ diagnostic sensitivity and specificity are both improved with the aid of AI; (3) when no time pressure, physicians with low self-efficacy benefit from AI assistance thus improving diagnostic accuracy but those with high self-efficacy do not, whereas physicians with low and high levels of self-efficacy both benefit from AI under time pressure.

Discussion

This study is one of the first to provide real-world evidence regarding the impact of AI on physicians’ decision-making performance, taking into account 2 boundary factors: clinical time pressure and physicians’ self-efficacy.

Conclusion

AI-assisted diagnosis should be prioritized for physicians working under time pressure or with low self-efficacy.
Impact of Clinical Data Veracity on Cancer Genomic Research
Authors: Mehta Sunali , Wright Deborah , Black Michael A , Merrie Arend , Anjomshoaa Ahmad , Munro Fran , Reeve Anthony , McCall John , Print Cristin
Published: October 2022

Genomic analysis of tumors is transforming our understanding of cancer. However, although a great deal of attention is paid to the accuracy of the cancer genomic data itself, less attention has been paid to the accuracy of the associated clinical information that renders the genomic data useful for research. In this brief communication, we suggest that omissions and errors in clinical annotations have a major impact on the interpretation of cancer genomic data. We describe our discovery of annotation omissions and errors when reviewing an already carefully annotated colorectal cancer gene expression dataset from our laboratory. The potential importance of clinical annotation omissions and errors was then explored using simulation analyses with an independent genomic dataset. We suggest that the completeness and veracity of clinical annotations accompanying cancer genomic data require renewed focus by the oncology research community, when planning new collections and when interpreting existing cancer genomic data.
The Subcapital Femoral Neck Stress Fracture: A Novel Subtype of Compression-sided Stress Fracture—A Report of Three Cases
Authors: Biolzi Francesco , Dinnen Ryan , Jacobs Bonamico , Doty Tyler , Barkley Colleen , Jackson Keith Lynn , Shaw K Aaron
Published: October 2022

Femoral neck stress fractures (FNSFs) are increasingly common, particularly in military training. The usual mode of classifying these injuries is based on the involvement of the compression or tension side of the femoral neck; however, this may oversimplify and fail to address factors such as the orientation of the fracture line. We present a novel subtype of a compression-sided FNSF affecting the subcapital femoral neck and report the treatment outcomes in a military trainee population. A retrospective analysis of patients with a subcapital, compression-sided FNSF was identified from a single U.S. Army basic trainee installation. Radiographic evaluation as well as treatment outcomes associated with the ability to complete military training were reported. A total of three patients with a subcapital compression-sided FNSF were identified in a military trainee population, accounting for 10% of all FNSFs that developed over a 3-month period. Of these individuals, one was treated operatively while the other two were treated non-operatively. Overall, one patient was able to return to and successfully complete military training.
Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations
Authors: Coughlan Jenn M , Dagilis Andrius J , Serrato-Capuchina Antonio , Elias Hope , Peede David , Isbell Kristin , Castillo Dean M , Cooper Brandon S , Matute Daniel R
Published: October 2022

Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.
Evaluation of activation criteria in paediatric multi-trauma
Authors: Cohen Neta , Davis Adrienne L , Test Gidon , Singer–Harel Dana , Pasternak Yehonatan , Beno Suzanne , Scolnik Dennis
Published: October 2022

Objective

To explore the optimal set of trauma activation criteria predicting paediatric patients’ need for acute care following multi-trauma, with particular attention to Glasgow Coma Scale (GCS) cut-off value.

Methods

A retrospective cohort study of paediatric multi-trauma patients aged 0 to 16 years, performed at a Level 1 paediatric trauma centre. Trauma activation criteria and GCS levels were examined with respect to patients’ need for acute care, defined as: direct to operating room disposition, intensive care unit admission, need for acute interventions in the trauma room, or in-hospital death.

Results

We enrolled 436 patients (median age 8.0 years). The following predicted need for acute care: GCS <14 (adjusted odds ratio [aOR] 23.0, 95% confidence interval [CI]: 11.5 to 45.9, P < 0.001), hemodynamic instability: (aOR 3.7, 95% CI: 1.2-8.1, P = 0.01), open pneumothorax/flail chest (aOR: 20.0, 95% CI: 4.0 to 98.7, P < 0.001), spinal cord injury (aOR 15.4, 95% CI; 2.4 to 97.1, P = 0.003), blood transfusion at the referring hospital (aOR: 7.7, 95% CI: 1.3 to 44.2, P = 0.02) and GSW to the chest, abdomen, neck, or proximal extremities (aOR 11.0, 95% CI; 1.7 to 70.8, P = 0.01). Using these activation criteria would have decreased over- triage by 10.7%, from 49.1% to 37.2% and under-triage by 1.3%, from 4.7% to 3.5%, in our cohort of patients.

Conclusions

Using GCS<14, hemodynamic instability, open pneumothorax/flail chest, spinal cord injury, blood transfusion at the referring hospital, and GSW to the chest, abdomen, neck of proximal extremities, as T1 activation criteria could decrease over- and under-triage rates. Prospective studies are needed to validate the optimal set of activation criteria in paediatric patients.
Implementation fidelity of the Promoting First Relationships intervention program in a Native community
Authors: Booth-LaForce Cathryn , Oxford Monica L , O’Leary Rae , Rees Jennifer , Petras Anthippy , Buchwald Dedra S
Published: October 2022

Promoting First Relationship (PFR) is an evidence-based intervention designed to promote positive, supportive relationships between primary caregivers and their young children. Implementing and testing the efficacy of PFR in a remote Native community is especially challenging and requires methods and tools for ensuring implementation fidelity. Tribal members of a Native community were successfully trained and certified to deliver PFR by university-based personnel. During PFR delivery, they achieved very high scores on adherence to intervention content (M = 0.99, SD = 0.02), and their quality of delivery uniformly exceeded established criteria. High attrition occurred before PFR was delivered. However, participants who remained in the study completed all 10 sessions of PFR content. Participants’ satisfaction with the program was very high (M = 3.90 [of 4 points], SD = 0.19). High implementation fidelity was attained in the face of many inherent challenges. The suite of methods and tools used for training, monitoring, and evaluating implementation fidelity in this study provides an example that may be useful in the evaluation of evidence-based programs more generally.
Illuminating Privacy and Security Concerns in Older Adults’ Technology Adoption
Authors: Knight Thora , Yuan Xiaojun , Bennett Gayle DeeDee
Published: October 2022

Privacy and security are among the salient factors that prevent older adults from adopting information communication technologies. Using the original APCO model (Antecedents, Privacy Concern, Outcomes), we conducted a PRISMA review on older adults’ perceptions of technology. This commentary draws upon findings from the PRISMA review and then proposes expansions to the APCO framework. More specifically, we advance that technology type is an antecedent to privacy concerns that contribute to older adults’ willingness to use or adopt technology. We also aggregate specific privacy and security concerns that older adults expressed are barriers to their technology use. Because these concerns vary according to technology type, we highlight methodological challenges for consideration in future research that investigates contextual relationships between technology and privacy-related factors.
Gastrointestinal Dysmotility in Critically Ill Patients
Authors: Salamone Silvia , Liu Rebecca , Staller Kyle
Published: October 2022

Disruption of normal gastrointestinal (GI) function in critical illness is linked to increased morbidity and mortality, and GI dysmotility is frequently observed in patients who are critically ill. Despite its high prevalence, the diagnosis and management of GI motility problems in the intensive care unit remain very challenging, given that critically ill patients often cannot verbalize symptoms and the general lack of understanding of underlying pathophysiology. Common clinical presentations of GI dysmotility issues among critically ill patients include: (1) high gastric residual volumes, acid reflux, and vomiting, (2) abdominal distention, and (3) diarrhea. In this review, we discuss the differential diagnosis for intensive care unit patients with symptoms and signs concerning GI motility issues. There are many myths and longstanding misconceptions about the diagnosis and management of GI dysmotility in critical illness. Here, we uncover these myths and discuss relevant evidence in each subject area, with the goal of re-conceptualizing GI motility disorders in critical care and providing evidence-based recommendations for clinical care.
Long-Term Efficacy and Safety of Fecal Microbiota Transplantation for C. difficile Infections Across Academic and Private Clinical Settings
Authors: Dogra Siddhant , Oneto Caterina , Sherman Alex , Varughese Resmi , Yuen Alexa , Sherman Isabel , Cohen Avi , Luo Yuying , Chen Lea Ann
Published: October 2022

Purpose:

Fecal microbiota transplant (FMT) is increasingly performed for Clostridioides difficile infection (CDI), although long-term efficacy and safety data are limited and are focused on results from academic medical centers rather than private settings where most patients receive care.

Methods:

Medical records of 165 patients who received FMTs for CDI were reviewed from an academic medical center and an adjacent, unaffiliated private practice. Of these patients, 68 also completed a survey regarding their long-term disease course and interval health.

Results:

CDI resolution occurred in 81.3% (100/123) at the academic center and 95.2% (40/42) in the private setting. Private practice patients were more likely to present with recurrent, rather than refractory, CDI (92.9% vs. 66.7% P<0.001). Those from the academic center were more likely to have comorbid IBD, recent hospitalization, recent proton pump inhibitor use, ongoing immunosuppression, and inpatient FMT (all P values <0.05).

Among surveyed patients, 29.4% developed interval comorbidities or changes to pre-existing conditions after a median follow-up of 33.7 months (IQR 13.2 to 44.3 mo). Of 30 patients requiring subsequent antibiotics, 13.3% suffered CDI relapse. All subjects who had initially responded to FMT but had a subsequent CDI (17.9%, 10/56) responded to another FMT.

Conclusions:

In a real-world setting, patients who underwent FMT at academic centers differed significantly in clinical characteristics from those treated at a private practice. In both settings, FMT is an effective treatment for CDI not responding to standard therapies, even after subsequent antibiotic use. New diagnoses following FMT, however, are common and merit further exploration.
Auxilliary Liver Transplantation According to the RAPID Procedure in Noncirrhotic Patients
Authors: Settmacher Utz , Ali-Deeb Aladdin , Coubeau Laurent , Cillo Umberto , Line Pål-Dag , Guba Markus , Nadalin Silvio , Rauchfuß Falk
Published: October 2022

Objective:

To present technical details and short-term experiences of liver transplantation as a 2-stage procedure using small for size grafts in a multicenter cohort study.

Background:

Two-stage liver transplantation using small for size grafts should be a feasible procedure with lower morbidity and mortality rates. Retrospective cohort study between 2015 and 2022 with multicenter experience. Twenty-three resection and partial liver transplantation with delayed total hepatectomy procedures for noncirrhotic indications were performed in 6 European centers (20 with grafts from living donors and 3 after deceased donation). Procedure’s feasibility, graft volumetric changes, morbidity, and mortality of donor and recipient were explored.

Results:

There was a low donor morbidity (4.3%) in our cohort. Hypertrophy of the graft was rapid (mean graft volume increases 107% between both stages) and offered the opportunity for remnant hepatectomy after a median of 14 days. In all cases, portomesenteric flow was routed to the graft by right remnant portal vein ligation. Portal vein inflow modulation to alleviate transient harmful portal hypertension was not needed in any case. Early postoperative mortality (4.3%) of the recipients were low. Ten patients suffered from complications ≥IIIb according to the Clavien-Dindo classification.

Conclusions:

Two-stage liver transplantation is a feasible option for noncirrhotic patients allowing the safe use of small for size grafts and could possibly be extended with caution to liver diseases with portal hypertension and cirrhosis. The resection and partial liver transplantation with delayed total hepatectomy technique might be a viable option for expanding the donor pool given the current organ shortage especially for low–model of end stage liver disease patients.
Prevent postoperative urinary retention in day surgery adult patients: evidence-based quality improvement project
Authors: Eddie Cristie Subang , Norzan Mohamad Norisham Bin , Mustafa Anith Al Bakri , Ong Shu Jie , Chan Jiah Hui , Bation Jeanibeth Molde , Owe Sze Ling , Goh Mien Li
Published: October 2022

Introduction and aims:

Postoperative urinary retention (POUR) is a complication that often leads to adverse outcomes and prolonged hospital stay if treatment is delayed. The aim of this project was to improve the competence of nurses in the provision of preoperative POUR education and ensure all patients received preoperative POUR education, and hence reduce the incidence of POUR.

Methods:

The evidence-based quality improvement project utilized JBI's Practical Application of Clinical Evidence System and Getting Research into Practice module, adopting two POUR best practice recommendations and two audit criteria. The first criterion was for nurses to conduct preoperative education on POUR and the second criterion was to initiate early ambulation of postoperative patients. The project was implemented in three phases from June 2019 to August 2020 in short-stayer and day surgery wards.

Results:

Criteria 1 and 2 revealed low compliance of 0 and 30%, respectively, during preimplementation audit. There were significant improvements in the first and second cycles of postimplementation audit for both criteria 1 and 2. Our results indicated that most of the patients who were ambulated early were able to void urine. However, there were a few incidents of urinary retention reported despite early ambulation. Following the audit of the third cycle of postimplementation, the compliance for both criteria were found to be satisfactory (criteria 1: 87%, criteria 2: 82%).

Conclusion:

The implementation of the evidence-based quality improvement project reduced the incidence of POUR. A standardized management would enable nurses to provide consistency in care and effective management and hence prevent the occurrence of POUR.
Red blood cell dynamics in extravascular biological tissues modelled as canonical disordered porous media
Authors: Zhou Qi , Schirrmann Kerstin , Doman Eleanor , Chen Qi , Singh Naval , Selvaganapathy P. Ravi , Bernabeu Miguel O. , Jensen Oliver E. , Juel Anne , Chernyavsky Igor L. , Krüger Timm
Published: October 2022

The dynamics of blood flow in the smallest vessels and passages of the human body, where the cellular character of blood becomes prominent, plays a dominant role in the transport and exchange of solutes. Recent studies have revealed that the microhaemodynamics of a vascular network is underpinned by its interconnected structure, and certain structural alterations such as capillary dilation and blockage can substantially change blood flow patterns. However, for extravascular media with disordered microstructure (e.g. the porous intervillous space in the placenta), it remains unclear how the medium’s structure affects the haemodynamics. Here, we simulate cellular blood flow in simple models of canonical porous media representative of extravascular biological tissue, with corroborative microfluidic experiments performed for validation purposes. For the media considered here, we observe three main effects: first, the relative apparent viscosity of blood increases with the structural disorder of the medium; second, the presence of red blood cells (RBCs) dynamically alters the flow distribution in the medium; third, symmetry breaking introduced by moderate structural disorder can promote more homogeneous distribution of RBCs. Our findings contribute to a better understanding of the cell-scale haemodynamics that mediates the relationship linking the function of certain biological tissues to their microstructure.
Performance Assessment of an Ultraviolet Light Emitting Semi-Conductor Device in Treating Apple Juice: Microbial Inactivation and Biochemical Assessment Study
Authors: Akwu Anita Scales , Patras Ankit , Pendyala Brahmiah , Kurup Anjali , Chen Fur-Chi , Vergne Matthew J.
Published: October 2022

Inactivation ofListeria monocytogenesATCC 19115 andSalmonella entericaserovar Muenchen ATCC BAA 1764 by a light emitting diodes (LED) operating at 279 nm was investigated. In addition, this investigation assessed the poly-phenolic and vitamin content of UV irradiated apple juice (AJ). Specific concentrations of bacteria were inoculated in AJ and irradiated at the designated UV doses of 0 to 10 mJ·cm-2forSalmonellaMuenchen and 0 to 12 mJ·cm-2forListeria monocytogenes.Results show that UV-C irradiation effectively inactivated pathogenic microbes in AJ. The log reduction kinetics of microorganisms followed log-linear and with higher R2(>0.95). The D10values of 3.50 and 3.56 mJ·cm-2were obtained from the inactivation ofSalmonellaMuenchen, andListeria monocytogenesin apple juice. In addition, quantifiable UV-C doses ranging from 0 to 160 mJ·cm-2were also delivered to AJ and polyphenols and vitamins were profiled. LC-MS/MS analysis was conducted to assess the stability of polyphenols or vitamins in UV-C exposed AJ. The polyphenol and vitamin results demonstrated that UV-C irradiation in AJ can cause significant reductions (p<0.05) if not properly delivered. Chlorogenic acid was reduced to 56%, at 80 mJ/cm2whereas 12% reduction was observed at 40 mJ/cm2. Choline was observed to be relatively stable as a function of UV-C dosage. In contrast thiamine was significantly reduced at higher doses. In addition, Epicatechin was significantly reduced at high exposure doses. In contrast minor changes were observed at 40 mJ/cm2. The results from this study imply that adequate log reduction of pathogens is achievable in AJ and suggest significant potential of using LED devices for UV-C treatment of highly turbid fluids.
Evaluating an epidemiologically motivated surrogate model of a multi-model ensemble
Authors: Abbott Sam , Sherratt Katharine , Bosse Nikos , Gruson Hugo , Bracher Johannes , Funk Sebastian
Published: October 2022

Multi-model and multi-team ensemble forecasts have become widely used to generate reliable short-term predictions of infectious disease spread. Notably, various public health agencies have used them to leverage academic disease modelling during the COVID-19 pandemic. However, ensemble forecasts are difficult to interpret and require extensive effort from numerous participating groups as well as a coordination team. In other fields, resource usage has been reduced by training simplified models that reproduce some of the observed behaviour of more complex models. Here we used observations of the behaviour of the European COVID-19 Forecast Hub ensemble combined with our own forecasting experience to identify a set of properties present in current ensemble forecasts. We then developed a parsimonious forecast model intending to mirror these properties. We assess forecasts generated from this model in real time over six months (the 15th of January 2022 to the 19th of July 2022) and for multiple European countries. We focused on forecasts of cases one to four weeks ahead and compared them to those by the European forecast hub ensemble. We find that the surrogate model behaves qualitatively similarly to the ensemble in many instances, though with increased uncertainty and poorer performance around periods of peak incidence (as measured by the Weighted Interval Score). The performance differences, however, seem to be partially due to a subset of time points, and the proposed model appears better probabilistically calibrated than the ensemble. We conclude that our simplified forecast model may have captured some of the dynamics of the hub ensemble, but more work is needed to understand the implicit epidemiological model that it represents.
Validation of a male-specific DNA marker confirms XX/XY-type sex determination in African catfish (Clarias gariepinus)
Authors: Balogh Réka Enikő , Csorbai Balázs , Guti Csaba , Keszte Szilvia , Urbányi Béla , Orbán László , Kovács Balázs
Published: October 2022

African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n=630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 2.69 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative ‘moderately sex-linked loci’ and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.
A novel pH-sensitive reporter reveals the cocaine-regulated trafficking of dopamine transporters in neuronal processes
Authors: Saenz Jacqueline , Yao Oscar , Aggarwal Meha , Zhou Xiaofeng , Barker David J. , DiCicco-Bloom Emanuel , Pan Ping-Yue
Published: October 2022

The dopamine transporter (DAT) mediated DA reuptake is a major molecular mechanism for termination of dopaminergic signaling in the brain. Psychoactive substances such as cocaine act by inhibition of plasma membrane DAT function as well as by altering its expression. The precise manner and mechanism by which cocaine regulates DAT trafficking, especially at neuronal processes, are poorly understood. We have now engineered a novel pH-sensitive reporter for DAT by conjugating pHluorin to the second exofacial loop of human DAT. We show that DAT-pHluorin can be used to study DAT localization and its dynamic trafficking at neuronal processes. Using DAT-pHluorin we show that unlike neuronal soma and dendrites, which contain majority of the DATs in weakly acidic intracellular compartments, axonal DATs at both shafts and boutons are primarily (75%) localized to the plasma membrane, while varicosities contain abundant intracellular DAT within acidic intracellular structures. Using this novel reporter, we show, for the first time, that cocaine exposure leads to a brief DAT internalization followed by membrane reinsertion that lasts for days. We further show that the cocaine-induced DAT trafficking is sensitive to the activities of Synaptojanin1 phosphatase. Thus, our study using the newly engineered DAT optical reporter reveals the previously unknown dynamics and molecular regulation for cocaine-regulated DAT trafficking in neuronal processes.
Development of novel cytoprotective small compounds inhibiting mitochondria-dependent apoptosis
Authors: Matsuyama Mieko , Ortega Joseph T. , Fedorov Yuri , Scott-McKean Jonah , Muller-Greven Jeannie , Buck Matthias , Adams Drew , Jastrzebska Beata , Greenlee William , Matsuyama Shigemi
Published: October 2022

We identified cyto-protective small molecules (CSMs) by a cell-based high-throughput screening of Bax inhibitors. Through a medicinal chemistry program, M109S was developed, which is orally bioactive and penetrates the blood-brain/retina barriers. M109S protected retinal cells in the mouse models of Stargardt disease and macular degeneration. M109S directly interacted with Bax and inhibited the conformational change and mitochondrial translocation of Bax. M109S inhibited ABT-737-induced apoptosis both in Bax-only and Bak-only MEFs. M109S also inhibited apoptosis induced by staurosporine (mouse embryonic fibroblasts), etoposide (Neuro2a cells), and obatoclax (ARPE19 cells). M109S is a novel small molecule protecting cells from mitochondria-dependent apoptosis bothin vitroandin vivo. M109S has the potential to become a new research tool for studying cell death mechanisms and to develop therapeutics targeting mitochondria-dependent cell death pathway. (128words)
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
Authors: Lea Amanda J. , Peng Julie , Ayroles Julien F.
Published: October 2022

There is increasing appreciation that, in addition to being shaped by an individual's genotype and environment, most complex traits are also determined by poorly understood interactions between these two factors. So-called “genotype × environment” (G×E) interactions remain difficult to map at the organismal level but can be uncovered using molecular phenotypes. To do so at large scale, we used TM3′seq to profile transcriptomes across 12 cellular environments in 544 immortalized B cell lines from the 1000 Genomes Project. We mapped the genetic basis of gene expression levels across environments and revealed a context-dependent genetic architecture: The average heritability of gene expression levels increased in treatment relative to control conditions, and on average, each treatment revealed new expression quantitative trait loci (eQTLs) at 11% of genes. Across our experiments, 22% of all identified eQTLs were context-dependent, and this group was enriched for trait- and disease-associated loci. Further, evolutionary analyses suggested that positive selection has shaped G×E loci involved in responding to immune challenges and hormones but not to man-made chemicals. We hypothesize that this reflects a reduced opportunity for selection to act on responses to molecules recently introduced into human environments. Together, our work highlights the importance of considering an exposure's evolutionary history when studying and interpreting G×E interactions, and provides new insight into the evolutionary mechanisms that maintain G×E loci in human populations.
Making programming part of teachers' everyday life – Programming affordances and constraints for K-12 mathematics and technology
Authors: Humble Niklas , Mozelius Peter
Published: October 2022

Purpose

The conducted examination of programming affordances and constraints had the purpose of adding knowledge and value that facilitate the on-going national curricula revision; knowledge that also could be of general interest outside the Swedish K-12 context.

Design/methodology/approach

With a qualitative approach, the study was conducted as a document analysis where submitted lesson plans were the base for a directed content analysis.

Findings

This study presents findings on how the involvement of programming in mathematics and technology have potential to foster engagement and motivation among students. Findings also indicate that the implementation of programming can develop important general skills that go beyond the boundaries of mathematics and technology. Moreover, the identified constraints could be valuable to improve the on-going curriculum development for K-12 mathematics and technology.

Research limitations/implications

This qualitative study was conducted on a relatively small number of teachers where the majority has taken the courses on a voluntary basis. An important complement would be to conduct a larger quantitative study with data from a more general sample of K-12 teachers.

Practical implications

Results and discussions provide guidance for K-12 teachers and other stakeholders who want to introduce programming as a complementary tool in teaching and learning activities.

Social implications

The study has a contribution to the on-going implementation of the Swedish national curricula for K-12 mathematics and technology.

Originality/value

During the last years, many studies have been published on teacher training in programming, and how the training can be improved. This study goes beyond the actual teacher training and examine aspects teachers translate to theirs daily work after completing the training.
Teachers' perceived sense of well-being through the lens of mattering: reclaiming the sense of community
Authors: Barrenechea Ignacio
Published: October 2022

Purpose

The concept of well-being has gained attention in the educational literature over time. Teachers around the globe are leaving the profession because they see their well-being being turned into ashes. Teachers' loss of well-being affects them and other actors of the educational system. The purpose of this paper is to look at teachers' sense of well-being through the lens of the construct of mattering.

Design/methodology/approach

Twenty-one South American Elementary Level teachers were interviewed for this qualitative study.

Findings

The paper's results suggest that teachers have experienced a loss of their sense of mattering—this sense of mattering impacts their overall level of well-being. If teachers do not feel valued or feel that they cannot add value, they will not function healthily. The author proposes that to regain their sense of mattering and increase their sense of well-being, teachers need to develop a sense of community further.

Originality/value

This paper seeks to look at the meta-construct from a more microscopic lens. Therefore, given the elusive nature of well-being, the purpose of this paper is to investigate well-being through the lens of mattering. In this paper, using the lens of mattering helps us focus on work-related manifestations of teachers' well-being in teachers working in elementary schools. Even though there are some empirical studies that have investigated the construct of mattering in educational settings, this author is not aware of empirical studies that have specifically focused on the documentation of teachers' perceived sense of mattering.
The political participation of local citizen in the elections of local leaders in Vietnam
Authors: Nguyen Thi Thuy Ngan , Nguyen Thi Phuong
Published: October 2022

Purpose

This study aims to identify the level of political participation of local citizen in 208 districts representing for 63 provinces and cities in Vietnam and consider the effects of candidate's attributes, local political contextual factors and other local citizen’s demographic characteristics on the elections of local leaders in Vietnam.

Design/methodology/approach

By using Probit model and data about provincial governance and public administration performance index and self-survey about local leaders in the districts, this paper shows the different effects of candidates’ attributes, local political context and other local citizen’s characteristics on the first and second elections of local leaders in Vietnam.

Findings

The result indicates the probability of candidates being elected in the first term depends on their characteristics, local political context and local citizen. However, the reelection of local leaders for a second term depends much on their characteristics and local political context not on demographic characteristics of local citizen. The satisfaction rate of local citizen and being an incumbent for the first term are driving forces for the local citizen to elect their leader for the second term. Meanwhile, local political context such as local transparency, local official development assistance project and citizen satisfaction will increase the likelihood of local leaders being elected for the first and second terms.

Research limitations/implications

The major limitation of this study is the data of the self-survey because it only provides basic but not complete characteristics of candidates and local contexts in some typical districts in 63 provinces and cities across the country.

Practical implications

This paper includes policy implications for candidates who want to be elected for both terms and local governance in Vietnam. The government needs to focus on building human resources for local administration to meet the requirements of building a clean, strong, modern and anticorruption administrative system.

Originality/value

This paper extends the analysis on examining the characteristics of candidates and local citizen as well as local political context influencing the elections of local leaders, getting involved in the Vietnam context, still underresearched, especially with reference to political participation of local citizen.
High‐efficiency and high‐precision seismic trace interpolation for irregularly spatial sampled data by combining an extreme gradient boosting decision tree and principal component analysis
Authors: Wu Shuliang , Wang Benfeng , Zhao Luanxiao , Liu Huaishan , Geng Jianhua
Published: October 2022

In seismic data acquisition, because of several factors, such as surface barriers, receiver failure, noise contamination and budget control, seismic records often exhibit irregular sampling in the space domain. As corrupted seismic records have a negative effect on seismic migration, inversion and interpretation, seismic trace interpolation is a key step in seismic data pre‐processing. In this paper, we propose a high‐efficiency and high‐precision seismic trace interpolation method for irregularly spatially sampled data by combining an extreme gradient boosting decision tree and principal component analysis in a semi‐supervised learning method. The adjacent trace number, sampling number and amplitudes of the effective seismic data were taken as features to build the training data set for the extreme gradient boosting decision tree. Principal component analysis is applied to remove redundant information and accelerate the training speed. This is different from the traditional trace interpolation method in that the proposed method is data‐driven; therefore, it does not require any assumptions. Compared with other deep learning‐based trace interpolation methods, the proposed method has fewer control parameters and learning labels and a smaller training cost. Experiments using synthetic and field data demonstrated the validity and flexibility of this trace interpolation method.
Distinguishing lone from group actor terrorists: A comparison of attitudes, ideologies, motivations, and risks
Authors: Dhumad Saleh , Candilis Philip J. , Cleary Sean D. , Dyer Allen R. , Khalifa Najat R.
Published: October 2022

The increasing recognition of the risks posed by lone‐actor terrorists provides the impetus for understanding the psychosocial and ideological characteristics that distinguish lone from group actors. This study examines differences between lone and group actor terrorists in two domains: (i) attitudes toward terrorism, ideology, and motivation for terrorist acts; and (ii) empirically derived risk factors for terrorism. Using a cross‐sectional research design and primary source data from 160 men convicted of terrorism in Iraq, this study applied bivariate and logistic regression analyses to assess group differences. It tested the hypothesis that there are no statistically significant differences between the groups. Bivariate analyses revealed that lone actors were less likely than group actors, to be unemployed, to cite personal or group benefit as the main motives for terrorist activity, and to believe that acts of terrorism achieved their goals. Regression analysis indicated that having an authoritarian father was the only factor that significantly predicted group membership, with group actors three times more likely to report this trait. Lone actors and group actors are almost indistinguishable except for certain differences in attitudes, motives, employment, and having an authoritarian father.
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data
Authors: Wang Yucheng , Korneliussen Thorfinn Sand , Holman Luke E. , Manica Andrea , Pedersen Mikkel Winther
Published: October 2022

Metagenomic data generated from environmental samples is increasingly common in the analysis of modern and ancient biological communities. To obtain taxonomic profiles from this type of data, DNA sequences are aligned against large genomic reference databases and the lowest common ancestor (LCA) needs to be inferred for each sequence with multiple alignments. To date, efforts have mainly focused on improving the speed, sensitivity and specificity of alignment tools, and little effort has been applied to the LCA algorithm that generates the taxonomic profiles from alignments.

We present ngsLCA, a command‐line toolkit with two separate modules: the main program (in C/C++) performing LCA inference, and an R package for generating tables and visualisations of the taxonomic profiles.

ngsLCA processed large datasets in BAM/SAM alignment format 4–11 times faster and used less memory compared to other available programs. It is compatible with the NCBI taxonomy and has flexible parameter settings. Furthermore, the toolkit offers functions for filtering, contamination removal, taxonomic clustering, and multiple ways of visualising the generated taxonomic profiles.

ngsLCA bridges a gap in current metagenomic analyses by supplying a computationally light, easy‐to‐use, accurate, fast and flexible LCA algorithm with R functions for processing and illustrating the taxonomic profiles
Use of specific agar plates for early detection of anaerobic bacteria in surgical site infections after spinal surgery: a prospective single centre study
Authors: Delaval Laure , Bouyer Benjamin , Rouis Karama , Pourbaix Annabelle , Fernandez‐Gerlinger Marie‐Paule , Podglajen Isabelle , Lebeaux David
Published: October 2022

To determine if additional agar plates could allow earlier detection of anaerobes in spinal surgical site infections (SSIs), we performed a prospective study (November 2017‐January 2019) of patients with early spinal SSIs. In addition to routine 14‐day cultures, surgical samples were inoculated onto three additional plates (CDC anaerobe agar with 5% sheep blood [CDC], CDC anaerobe laked sheep blood agar with kanamycin/vancomycin [BBL], and Bacteroides bile esculin [BBE] agar with amikacin (BD, USA)) incubated under anaerobic conditions (72 h, 37°C). The primary endpoint was detection of anaerobes by these methods, as compared to routine culture. Anaerobes were identified in 7/61 patients (11%) using the routine procedure and in one extra case with additional plates (overall detection rate 8/61, 13%). Sensitivity was greater for the CDC plate than for the BBL and BBE plates. When routine culture was positive, the CDC plate was always positive, and in three cases showed at least one additional anaerobe. Using additional agar plates, anaerobes were identified in early spinal SSI in 13% of patients. Within 3 days, CDC agar plate enabled detection of anaerobes in one extra case and at least one additional anaerobe in three other cases, compared to routine 14‐day culture.
Dodo dilemmas: Conflicting ethical loyalties in conservation social science research
Authors: Fair Hannah , Schreer Viola , Keil Paul , Kiik Laur , Rust Niki
Published: October 2022

In a time of deepening social and ecological crises, the question of research ethics is more pertinent than ever. Our intervention grapples with the specific personal, ethical, and methodological challenges that arise at the interface of conservation and social science. We expose these challenges through the figure of Chris, a fictional anonymised composite of our fraught diverse fieldwork experiences in Australia, Burma, Indonesian Borneo, Namibia, and Vanuatu. Fundamentally, we explore fieldwork as a series of contested loyalties: loyalties to our different human and non‐human research participants, to our commitments to academic rigour, and to the project of wildlife conservation itself, while reckoning with conservation's spotted (neo)colonial past. Our struggles and reflections illustrate, first, that practical research ethics do not predetermine forms of reciprocity. Second, while we need to choose our concealments carefully and follow the principle of not doing harm, we also have the responsibility to reveal social and environmental injustices. Third, we must acknowledge that as researchers we are complicit in the practices of human and non‐human violence and exclusion that suffuse conservation. Finally, given how these responsibilities move the researcher beyond a position of innocence or neutrality, academic institutions should adjust their ethics support. This intervention highlights the need for greater openness about research challenges emerging from conflicting personal, ethical, and disciplinary loyalties, in order to facilitate greater cross‐disciplinary understanding. Active engagement with these ethical questions through collaborative dialogue‐based fora, both before and after fieldwork, would enable learning and consequently transform research practices.
Replacement Adaptor 09106 for patients with a dynamic graciloplasty or patients with sacral neuromodulation and abdominal implantable pulse generators: a retrospective, single centre, Stage 2a/2b development IDEAL case series
Authors: Assmann Roman , Douven Perla , Joosten Elbert A. , van Koeveringe Gommert A. , Breukink Stephanie O. , Melenhorst Jarno
Published: October 2022

Aim

Due to the introduction of a new implantable pulse generator (IPG), the Interstim II, patients with either a dynamic graciloplasty or an abdominally placed IPG for sacral neuromodulation could not undergo surgery to replace their IPG in the case of end of battery life. For these patients, the Medtronic Replacement Adaptor 09106 was created. This retrospective case series aims to study safety and feasibility of the Medtronic Replacement Adaptor 09106 in patients with abdominally placed IPGs.

Methods

Seventeen patients (11 women, six men) received a replacement adaptor with a follow‐up of 6 months. Outcome measures consisted of a bowel habit diary. Adverse events were classified using the Clavien–Dindo classification.

Results

Outcome measures in the bowel habit diaries after replacement (feasibility) did not differ significantly from outcome measures before replacement. Adverse events occurred in four out of 17 patients (24%): two patients initially showed pocket site pain (Clavien–Dindo Grade I), which resolved without intervention. One patient suffered from poor wound closure (Clavien–Dindo Grade II) and one patient had persisting pocket pain (Clavien–Dindo Grade IIIa) for which a pocket revision was performed. Statistical analyses were performed making paired comparisons using a Wilcoxon signed rank test.

Conclusion

The Medtronic Replacement Adaptor 09106 is a valuable option for patients with dynamic graciloplasty or sacral neuromodulation and abdominal IPG and has complication rates similar to replacement of the Interstim without Replacement Adaptor 09106.