bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
Authors: Peris David , Lu Dabao Sun , Kinneberg Vilde Bruhn , Methlie Ine-Susanne , Dahl Malin Stapnes , James Timothy Y. , Kauserud Håvard , Skrede Inger
Published: March 2022

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci,MATAandMATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genusTrichaptum(Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of threeTrichaptumspecies. We characterized the chromosomal location ofMATAandMATB, the molecular structure ofMATregions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multipleMATalleles segregating before the speciation event ofTrichaptumspecies. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes.In vitrocrosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci inTrichaptumis due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.
Ongoing viral replication and production of infectious virus in patients with chronic hepatitis B virus suppressed below the limit of quantitation on long-term nucleos(t)ide therapy
Authors: Burdette Dara L , Lazerwith Scott , Yang Jenny , Chan Henry L. Y. , Delaney IV William E. , Fletcher Simon P. , Cihlar Tomas , Feierbach Becket
Published: April 2022

Nucleos(t)ide analogs are standard-of-care for the treatment of chronic hepatitis B and can effectively reduce hepatitis B virus (HBV) replication but rarely leads to cure. Nucleos(t)ide analogs do not directly eliminate the viral episome, therefore treatment cessation typically leads to rapid viral rebound. While treatment is effective, HBV DNA is still detectable (although not quantifiable) in the periphery of the majority of nucleos(t)ide analog treated HBV patients, even after prolonged treatment. Addressing whether the detectable HBV DNA represents infectious virus is a key unknown and has important implications for the development of a curative treatment for HBV. The minimum HBV genome equivalents required to establish infection in human liver chimeric mice was determined by titration of HBV patient sera and the infectivity in chimeric mice of serum from patients (n = 7) suppressed to the limit of detection on nucleos(t)ide analog therapy was evaluated. A minimum of 5 HBV genome equivalents were required to establish infection in the chimeric mice, confirming this model has sufficient sensitivity to determine whether serum from virally suppressed patients contains infectious virus. Strikingly, serum from 75% (n = 3 out of 4) of nucleos(t)ide-treated HBV patients with DNA that was detectable, but below the lower limit of quantitation, also established infection in the chimeric mice. These results demonstrate that infectious virus is still present in some HBV patients on suppressive nucleos(t)ide therapy. This residual virus may support viral persistence via continuous infection and explain the ongoing risk for HBV-related complications despite long-term suppression on therapy. Thus, additional treatment intensification may facilitate HBV cure.
Carex borealifujianica (Cyperaceae), a new species of the core Carex clade from Fujian, southeastern China
Authors: Lu Yi-Fei , Jin Xiao-Feng , Yu Ming-Jian
Published: March 2022

A new species, Carex borealifujianica Y.F. Lu & X.F. Jin (Cyperaceae, sect. Occlusae of core Carex clade) is described and illustrated from northern Fujian, China. In addition to morphological comparisons with its relatives, comparative micromorphology of utricles and achenes of seven species in Carex sect. Occlusae was examined. Micromorphology of utricles and achenes revealed the similarity of Carex borealifujianica and C. ligulata. Morphologically, this new species is similar to Carex ligulata in having lateral spikes remote and densely flowered, as well as utricles densely hispidulous, but differs in having 2 or 3 narrowly clavate staminate spikes, leaves 2.5–5 mm wide with sheaths sparsely pilose, and achenes emarginate at the apex. The phylogenetic analysis from two nuclear DNA regions (ETS and ITS) and two chloroplast DNA regions (matK and trnL-F) of 68 taxa resolved C. borealifujianica as a distinct species.
Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy
Authors: Rossi Rachele , Fang Mingyan , Zhu Lin , Jiang Chongyi , Yu Cong , Flesia Cristina , Nie Chao , Li Wenyan , Ferlini Alessandra
Published: March 2022

We designed a novel strategy to define codon usage bias (CUB) in 6 specific small cohorts of human genes. We calculated codon usage (CU) values in 29 non-disease-causing (NDC) and 31 disease-causing (DC) human genes which are highly expressed in 3 distinct tissues, kidney, muscle, and skin. We applied our strategy to the same selected genes annotated in 15 mammalian species. We obtained CUB hierarchical clusters for each gene cohort which showed tissue-specific and disease-specific CUB fingerprints. We showed that DC genes (especially those expressed in muscle) display a low CUB, well recognizable in codon hierarchical clustering. We defined the extremely biased codons as “zero codons” and found that their number is significantly higher in all DC genes, all tissues, and that this trend is conserved across mammals. Based on this calculation in different gene cohorts, we identified 5 codons which are more differentially used across genes and mammals, underlining that some genes have favorite synonymous codons in use. Since of the muscle genes clear clusters, and, among these, dystrophin genesurprisinglydoes not show any “zero codon” we adopted a novel approach to study CUB, we called “mapping-on-codons”. We positioned 2828 dystrophin missense and nonsense pathogenic variations on their respective codon, highlighting that its frequency and occurrence is not dependent on the CU values. We conclude our strategy consents to identify a hierarchical clustering of CU values in a gene cohort-specific fingerprints, with recognizable trend across mammals. In DC muscle genes also a disease-related fingerprint can be observed, allowing discrimination between DC and NDC genes. We propose that using our strategy which studies CU in specific gene cohorts, as rare disease genes, and tissue specific genes, may provide novel information about the CUB role in human and medical genetics, with implications on synonymous variations interpretation and codon optimization algorithms.
A prospective multicenter validation study of a machine learning algorithm classifier on quantitative electroencephalogram for differentiating between dementia with Lewy bodies and Alzheimer’s dementia
Authors: Suzuki Yukiko , Suzuki Maki , Shigenobu Kazue , Shinosaki Kazuhiro , Aoki Yasunori , Kikuchi Hirokazu , Baba Toru , Hashimoto Mamoru , Araki Toshihiko , Johnsen Kristinn , Ikeda Manabu , Mori Etsuro
Published: March 2022

Background and purpose

An early and accurate diagnosis of Dementia with Lewy bodies (DLB) is critical because treatments and prognosis of DLB are different from Alzheimer’s disease (AD). This study was carried out in Japan to validate an Electroencephalography (EEG)-derived machine learning algorithm for discriminating DLB from AD which developed based on a database of EEG records from two different European countries.

Methods

In a prospective multicenter study, patients with probable DLB or with probable AD were enrolled in a 1:1 ratio. A continuous EEG segment of 150 seconds was recorded, and the EEG data was processed using MC-004, the EEG-based machine learning algorithm, with all clinical information blinded except for age and gender.

Results

Eighteen patients with probable DLB and 21 patients with probable AD were the included for the analysis. The performance of MC-004 differentiating probable DLB from probable AD was 72.2% (95% CI 46.5–90.3%) for sensitivity, 85.7% (63.7–97.0%) for specificity, and 79.5% (63.5–90.7%) for accuracy. When limiting to subjects taking ≤5 mg donepezil, the sensitivity was 83.3% (95% CI 51.6–97.9), the specificity 89.5% (66.9–98.7), and the accuracy 87.1% (70.2–96.4).

Conclusions

MC-004, the EEG-based machine learning algorithm, was able to discriminate between DLB and AD with fairly high accuracy. MC-004 is a promising biomarker for DLB, and has the potential to improve the detection of DLB in a diagnostic process.
The stress sigma factor σS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of Salmonella enterica serovar Typhimurium
Authors: Metaane Selma , Monteil Véronique , Ayrault Sophie , Bordier Louise , Levi-Meyreuis Corinne , Norel Françoise
Published: March 2022

In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have previously identified sRNAs genes positively controlled by σS in Salmonella, including the two paralogous sRNA genes, ryhB1 and ryhB2/isrE. Expression of ryhB1 and ryhB2 is repressed by the ferric uptake regulator Fur when iron is available. In this study, we show that σS alleviates Fur-mediated repression of the ryhB genes and of additional Fur target genes. Moreover, σS induces transcription of the manganese transporter genes mntH and sitABCD and prevents their repression, not only by Fur, but also by the manganese-responsive regulator MntR. These findings prompted us to evaluate the impact of a ΔrpoS mutation on the Salmonella ionome. Inductively coupled plasma mass spectrometry analyses revealed a significant effect of the ΔrpoS mutation on the cellular concentration of manganese, magnesium, cobalt and potassium. In addition, transcriptional fusions in several genes involved in the transport of these ions were regulated by σS. This study suggests that σS controls fluxes of ions that might be important for the fitness of quiescent cells. Consistent with this hypothesis, the ΔrpoS mutation extended the lag phase of Salmonella grown in rich medium supplemented with the metal ion chelator EDTA, and this effect was abolished when magnesium, but not manganese or iron, was added back. These findings unravel the importance of σS and magnesium in the regrowth potential of quiescent cells.
DeBoNet: A deep bone suppression model ensemble to improve disease detection in chest radiographs
Authors: Rajaraman Sivaramakrishnan , Cohen Gregg , Spear Lillian , Folio Les , Antani Sameer
Published: March 2022

Automatic detection of some pulmonary abnormalities using chest X-rays may be impacted adversely due to obscuring by bony structures like the ribs and the clavicles. Automated bone suppression methods would increase soft tissue visibility and enhance automated disease detection. We evaluate this hypothesis using a custom ensemble of convolutional neural network models, which we call DeBoNet, that suppresses bones in frontal CXRs. First, we train and evaluate variants of U-Nets, Feature Pyramid Networks, and other proposed custom models using a private collection of CXR images and their bone-suppressed counterparts. The DeBoNet, constructed using the top-3 performing models, outperformed the individual models in terms of peak signal-to-noise ratio (PSNR) (36.7977±1.6207), multi-scale structural similarity index measure (MS-SSIM) (0.9848±0.0073), and other metrics. Next, the best-performing bone-suppression model is applied to CXR images that are pooled from several sources, showing no abnormality and other findings consistent with COVID-19. The impact of bone suppression is demonstrated by evaluating the gain in performance in detecting pulmonary abnormality consistent with COVID-19 disease. We observe that the model trained on bone-suppressed CXRs (MCC: 0.9645, 95% confidence interval (0.9510, 0.9780)) significantly outperformed (p < 0.05) the model trained on non-bone-suppressed images (MCC: 0.7961, 95% confidence interval (0.7667, 0.8255)) in detecting findings consistent with COVID-19 indicating benefits derived from automatic bone suppression on disease classification. The code is available at https://github.com/sivaramakrishnan-rajaraman/Bone-Suppresion-Ensemble.
Cardiovascular risk scores in asymptomatic carotid stenosis: A validation study with ultrasonographic parameters
Authors: Kang Min Kyoung , Nam Ki-Woong , Shin Jung Hwan , Kwon Hyung-Min , Lee Yong-Seok
Published: April 2022

We evaluated the feasibility of the Framingham stroke risk score (FSRS) and atherosclerotic cardiovascular disease (ASCVD) risk scores for asymptomatic carotid stenosis (ACS). In addition, we developed novel risk prediction models for ischemic stroke and composite outcomes by combining ultrasonographic parameters and conventional cardiovascular risk scores. We retrospectively enrolled 612 patients with ACS greater than 50% over 7 years and evaluated them using transcranial Doppler and carotid duplex ultrasonography. In total, 150 patients were included in the analysis. During the mean 5-year follow-up, 6 ischemic strokes and 25 composite events were detected. Among all ultrasonographic parameters, only a higher peak-systolic velocity/end-diastolic velocity ratio was detected and significantly associated with an increased risk of relevant ischemic stroke (hazard ratio: 1.502, 95% confidence interval: 1.036–1.968). The C-statistics of the FSRS and ASCVD risk scores were 0.646 and 0.649, respectively, for relevant ischemic stroke, and 0.612 and 0.649, respectively, for composite outcomes. C-statistics of the FSRS and ASCVD risk scores combined with ultrasonographic parameters increased to 0.937 and 0.941, respectively, for ischemic stroke, and 0.856 and 0.886, respectively, for composite outcomes. The study suggests that inclusion of ultrasonographic parameters in conventional cardiovascular scores helps identify the risk of further vascular events in ACS patients.
Response of runoff towards land use changes in the Yellow River Basin in Ningxia, China
Authors: Wang Zhanping , Tian Juncang , Feng Kepeng
Published: April 2022

Since the Yellow River is a main source of water in Ningxia China, maintaining its healthy ecological environment is vital to Ningxia and the neighboring areas. Changes of land use caused by human activities such as population growth, urbanizing process, and industrial and mining construction would affect the balance and cycle of water in the Basin. Therefore, investigating hydrological responses of land use changes can provide insights into the characteristics and evolution of runoff the Yellow River Basin in the Ningxia section. This has imperative and practical significance to the rational use, allocation, and planning of water resources in a changing environment. In this paper, we analyzed the meteorological and hydrological elements of changing characteristics of the Yellow River Basin in the Ningxia section. Then we selected a distribution-based hydrology model of SWAT in combination with GIS to simulate annual and monthly runoff under different land use scenarios. Finally, we analyzed the influence caused by the changes of land use on runoff. We concluded that it is appropriate to lay a decision-making foundation to manage water resources of the Yellow River Basin in the Ningxia section.
Exploring a peptide nucleic acid-based antisense approach for CD5 targeting in chronic lymphocytic leukemia
Authors: Cesaro Elena , Falanga Andrea Patrizia , Catapano Rosa , Greco Francesca , Romano Simona , Borbone Nicola , Pastore Arianna , Marzano Maria , Chiurazzi Federico , D’Errico Stefano , Piccialli Gennaro , Oliviero Giorgia , Costanzo Paola , Grosso Michela
Published: March 2022

We herein report an innovative antisense approach based on Peptide Nucleic Acids (PNAs) to down-modulate CD5 expression levels in chronic lymphocytic leukemia (CLL). Using bioinformatics tools, we selected a 12-mer tract of the CD5 mRNA as the molecular target and synthesized the complementary and control PNA strands bearing a serine phosphate dipeptide tail to enhance their water solubility and bioavailability. The specific recognition of the 12-mer DNA strand, corresponding to the target mRNA sequence by the complementary PNA strand, was confirmed by non-denaturing polyacrylamide gel electrophoresis, thermal difference spectroscopy, circular dichroism (CD), and CD melting studies. Cytofluorimetric assays and real-time PCR analysis demonstrated the downregulation of CD5 expression due to incubation with the anti-CD5 PNA at RNA and protein levels in Jurkat cell line and peripheral blood mononuclear cells from B-CLL patients. Interestingly, we also observed that transfection with the anti-CD5 PNA increases apoptotic response induced by fludarabine in B-CLL cells. The herein reported results suggest that PNAs could represent a potential candidate for the development of antisense therapeutic agents in CLL.
On the relationship between predictive coding and backpropagation
Authors: Rosenbaum Robert
Published: March 2022

Artificial neural networks are often interpreted as abstract models of biological neuronal networks, but they are typically trained using the biologically unrealistic backpropagation algorithm and its variants. Predictive coding has been proposed as a potentially more biologically realistic alternative to backpropagation for training neural networks. This manuscript reviews and extends recent work on the mathematical relationship between predictive coding and backpropagation for training feedforward artificial neural networks on supervised learning tasks. Implications of these results for the interpretation of predictive coding and deep neural networks as models of biological learning are discussed along with a repository of functions, Torch2PC, for performing predictive coding with PyTorch neural network models.
Training and mentorship as a tool for building African researchers’ capacity in knowledge translation
Authors: Oronje Rose N. , Mukiira Carol , Kahurani Elizabeth , Murunga Violet
Published: March 2022

As one of the main knowledge producers, researchers can play an important role in contributing to efforts that bridge the gap between knowledge, policy and practice. However, for researchers to play this role, they need knowledge translation (KT) capacities that many typically lack. Furthermore, research has confirmed that little is known on KT training approaches for LMICs researchers and their effectiveness. This paper seeks to contribute to filling this knowledge gap on KT training approaches for LMIC researchers by assessing the effectiveness of a training and mentorship intervention to build African researchers’ KT capacity. We conducted KT training and mentorship for 23 early and mid-career researchers from 20 universities in sub-Saharan Africa. This comprised a 5-day intense residential training workshop, followed by a 6-months mentorship. A pre- and post-training test was used to assess the immediate effect of the workshop. The intermediate effect of the training following a 6-month mentorship was assessed by the number of researchers who completed policy briefs during this period and those who participated in the webinar series conducted during this period. Overall, the aggregate average point change in the self-reported learning between the pre-training and the post-training survey was 1.9, which demonstrated the effectiveness of the training workshop. This was confirmed by a 33.7% increase in the aggregate average percentage of participants that responded correctly to questions assessing topics covered in the training between the pre-training and the post-training survey. During the mentorship period, 19 of the 23 researchers prepared and submitted complete drafts of their policy briefs within two months after the training. Fewer (4) researchers revised and submitted final policy briefs. More than half of the trained researchers participated in the webinars conducted in the first three months of the mentorship, whereas less than half of the researchers participated in the webinars conducted in the last three months. KT training and mentorship can be an effective intervention for addressing researchers’ KT capacity gaps. For sustainability, KT training and mentorship need to be integrated in graduate training programmes in universities so that future LMIC researchers leave training institutions with the KT capacities they need for influencing policy and programme decisions and actions.
Relative effectiveness of medications for opioid-related disorders: A systematic review and network meta-analysis of randomized controlled trials
Authors: Lim Jihoon , Farhat Imen , Douros Antonios , Panagiotoglou Dimitra
Published: March 2022

Introduction

Several pharmacotherapeutic interventions are available for maintenance treatment for opioid-related disorders. However, previous meta-analyses have been limited to pairwise comparisons of these interventions, and their efficacy relative to all others remains unclear. Our objective was to unify findings from different healthcare practices and generate evidence to strengthen clinical treatment protocols for the most widely prescribed medications for opioid-use disorders.

Methods

We searched Medline, EMBASE, PsycINFO, CENTRAL, and ClinicalTrials.gov for all relevant randomized controlled trials (RCT) from database inception to February 12, 2022. Primary outcome was treatment retention, and secondary outcome was opioid use measured by urinalysis. We calculated risk ratios (RR) and 95% credible interval (CrI) using Bayesian network meta-analysis (NMA) for available evidence. We assessed the credibility of the NMA using the Confidence in Network Meta-Analysis tool.

Results

Seventy-nine RCTs met the inclusion criteria. Due to heterogeneity in measuring opioid use and reporting format between studies, we conducted NMA only for treatment retention. Methadone was the highest ranked intervention (Surface Under the Cumulative Ranking [SUCRA] = 0.901) in the network with control being the lowest (SUCRA = 0.000). Methadone was superior to buprenorphine for treatment retention (RR = 1.22; 95% CrI = 1.06–1.40) and buprenorphine superior to naltrexone (RR = 1.39; 95% CrI = 1.10–1.80). However, due to a limited number of high-quality trials, confidence in the network estimates of other treatment pairs involving naltrexone and slow-release oral morphine (SROM) remains low.

Conclusion

All treatments had higher retention than the non-pharmacotherapeutic control group. However, additional high-quality RCTs are needed to estimate more accurately the extent of efficacy of naltrexone and SROM relative to other medications. For pharmacotherapies with established efficacy profiles, assessment of their long-term comparative effectiveness may be warranted.

Trial Registration

This systematic review has been registered with PROSPERO (https://www.crd.york.ac.uk/prospero) (identifierCRD42021256212).
Factors affecting fisher decisions: The case of the inshore fishery for European sea bass (Dicentrarchus labrax)
Authors: Watson Joseph W. , Muench Angela , Hyder Kieran , Sibly Richard
Published: March 2022

Fishery management relies on forecasts of fish abundance over time and space, on scales of months and kilometres. While much research has focussed on the drivers of fish populations, there has been less investigation of the decisions made day-to-day by fishers and their subsequent impact on fishing pressure. Studies that focus on the fisher decisions of smaller vessels may be particularly important due to the prevalence of smaller vessels in many fisheries and their potential vulnerability to bad weather and economic change. Here we outline a methodology with which to identify the factors affecting fisher decisions and success as well as quantifying their effects. We analyse first the decision of when to leave port, and then the success of the fishing trip. Fisher behaviour is here analysed in terms of the decisions taken by fishers in response to bio-physical and socio-economic changes and to illustrate our method, we describe its application to the under 10-meter fleet targeting sea bass in the UK. We document the effects of wave height and show with increasing wave height fewer vessels left port to go fishing. The decision to leave port was only substantially affected by time of high tide at one of the four ports investigated. We measured the success of fishing trips by the landings of sea bass (kg) per metre of vessel length. Fishing success was lower when wave height was greater and when fish price had increased relative to the previous trip. Fuel price was unimportant, but a large proportion of the variation in success was explained by variation between individual vessels, presumably due to variation in skipper ability or technical restrictions due to vessel characteristics. The results are discussed in the context of management of sea bass and other small-scale inshore fisheries.
An integrated hospital-district performance evaluation for communicable diseases in low-and middle-income countries: Evidence from a pilot in three sub-Saharan countries
Authors: Tavoschi Lara , Belardi Paolo , Mazzilli Sara , Manenti Fabio , Pellizzer Giampietro , Abebe Desalegn , Azzimonti Gaetano , Nsubuga John Bosco , Dall’Oglio Giovanni , Vainieri Milena
Published: March 2022

Introduction

The last two decades saw an extensive effort to design, develop and implement integrated and multidimensional healthcare evaluation systems in high-income countries. However, in low- and middle-income countries, few experiences of such systems implementation have been reported in the scientific literature. We developed and piloted an innovative evaluation tool to assess the performance of health services provision for communicable diseases in three sub-Saharan African countries.

Material and methods

A total of 42 indicators, 14 per each communicable disease care pathway, were developed. A sub-set of 23 indicators was included in the evaluation process. The communicable diseases care pathways were developed for Tuberculosis, Gastroenteritis, and HIV/AIDS, including indicators grouped in four care phases: prevention (or screening), diagnosis, treatment, and outcome. All indicators were calculated for the period 2017–2019, while performance evaluation was performed for the year 2019. The analysis involved four health districts and their relative hospitals in Ethiopia, Tanzania, and Uganda.

Results

Substantial variability was observed over time and across the four different districts. In the Tuberculosis pathway, the majority of indicators scored below the standards and below-average performance was mainly reported for prevention and diagnosis phases. Along the Gastroenteritis pathway, excellent performance was instead evaluated for most indicators and the highest scores were reported in prevention and treatment phases. The HIV/AIDS pathway indicators related to screening and outcome phases were below the average score, while good or excellent performance was registered within the treatment phase.

Conclusions

The bottom-up approach and stakeholders’ engagement increased local ownership of the process and the likelihood that findings will inform health services performance and quality of care. Despite the intrinsic limitations of data sources, this framework may contribute to promoting good governance, performance evaluation, outcomes measurement and accountability in settings characterised by multiple healthcare service providers.
Medical residents’ mental distress in the COVID-19 pandemic: An urgent need for mental health care
Authors: Steil Amanda , Pereira Tokeshi Ana Bresser , Bernardo Luca Silveira , da Silva Neto Geraldo Pio , Davi Ronald Ferreira , Bárbara Amanda Ferreira Santa , Mendonca Vitor S. , Fidalgo Thiago M. , Teixeira Gois Aécio Flávio
Published: March 2022

Purpose

Medical residents’ mental health is currently an issue of concern for medical educators worldwide. The COVID-19 pandemic has raised the greatest concerns given the psychological effects of this scenario on medical residents on the frontlines of the pandemic. To assess the psychological impact of the COVID-19 pandemic on physicians in residency training, the collective symptoms of burnout, depression and anxiety are used to identify the residents’ beliefs and clinical practices related to COVID-19 patients and their behaviors concerning disease prevention.

Method

This observational study involved 3071 medical residents from all regions of Brazil. An online questionnaire assessed the presence of burnout using the Oldenburg Burnout Inventory, depressive symptoms using the Patient Health Questionaire-9, anxiety symptoms using the Generalized Anxiety Disorder-7, and COVID-19 Impact Questions to assess the residents’ beliefs and clinical practices related to COVID-19 patients. Exploratory analyses, logistic regression and multinomial regression analysis were performed in this investigation.

Results

Moderate and severe depressive symptoms were the most common (67.7%) followed by anxiety symptoms (52.8%) and burnout (48.6%). The difference between residents with or without contact with COVID-19 patients was significant increased when analyzing different aspects of clinical practice, behavior, substance use and mental health.

Conclusions

These results suggest an increase in depression and anxiety symptoms among medical residents dealing with COVID-19, upstaging previous concerns about medical residents’ mental health. The prevalence of burnout is similar to that of a nonpandemic scenario. Considering the severity of the pandemic scenario and the overburden of healthcare services, medical residents’ mental health deserves special care.
Social-ecological factors related to preventive behaviors during the COVID-19 pandemic in South Korea
Authors: Jang Sou Hyun
Published: March 2022

Most studies on COVID-19 preventive behaviors have focused on single-level factors such as national policy, community social capital, or individuals’ sociodemographic characteristics. Through a social-ecological model, this study attempts to comprehensively examine the multilevel factors associated with COVID-19 preventive practices in South Korea. Accordingly, a web survey involving 1,500 participants was conducted in December 2020. An ordinary least squares (OLS) regression was used to examine the multilevel factors (individual, interpersonal, community, and policy levels) related to COVID-19 preventive measures, which are based on wearing a mask, washing hands, covering the mouth when coughing or sneezing, and social distancing. When factors at each level were investigated, higher scores of COVID-19 fear and correct knowledge at the individual level, COVID-19 information share at the interpersonal level, and better evaluation of the national government policies in regard to COVID-19 at the policy level were positively associated with COVID-19 preventive behaviors. Community-level factors—neighborhood perception and community participation—were negatively significantly related to COVID-19 preventive behaviors. Additionally, older age, being female, and having a graduate-level education were positively related to better preventive behaviors. The findings of the current study suggest that multilevel efforts are needed to promote preventive behaviors. Specifically, more effort to alleviate COVID-19-related fear and disseminate correct knowledge among Korean citizens is needed as the individual-level characteristics explained the preventive behaviors more than the factors at upper levels.
Association between miRNA-499 gene polymorphism and autoimmune diseases: A meta-analysis
Authors: Kong Xiangjian , Diao Shuling , Xu Huipu , Sun Junming , Ma Baoxin
Published: March 2022

Introduction

The association between miRNA-499 rs3746444 and a variety of autoimmune diseases has been reported. However, these results were contradictory and just focused on one or two autoimmune diseases. The present study aims to examine the possible association between rs3746444 polymorphism and the risk of autoimmune diseases.

Methods

The studies that evaluated the association between miRNA-499 gene polymorphism and autoimmune diseases were retrieved. Five different genetic models were used to evaluate the association. The random-effects model was used to pool the effect sizes. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the associations. Stratification analyses were performed by ethnicity and type of autoimmune diseases. False-positive report probability (FPRP) was performed for determining noteworthy associations.

Results

Seventeen articles (twenty studies) involving 4,376 cases and 4,991 controls were identified and included in our meta-analysis. The pooled ORs of all eligible case-control studies indicated a significant association between miRNA-499 gene polymorphism and autoimmune diseases: (T vs. C: OR = 0.877; 95% CI: 0.774, 0.993; P = 0.039). Stratified analysis indicated a significant association across both Caucasian (TT vs. TC+CC: OR = 0.779; 95% CI: 0.622, 0.976; P = 0.030) and Asian (T vs. C: OR = 0.895; 95% CI: 0.808, 0.992; P = 0.035) populations. There was also a significant association in Behcet’s disease, rheumatoid arthritis, systemic lupus erythematosus, and ulcerative colitis populations.

Conclusions

Our meta-analysis suggested that the miRNA-499 rs3746444 polymorphism was associated with an elevated risk of autoimmune diseases in the overall analysis as well as Caucasian and Asian populations.
The effect of COVID-19 on public hospital revenues in Iran: An interrupted time-series analysis
Authors: Behzadifar Masoud , Aalipour Afshin , Kehsvari Mohammad , Darvishi Teli Banafsheh , Ghanbari Mahboubeh Khaton , Gorji Hasan Abolghasem , Sheikhi Alaeddin , Azari Samad , Heydarian Mohammad , Ehsanzadeh Seyed Jafar , Kong Jude Dzevela , Ahadi Maryam , Bragazzi Nicola Luigi
Published: March 2022

Background

The “Coronavirus Disease 2019” (COVID-19) pandemic has become a major challenge for all healthcare systems worldwide, and besides generating a high toll of deaths, it has caused economic losses. Hospitals have played a key role in providing services to patients and the volume of hospital activities has been refocused on COVID-19 patients. Other activities have been limited/repurposed or even suspended and hospitals have been operating with reduced capacity. With the decrease in non-COVID-19 activities, their financial system and sustainability have been threatened, with hospitals facing shortage of financial resources. The aim of this study was to investigate the effects of COVID-19 on the revenues of public hospitals in Lorestan province in western Iran, as a case study.

Method

In this quasi-experimental study, we conducted the interrupted time series analysis to evaluate COVID-19 induced changes in monthly revenues of 18 public hospitals, from April 2018 to August 2021, in Lorestan, Iran. In doing so, public hospitals report their earnings to the University of Medical Sciences monthly; then, we collected this data through the finance office.

Results

Due to COVID-19, the revenues of public hospitals experienced an average monthly decrease of $172,636 thousand (P-value = 0.01232). For about 13 months, the trend of declining hospital revenues continued. However, after February 2021, a relatively stable increase could be observed, with patient admission and elective surgeries restrictions being lifted. The average monthly income of hospitals increased by $83,574 thousand.

Conclusion

COVID-19 has reduced the revenues of public hospitals, which have faced many problems due to the high costs they have incurred. During the crisis, lack of adequate fundings can damage healthcare service delivery, and policymakers should allocate resources to prevent potential shocks.
Electrical activity and fatigue of respiratory and locomotor muscles in obstructive respiratory diseases during field walking test
Authors: Cavalcanti Jéssica D. , Fregonezi Guilherme Augusto F. , Sarmento Antonio J. , Bezerra Thiago , Gualdi Lucien P. , Pennati Francesca , Aliverti Andrea , Resqueti Vanessa R.
Published: April 2022

Introduction

In subjects with obstructive respiratory diseases the increased work of breathing during exercise can trigger greater recruitment and fatigue of respiratory muscles. Associated with these changes, lower limb muscle dysfunctions, further contribute to exercise limitations. We aimed to assess electrical activity and fatigue of two respiratory and one locomotor muscle during Incremental Shuttle Walking Test (ISWT) in individuals with obstructive respiratory diseases and compare with healthy.

Methods

This is a case-control study. Seventeen individuals with asthma (asthma group) and fifteen with chronic obstructive pulmonary disease (COPD group) were matched with healthy individuals (asthma and COPD control groups). Surface electromyographic (sEMG) activity of sternocleidomastoid (SCM), scalene (ESC), and rectus femoris (RF) were recorded during ISWT. sEMG activity was analyzed in time and frequency domains at baseline and during the test (33%, 66%, and 100% of ISWT total time) to obtain, respectively, signal amplitude and power spectrum density (EMG median frequency [MF], high- and low-frequency bands, and high/low [H/L] ratio).

Results

Asthma group walked a shorter distance than controls (p = 0.0007). sEMG amplitudes of SCM, ESC, and RF of asthma and COPD groups were higher at 33% and 66% of ISWT compared with controls groups (all p<0.05). SCM and ESC of COPD group remained higher until 100% of the test. MF of ESC and RF decreased in asthma group (p = 0.016 and p < 0.0001, respectively) versus controls, whereas MF of SCM (p < 0.0001) decreased in COPD group compared with controls. H/L ratio of RF decreased (p = 0.002) in COPD group versus controls.

Conclusion

Reduced performance is accompanied by increased electromyographic activity of SCM and ESC and activation of RF in individuals with obstructive respiratory diseases during ISWT. These are susceptible to be more pronounced respiratory and peripheral muscle fatigue than healthy subjects during exercise.
Characterization of locomotor phenotypes in zebrafish larvae requires testing under both light and dark conditions
Authors: Tuz-Sasik Melek Umay , Boije Henrik , Manuel Remy
Published: April 2022

Despite growing knowledge, much remains unknown regarding how signaling within neural networks translate into specific behaviors. To pursue this quest, we need better understanding of the behavioral output under different experimental conditions. Zebrafish is a key model to study the relationship between network and behavior and illumination is a factor known to influence behavioral output. By only assessing behavior under dark or light conditions, one might miss behavioral phenotypes exclusive to the neglected illumination setting. Here, we identified locomotor behavior, using different rearing regimes and experimental illumination settings, to showcase the need to assess behavior under both light and dark conditions. Characterization of free-swimming zebrafish larvae, housed under continuous darkness or a day/night cycle, did not reveal behavioral differences; larvae were most active during light conditions. However, larvae housed under a day/night cycle moved a shorter distance, had lower maximum velocity and maximum acceleration during the startle response under light conditions. Next, we explored if we could assess behavior under both dark and light conditions by presenting these conditions in sequence, using the same batch of larvae. Our experiments yielded similar results as observed for naïve larvae: higher activity during light conditions, regardless of order of illumination (i.e. dark-light or light-dark). Finally, we conducted these sequenced illumination conditions in an experimental setting by characterizing behavioral phenotypes in larvae following neuromast ablation. Depending on the illumination during testing, the behavioral phenotype following ablation was characterized differently. In addition, the results indicate that the order in which the light and dark conditions are presented has to be considered, as habituation may occur. Our study adds to existing literature on illumination-related differences in zebrafish behavior and emphasize the need to explore behavioral phenotypes under both light and dark condition to maximize our understanding of how experimental permutations affect behavior.
Unraveling the molecular determinants of the anti-phagocytic protein cloak of plague bacteria
Authors: Peters Daniel T. , Reifs Antonio , Alonso-Caballero Alvaro , Madkour Azzeldin , Waller Helen , Kenny Brendan , Perez-Jimenez Raul , Lakey Jeremy H.
Published: March 2022

The pathogenic bacteriumYersina pestisis protected from macrophage engulfment by a capsule like antigen, F1, formed of long polymers of the monomer protein, Caf1. However, despite the importance of this pathogen, the mechanism of protection was not understood. Here we demonstrate how F1 protects the bacteria from phagocytosis. First, we show thatEscherichia coliexpressing F1 showed greatly reduced adherence to macrophages. Furthermore, the few cells that did adhere remained on the macrophage surface and were not engulfed. We then inserted, by mutation, an “RGDS” integrin binding motif into Caf1. This did not change the number of cells adhering to macrophages but increased the fraction of adherent cells that were engulfed. Therefore, F1 protects in two separate ways, reducing cell adhesion, possibly by acting as a polymer brush, and hiding innate receptor binding sites needed for engulfment. F1 is very robust and we show thatE.coliexpressing weakened mutant polymers are engulfed like the RGDS mutant. This suggests that innate attachment sites on the native cell surface are exposed if F1 is weakened. Single-molecule force spectroscopy (SMFS) experiments revealed that wild-type F1 displays a very high mechanical stability of 400 pN. However, the mechanical resistance of the destabilised mutants, that were fully engulfed, was only 20% weaker. By only marginally exceeding the mechanical force applied to the Caf1 polymer during phagocytosis it may be that the exceptional tensile strength evolved to resist the forces applied at this stage of engulfment.
The interplay between authenticity, realism and cultural proximity in the reception of Turkish drama serials among Qatari audiences
Authors: Berg Miriam
Published: April 2022

This article explores how young Qatari audiences perceive authenticity in Turkish television dramas. The concepts of authenticity and realism are used as analytical tools to examine empirical findings from twenty focus group discussions with students, in 2016 and 2017. The results reveal that young Qataris see Turkish serials as offering a more authentic representation of real life than local and regional television serials. Although Turkish drama serials do not provide a window into actual life within Turkish society, they are perceived as offering a realistic depiction of characters and storylines representing Turkey’s social life and culture. This article establishes that Turkish serials’ dubbing into a colloquial Syrian dialect has heightened audience experience of authenticity. The fact that Turkish dramas were created against the backdrop of a Muslim country with significant ethnic and cultural similarities further elevated the Arab audiences’ perception of authenticity.
Fecobionics Evaluation of Biofeedback Therapy in Patients With Fecal Incontinence
Authors: Futaba Kaori , Chen Ssu-Chi , Leung Wing Wa , Wong Cherry , Mak Tony , Ng Simon , Gregersen Hans
Published: April 2022

INTRODUCTION:

Biofeedback therapy (BFT) is a well-known treatment for functional anorectal disorders. The effect of BFT was monitored in fecal incontinence (FI) patients with the Fecobionics test and with the conventional technologies, anorectal manometry (ARM) and balloon expulsion test (BET).

METHODS:

Studies were performed in 12 patients before and after 8 weeks of biofeedback training. The Fecal Incontinence Severity Index (FISI) score was obtained. Anal resting and squeeze pressures were measured before the bag was distended in the rectum until urge to defecate. Pressure recordings were made during Fecobionics evacuation.

RESULTS:

BFT resulted in 24% reduction in FISI scores (P < 0.01). Seven patients were characterized as responders. Anal pressures, the urge-to-defecate volume, and defecatory parameters did not change significantly during BFT. For ARM-BET, the maximum anal squeeze pressure, the urge-to-defecate volume, and the expulsion time were lower after BFT compared with those before BFT (P < 0.05). For Fecobionics, the change in urge volume (r = 0.74, P < 0.05) and the change in defecation index (r = 0.79, P < 0.01) were associated with the change in FISI score. None of the ARM-BET parameters were associated with the change in FISI score. It was studied whether any pre-BFT data could predict treatment success. The Fecobionics expulsion duration and the defecation index predicted the outcome (P < 0.05). The defecation index had a sensitivity of 100% and a specificity of 72%. None of the ARM-BET parameters predicted the outcome (all P > 0.2).

DISCUSSION:

Fecobionics was used as a tool to monitor the effect of BFT and proved better than conventional technologies for monitoring and predicting the outcome in the FISI score.