bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotype–Phenotype correlations of SCARB2 associated clinical presentation: a case report and in-depth literature review
Authors: Atasu Burcu , Acarlı Ayse Nur Ozdag , Bilgic Basar , Baykan Betül , Demir Erol , Ozluk Yasemin , Turkmen Aydin , Hauser Ann-Kathrin , Guven Gamze , Hanagasi Hasmet , Gurvit Hakan , Emre Murat , Gasser Thomas , Lohmann Ebba
Published: March 2022

Background

Biallelic pathogenic variants in the SCARB2 gene have been associated with action myoclonus-renal failure (AMRF) syndrome. Even though SCARB2 associated phenotype has been reported to include typical neurological characteristics, depending on the localization and the feature of the pathogenic variants, clinical course and the presentations have been shown to differ.

Case presentation

Whole exome sequencing (WES) analysis revealed a homozygous truncating variant (p.N45MfsX88) in SCARB2 gene in the index case, and subsequent sanger sequencing analysis validated the variant in all affected family members from a Turkish family with the clinical characteristics associated with AMRF and related disorders. Intrafamilial clinical heterogeneity with common features including dysarthria, tremor and proteinuria, and distinct features such as peripheral neuropathy (PNP), myoclonus and seizures between the affected cases, was observed in the family.

In-depth literature review enabled the detailed investigation of the reported variants associated with AMRF and suggested that while the type of the variant did not have a major impact on the course of the clinical characteristics, only the C terminal localization of the pathogenic variant significantly affected the clinical presentation, particularly the age at onset (AO) of the disease.

Conclusions

In this study we showed that biallelic SCARB2 pathogenic variants might cause a spectrum of common and distinct features associated with AMRF. Of those features while the common features include myoclonus (100%), ataxia (96%), tonic clonic seizures (82%), dysarthria (68%), tremor (65%), and renal impairment (62%), the uncommon features involve PNP (17%), hearing loss (6.8%), and cognitive impairment (13.7%). AO has been found to be significantly higher in the carriers of the p.G462DfsX34 pathogenic variant.

SCARB2 pathogenic variants have not been only implicated in AMRF but also in the pathogenesis of Parkinson’s disease (PD) and Gaucher disease (GD), suggesting the importance of genetic and functional studies in the clinical and the diagnostic settings.

Given the proven role of SCARB2 gene in the pathogenesis of AMRF, PD and GD with a wide spectrum of clinical symptoms, investigation of the possible modifiers, such as progranulin and HSP7, has a great importance.
Facilitating stress prevention in micro and small-sized enterprises: protocol for a mixed method study to evaluate the effectiveness and implementation process of targeted web-based interventions
Authors: Engels Miriam , Boß Leif , Engels Judith , Kuhlmann Rebekka , Kuske Johanna , Lepper Sarah , Lesener Lutz , Pavlista Valeria , Diebig Mathias , Lunau Thorsten , Ruhle Sascha A. , Zapkau Florian B. , Angerer Peter , Hoewner Jörg , Lehr Dirk , Schwens Christian , Süß Stefan , Wulf Ines C. , Dragano Nico
Published: March 2022

Background

Workplace-related stress is a major risk factor for mental and physical health problems and related sickness absence and productivity loss. Despite evidence regarding the effectiveness of different workplace-based interventions, the implementation of stress prevention interventions is rare, especially in micro and small-sized enterprises (MSE) with fewer than 50 employees. The joint research project “PragmatiKK”+ aims to identify and address the specific barriers to the implementation of stress prevention interventions in MSE. This study protocol describes a mixed method study design to evaluate the effectiveness of adapted stress prevention interventions and the implementation process via an integrated web-based platform (“System P”) specifically targeted at MSE.

Methods

First, we develop a web-based intervention, which accounts for the specific working conditions in MSE and addresses stress prevention at a structural and behavioral level. Second, we use common methods of implementation research to perform an effect and process evaluation. We analyze the effectiveness of the web-based stress prevention interventions by comparing depressive symptoms at baseline and follow-up (after 6 months and 12 months). Indicators for a successful implementation process include acceptability, adoption, feasibility, reach, dose, and fidelity, which we will measure with quantitative web-based questionnaires and qualitative interviews. We will also analyze the accumulated usage data from the web-based platform.

Discussion

Collecting data on the implementation process and the effectiveness of a web-based intervention will help to identify and overcome common barriers to stress prevention in MSE. This can improve the mental health of employees in MSE, which constitute more than 90% of all enterprises in Germany.

+ Full Project Name: „PragmatiKK - Pragmatische Lösungen für die Implementation von Maßnahmen zur Stressprävention in Kleinst- und Kleinbetrieben “(= Pragmatic solutions for the implementation of stress prevention interventions in micro and small-sized enterprises).

Trial registration

German Register of Clinical Studies (DRKS): DRKS00026154, date of registration: 2021-09-16.
Parental education moderates the association between indoor moisture environment and asthma in adolescents: the Greek Global Asthma Network (GAN) cross-sectional study
Authors: Antonogeorgos George , Liakou Evangelia , Koutsokera Alexandra , Drakontaeidis Pavlos , Thanasia Marina , Mandrapylia Maria , Fouzas Sotirios , Ellwood Philippa , García-Marcos Luis , Panagiotakos Demosthenes B. , Priftis Kostas N. , Douros Konstantinos
Published: March 2022

Objective

Asthma is a major contributor to childhood morbidity. Several environmental and socioeconomic status (SES) factors have been implicated in its etiopathogeneses such as indoor moisture and parental education level. Our study examined the association between exposure to indoor dampness and/or mould (IDM) with adolescent asthma and how parental education could modify or mediate this relationship.

Method

A total of 1934 adolescents (boys: 47.5%, mean age (standard variation): 12.7(0.6) years) and their parents were voluntarily enrolled and completed a validated questionnaire on adolescents’ asthma status, parental educational level, and adolescents’ indoor exposure to IDM during three different lifetime periods, i.e., pregnancy, the first year of life and the current time.

Results

There was a significant modification effect of parental education only for the current exposure; higher parental education lowered almost 50% the odds of IDM and asthma (adjusted odds ratio (aOR): 1.96, 95% Confidence Intervals (CI): (1.05–3.68) and aOR:1.55, 95% CI (1.04–2.32), for primary/secondary and tertiary parental education, respectively).

Conclusion

Adolescents whose parents had a higher education level had lesser odds to have asthma, even if they were exposed to a moisture home environment. This could be attributed to the increased knowledge about asthma risk factors and the improved measures for the amelioration of moisture-home environment that highly educated parents are more likely to take. Further research is needed in order to elucidate the interweaved role of family SES in the aforementioned relation.
Healthcare costs of patients with chronic obstructive pulmonary disease in Denmark – specialist care versus GP care only
Authors: Lykkegaard Jesper , Nielsen Jesper Bo , Storsveen Maria Munch , Jarbøl Dorte Ejg , Søndergaard Jens
Published: March 2022

Background

Many patients with chronic obstructive pulmonary disease (COPD) are treated in general practice only and have never received specialist care for COPD. They are seldom included in COPD cost studies but may account for a substantial proportion of the total costs.

Objective

To estimate and specify the total healthcare costs of patients who are treated for COPD in Denmark comparing those who have- and have not had specialist care for COPD.

Setting

Denmark, population 5.7 million citizens.

Methods

Via national registers, we specified the total healthcare costs of all + 30-years-old current users of respiratory pharmaceuticals. We identified the patients with COPD and compared those with at least one episode of pulmonary specialist care to those with GP care only.

Results

Among totally 329,428 users of respiratory drugs, we identified 46,084 with specialist-care- and 68,471 with GP-care-only COPD. GP-care-only accounted for 40% of the two populations’ total healthcare costs. The age- and gender-adjusted coefficient relating the individual total costs specialist-care versus GP-care-only was 2.19. The individual costs ranged widely and overlapped considerably (p25-75: specialist-care €2,175—€12,625, GP-care-only €1,110—€4,350). Hospital treatment accounted for most of the total cost (specialist-care 78%, GP-care-only 62%; coefficient 2.81), pharmaceuticals (specialist-care 16%, GP-care-only 27%; coefficient 1.28), and primary care costs (specialist-care 6%, GP-care-only 11%; coefficient 1.13). The total costs of primary care pulmonary specialists were negligible.

Conclusion

Healthcare policy makers should consider the substantial volume of patients who are treated for COPD in general practice only and do not appear in specialist statistics.
Development of the European Healthcare and Social Cost Database (EU HCSCD) for use in economic evaluation of healthcare programs
Authors: Espín Jaime , Špacírová Zuzana , Rovira Joan , Epstein David , Olry de Labry Lima Antonio , García-Mochón Leticia
Published: March 2022

Introduction

Costs are one of the critical factors for the transferability of the results in health technology assessment and economic evaluation. The objective is to develop a cost database at the European level to facilitate cross-border cost comparisons in different settings and explains the factors that lead to differences in healthcare costs in different countries, taking into account the differences between health systems and other factors.

Methodology

The core of the database is compounded of three main categories (primary resources, composite goods and services, and complex processes and interventions) organized into 13 subcategories. A number of elements providing as detailed information of unit cost as possible were identified in order to mitigate the problem of comparability. Consortium partners validated both the database structure and selected costing items.

Results

Twenty-seven costing items included in the EU HCSCD resulted in 1450 unit costs when taking into account all item subtypes and countries. Cross-country differences in costs are driven by the type of resources included in the costing items (e.g., overhead costs in case of complex processes and interventions) or by the variety of existing brands and/or models and the type of unit value in most of the primary resources.

Conclusion

The EU HCSCD is the only public unit healthcare and social cost database at European level that gather data on unit costs and explains differences in costs across countries. Its maintenance and regular data updating will enable establishing specific systems for generating and recording information that will meet many of its current limitations.
Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates
Authors: Stiller Josefin , Short Graham , Hamilton Healy , Saarman Norah , Longo Sarah , Wainwright Peter , Rouse Greg W. , Simison W. Brian
Published: March 2022

Background

Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved.

Results

Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea.

Conclusions

Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events.
How do people who use drugs receiving Opioid Medication Therapy perceive their treatment ? A multicentre study
Authors: Guillou Landreat Morgane , Dany Antoine , Challet Bouju Gaelle , Laforgue Edouard-Jules , Cholet J. , Leboucher Juliette , Hardouin Jean Benoit ,   the OPAL Group, Bodenez Pierre , Grall-Bronnec Marie , Guillou-Landreat Morgane , Le Geay Bertrand , Martineau Isabelle , Levassor Philippe , Bolo Paul , Guillet Jean-Yves , Guillery Xavier , Dano Corine , Victorri Vigneau Caroline , Grall Bronnec Marie
Published: March 2022

Background

The resurgence of heroin use and the misuse of pharmaceutical opioids are some of the reasons for a worldwide increase in opioid dependence. Opioid Medication Therapies (OMT) have amply demonstrated their efficacy. From a medical point of view, the main objectives of OMT concern medical and social outcomes, centred on risk reduction and the cessation of opioid use. But patient points of view can differ and few studies have explored opioid-dependent patient viewpoints on their OMT. This variable seems important to consider in a patient-centred approach. The aim of our study was to explore points of view of people who use drugs (PWUD) treated with OMT, in a large multicentre sample.

Method

A cross-sectional multicentre study explored the points of view of PWUD with Opioid Use Disorder following OMT. Data regarding the patients’ points of view were collected using a self-administered questionnaire developed by the scientific committee of the study. A descriptive analysis and an exploratory factor analysis were performed to explore the structure of items exploring patient viewpoints.

Results

263 opioid dependent PWUD were included, a majority were men consuming heroin prior to being prescribed OMT. 68% were on methadone, 32% were on buprenorphine. Most PWUD identified a positive impact on their lives, with 92.8% agreeing or strongly agreeing that OMT had changed a lot of things in their lives. The exploratory factor analysis identified three factors: (F1) items related to points of views concerning the objectives and efficacy of OMT; (F2) items related to the legitimacy of OMT as a treatment compared to a drug, (F3) items related to experiences and relationships with OMT.

Conclusion

Patient viewpoints on efficacy were correlated with the pharmacological benefits of OMT and with the associated psychosocial measures. The implications of OMT in relationships, such as the feeling of being judged, concerned a majority. Points of view were ambivalent concerning the role of OMT as a treatment or as a drug. Involving patient points of view in therapeutic strategies decisions could help enhance positive views among PWUD on OMT and help PWUD towards their recovery.

Trial registration: OPAL study was registered: (NCT01847729).
Co-targeting WIP1 and PARP induces synthetic lethality in hepatocellular carcinoma
Authors: Chen Miaoqin , Wang Weikai , Hu Shiman , Tong Yifan , Li Yiling , Wei Qi , Yu Lei , Zhu Liyuan , Zhu Yiran , Liu Leiming , Ju Zhenyu , Wang Xian , Jin Hongchuan , Feng Lifeng
Published: March 2022

Background

Hepatocellular carcinoma (HCC) is one of the most fatal cancers. Due to limited strategies for effective treatments, patients with advanced HCC have a very poor prognosis. This study aims to identify new insights in HCC to develop novel strategies for HCC management.

Methods

The role of WIP1 (wild type p53 induced protein phosphatase1) in HCC was analyzed in HCC cells, xenograft model, DEN (Diethylnitrosamine) induced mice liver cancer model with WIP1 knockout mice, and TCGA database. DNA damage was evaluated by Gene Set Enrichment Analysis, western blotting, comet assay, and Immunofluorescence.

Results

High expression of WIP1 is associated with the poor prognosis of patients with HCC. Genetically and chemically suppression of WIP1 drastically reduced HCC cell proliferation. Besides, WIP1 knockout retarded DEN induced mice hepato-carcinogenesis. Mechanically, WIP1 inhibition induced DNA damage by increasing H2AX phosphorylation (γH2AX). Therefore, suppression of WIP1 and PARP induced synthetic lethality in HCC in vitro and in vivo by augmenting DNA damage.

Conclusion

WIP1 plays an oncogenic effect in HCC development, and targeting WIP1-dependent DNA damage repair alone or in combination with PARP inhibition might be a reasonable strategy for HCC management.
Prediction of 3-year risk of diabetic kidney disease using machine learning based on electronic medical records
Authors: Dong Zheyi , Wang Qian , Ke Yujing , Zhang Weiguang , Hong Quan , Liu Chao , Liu Xiaomin , Yang Jian , Xi Yue , Shi Jinlong , Zhang Li , Zheng Ying , Lv Qiang , Wang Yong , Wu Jie , Sun Xuefeng , Cai Guangyan , Qiao Shen , Yin Chengliang , Su Shibin , Chen Xiangmei
Published: March 2022

Background

Established prediction models of Diabetic kidney disease (DKD) are limited to the analysis of clinical research data or general population data and do not consider hospital visits. Construct a 3-year diabetic kidney disease risk prediction model in patients with type 2 diabetes mellitus (T2DM) using machine learning, based on electronic medical records (EMR).

Methods

Data from 816 patients (585 males) with T2DM and 3 years of follow-up at the PLA General Hospital. 46 medical characteristics that are readily available from EMR were used to develop prediction models based on seven machine learning algorithms (light gradient boosting machine [LightGBM], eXtreme gradient boosting, adaptive boosting, artificial neural network, decision tree, support vector machine, logistic regression). Model performance was evaluated using the area under the receiver operating characteristic curve (AUC). Shapley additive explanation (SHAP) was used to interpret the results of the best performing model.

Results

The LightGBM model had the highest AUC (0.815, 95% CI 0.747–0.882). Recursive feature elimination with random forest and SHAP plot based on LightGBM showed that older patients with T2DM with high homocysteine (Hcy), poor glycemic control, low serum albumin (ALB), low estimated glomerular filtration rate (eGFR), and high bicarbonate had an increased risk of developing DKD over the next 3 years.

Conclusions

This study constructed a 3-year DKD risk prediction model in patients with T2DM and normo-albuminuria using machine learning and EMR. The LightGBM model is a tool with potential to facilitate population management strategies for T2DM care in the EMR era.
Intimate partner violence against married and cohabiting women in sub-Saharan Africa: does sexual autonomy matter?
Authors: Aboagye Richard Gyan , Dadzie Louis Kobina , Arthur-Holmes Francis , Okyere Joshua , Agbaglo Ebenezer , Ahinkorah Bright Opoku , Seidu Abdul-Aziz
Published: March 2022

Background

Literature shows that women’s sexual autonomy, which refers to women’s capacity to refuse sex and ask a partner to use condom, has significant implications on the sexual and reproductive health outcomes and sexual-and-gender based violence. Nevertheless, there is scarcity of empirical evidence to support the association between women’s sexual autonomy and intimate partner violence (IPV) in sub-Saharan Africa.

Methods

Data for the study were extracted from the recent Demographic and Health Surveys in 24 countries in sub-Saharan Africa between 2010 and 2019. Bivariable and multivariable binary logistic regression analyses were performed to examine the association between sexual autonomy and IPV in all the studied countries. Statistical significance was set at p < 0.05.

Results

The pooled prevalence of IPV and sexual autonomy in the 24 countries were 38.5% and 73.0% respectively. Overall, the odds of exposure to IPV were higher among women with sexual autonomy, compared to those without sexual autonomy even after controlling for covariates (age, level of education, marital status, current working status, place of residence, wealth quintile and media exposure). At the country-level, women from Angola, Cameroon, Chad, Gabon, Cote d’lvoire, Gambia, Mali, Nigeria, Kenya, Comoros, Zambia, and South Africa who had sexual autonomy were more likely to experience IPV whilst those in Burundi were less likely to experience IPV. The study showed that sexual autonomy increases women’s exposure to IPV and this occurred in many countries except Burundi where women with sexual autonomy were less likely to experience IPV.

Conclusion

The findings highlight the need for serious programs and policies to fight against IPV in the sub-region. Additionally, laws need to be passed and implemented, with law enforcement agencies provided with the necessary resources to reduce intimate partner violence among women with sexual autonomy.
Prosthetic embodiment: systematic review on definitions, measures, and experimental paradigms
Authors: Zbinden Jan , Lendaro Eva , Ortiz-Catalan Max
Published: March 2022

The term embodiment has become omnipresent within prosthetics research and is often used as a metric of the progress made in prosthetic technologies, as well as a hallmark for user acceptance. However, despite the frequent use of the term, the concept of prosthetic embodiment is often left undefined or described incongruently, sometimes even within the same article. This terminological ambiguity complicates the comparison of studies using embodiment as a metric of success, which in turn hinders the advancement of prosthetics research. To resolve these terminological ambiguities, we systematically reviewed the used definitions of embodiment in the prosthetics literature. We performed a thematic analysis of the definitions and found that embodiment is often conceptualized in either of two frameworks based on body representations or experimental phenomenology. We concluded that treating prosthetic embodiment within an experimental phenomenological framework as the combination of ownership and agency allows for embodiment to be a quantifiable metric for use in translational research. To provide a common reference and guidance on how to best assess ownership and agency, we conducted a second systematic review, analyzing experiments and measures involving ownership and agency. Together, we highlight a pragmatic definition of prosthetic embodiment as the combination of ownership and agency, and in an accompanying article, we provide a perspective on a multi-dimensional framework for prosthetic embodiment. Here, we concluded by providing recommendations on metrics that allow for outcome comparisons between studies, thereby creating a common reference for further discussions within prosthetics research.
Conventional, functional and radiomics assessment for intrahepatic cholangiocarcinoma
Authors: Granata Vincenza , Fusco Roberta , Belli Andrea , Borzillo Valentina , Palumbo Pierpaolo , Bruno Federico , Grassi Roberta , Ottaiano Alessandro , Nasti Guglielmo , Pilone Vincenzo , Petrillo Antonella , Izzo Francesco
Published: March 2022

Background

This paper offers an assessment of diagnostic tools in the evaluation of Intrahepatic Cholangiocarcinoma (ICC).

Methods

Several electronic datasets were analysed to search papers on morphological and functional evaluation in ICC patients. Papers published in English language has been scheduled from January 2010 to December 2021.

Results

We found that 88 clinical studies satisfied our research criteria. Several functional parameters and morphological elements allow a truthful ICC diagnosis. The contrast medium evaluation, during the different phases of contrast studies, support the recognition of several distinctive features of ICC. The imaging tool to employed and the type of contrast medium in magnetic resonance imaging, extracellular or hepatobiliary, should change considering patient, departement, and regional features. Also, Radiomics is an emerging area in the evaluation of ICCs.

Post treatment studies are required to evaluate the efficacy and the safety of therapies so as the patient surveillance.

Conclusions

Several morphological and functional data obtained during Imaging studies allow a truthful ICC diagnosis.
Can producer groups improve technical efficiency among artisanal shrimpers in Nigeria? A study accounting for observed and unobserved selectivity
Authors: Adetoyinbo Ayobami , Otter Verena
Published: March 2022

It is widely recognized that participation in producer groups is advantageous for smallholders who must deal with complex production and marketing constraints and dynamic business environments. However, available data on this process are scarce in the fishery sector, while existing evidence is limited by smallholders’ potential self-selection into producer groups. This study, therefore, examined the selectivity-corrected role of fisher groups in improving shrimpers’ technological and technical efficiency. Using the latest primary data from artisan shrimpers in Nigeria, we applied propensity score matching and Greene’s selectivity stochastic production frontier model to control for selection bias from both observable and unobservable factors. Empirical results from our metafrontier approach show that technical efficiency scores for members tend to be overestimated if selectivity is not properly controlled. However, the technical efficiencies and productivities of members were significantly higher regardless of how biases were corrected, implying that participation in fisher groups is positively related to increases in shrimpers’ capture and technical efficiency. Further findings suggest that current artisanal fisher groups are “production-oriented” as they ensure that members access vital shrimping inputs at lower costs. With declining returns to scale for members, the study concludes that without public and private support for collective action in the fishery sector, membership in artisanal fisher groups may not lead to significant improvement in shrimpers’ productivity. The study discusses several recommendations on how collective action can be further encouraged and developed among artisan fishers.
The plant microbiota signature of the Anthropocene as a challenge for microbiome research
Authors: Berg Gabriele , Cernava Tomislav
Published: March 2022

Background

One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

Results

Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.

Conclusions

Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Hybridization increases genetic diversity in Schistosoma haematobium populations infecting humans in Cameroon
Authors: Teukeng Félicité Flore Djuikwo , Blin Manon , Bech Nicolas , Gomez Marta Reguera , Zein-Eddine Rima , Simo Alain Michel Kouam , Allienne Jean-Francois , Tchuem-Tchuenté Louis Albert , Boissier Jérôme
Published: March 2022

Background

Hybrids between Schistosoma haematobium (Sh) and S. bovis (Sb) have been found in several African countries as well as in Europe. Since the consequences of this hybridization are still unknown, this study aims to verify the presence of such hybrids in Cameroonian humans, to describe the structure of S. haematobium populations on a large geographic scale, and to examine the impact of these hybrids on genetic diversity and structure of these populations.

Methods

From January to April 2019, urine from infected children was collected in ten geographically distinct populations. Miracidia were collected from eggs in this urine. To detect the presence of hybrids among these miracidia we genotyped both Cox1 (RD-PCR) and ITS2 gene (PCR-RFLP). Population genetic diversity and structure was assessed by genotyping each miracidium with a panel of 14 microsatellite markers. Gene diversity was measured using both heterozygosity and allelic richness indexes, and genetic structure was analyzed using paired Fst, PCA and Bayesian approaches.

Results

Of the 1327 miracidia studied, 88.7% were identified as pure genotypes of S. haematobium (Sh_Sh/Sh) while the remaining 11.3% were hybrids (7.0% with Sh_Sh/Sb, 3.7% with Sb_Sb/Sh and 0.4% with Sb_Sh/Sb). No miracidium has been identified as a pure genotype of S. bovis. Allelic richness ranged from 5.55 (Loum population) to 7.73 (Matta-Barrage) and differed significantly between populations. Mean heterozygosity ranged from 53.7% (Loum) to 59% (Matta Barrage) with no significant difference. The overall genetic differentiation inferred either by a principal component analysis or by the Bayesian approach shows a partial structure. Southern populations (Loum and Matta Barrage) were clearly separated from other localities but genetic differentiation between northern localities was limited, certainly due to the geographic proximity between these sites.

Conclusions

Hybrids between S. haematobium and S. bovis were identified in 11.3% of miracidia that hatched from eggs present in the urine of Cameroonian schoolchildren. The percentages of these hybrids are correlated with the genetic diversity of the parasite, indicating that hybridization increases genetic diversity in our sampling sites. Hybridization is therefore a major biological process that shapes the genetic diversity of S. haematobium.

Graphical Abstract
Alterations of gut microbiota diversity, composition and metabonomics in testosterone-induced benign prostatic hyperplasia rats
Authors: Li Lu-Yao , Han Jie , Wu Lan , Fang Cheng , Li Wei-Guang , Gu Jia-Min , Deng Tong , Qin Chang-Jiang , Nie Jia-Yan , Zeng Xian-Tao
Published: March 2022

Background

Studies had shown many diseases affect the stability of human microbiota, but how this relates to benign prostatic hyperplasia (BPH) has not been well understood. Hence, this study aimed to investigate the regulation of BPH on gut microbiota composition and metabonomics.

Methods

We analyzed gut samples from rats with BPH and healthy control rats, the gut microbiota composition and metabonomics were detected by 16S rDNA sequencing and liquid chromatography tandem mass spectrometry (LC–MS/MS).

Results

High-throughput sequencing results showed that gut microbiota beta-diversity increased (P < 0.01) in the BPH group vs. control group. Muribaculaceae (P < 0.01), Turicibacteraceae (P < 0.05), Turicibacter (P < 0.01) and Coprococcus (P < 0.01) were significantly decreased in the BPH group, whereas that of Mollicutes (P < 0.05) and Prevotella (P < 0.05) were significantly increased compared with the control group. Despite profound interindividual variability, the levels of several predominant genera were different. In addition, there were no statistically significant differences in several bacteria. BPH group vs. control group: Firmicutes (52.30% vs. 57.29%, P > 0.05), Bacteroidetes (46.54% vs. 41.64%, P > 0.05), Clostridia (50.89% vs. 54.66%, P > 0.05), Ruminococcaceae (25.67% vs. 20.56%, P > 0.05). LC–MS/MS of intestinal contents revealed that differential metabolites were mainly involved in cellular processes, environmental information processing, metabolism and organismal systems. The most important pathways were global and overview maps, lipid metabolism, amino acid metabolism, digestive system and endocrine system. Through enrichment analysis, we found that the differential metabolites were significantly enriched in metabolic pathways, steroid hormone biosynthesis, ovarian steroidogenesis, biosynthesis of unsaturated fatty acids and bile secretion. Pearson correlation analysis (R = 0.94) showed that there was a strong correlation between Prevotellaceae, Corynebacteriaceae, Turicibacteraceae, Bifidobacteriaceae and differential metabolites.

Conclusion

Our findings suggested an association between the gut microbiota and BPH, but the causal relationship between the two groups is unclear. Thus, further studies are warranted to elucidate the potential mechanisms and causal relationships between BPH and gut microbiota.
DCAU-Net: dense convolutional attention U-Net for segmentation of intracranial aneurysm images
Authors: Yuan Wenwen , Peng Yanjun , Guo Yanfei , Ren Yande , Xue Qianwen
Published: March 2022

Segmentation of intracranial aneurysm images acquired using magnetic resonance angiography (MRA) is essential for medical auxiliary treatments, which can effectively prevent subarachnoid hemorrhages. This paper proposes an image segmentation model based on a dense convolutional attention U-Net, which fuses deep and rich semantic information with shallow-detail information for adaptive and accurate segmentation of MRA-acquired aneurysm images with large size differences. The U-Net model serves as a backbone, combining dense block and convolution block attention module (CBAM). The dense block is composed of a batch normalization layer, an randomly rectified linear unit activation function, and a convolutional layer, for mitigation of vanishing gradients, for multiplexing of aneurysm features, and for improving the network training efficiency. The CBAM is composed of a channel attention module and a spatial attention module, improving the segmentation performance of feature discrimination and enhancing the acquisition of key feature information. Owing to the large variation of aneurysm sizes, multi-scale fusion is performed during up-sampling, for adaptive segmentation of MRA-acquired aneurysm images. The model was tested on the MICCAI 2020 ADAM dataset, and its generalizability was validated on the clinical aneurysm dataset (aneurysm sizes: < 3 mm, 3–7 mm, and > 7 mm) supplied by the Affiliated Hospital of Qingdao University. A good clinical application segmentation performance was demonstrated.
First-principles phonon calculations for lattice dynamics, thermal expansion and lattice thermal conductivity of CoSi in the high temperature region
Authors: Sk Shamim , Pandey Sudhir K.
Published: March 2022

This study presents the first-principles phonon calculations to understand the experimental thermal expansion (

) and lattice thermal conductivity

of CoSi in the high temperature region. Phonon dispersion is computed using the finite displacement method and supercell approach by taking the equilibrium crystal structures obtained from DFT. The calculation of

is done under quasi-harmonic approximation. The

is calculated using first-principle anharmonic lattice dynamics calculations under single-mode relaxation time approximation. The calculated

in the temperature range 0–1300 K gives a good match with existing experimental data. The calculated value of

(∼8.0 W/mK) at 300 K is found to be in good agreement with the experimental value of ∼8.3 W/mK. The temperature dependence of phonon lifetime due to phonon-phonon interaction is calculated to understand the behaviour of

. The present study suggests that ground state phonon dispersion obtained from DFT-based methods gives reasonably good explanation of experimental

and

.
The Other Kind of Reclamation: Wetlands Drainage and National Water Policy, 1902–1912
Authors: CARLSON ANTHONY E.
Published: March 2022

This essay evaluates national wetlands policy during the first decade of the twentieth century. Beginning in the 1890s the national government began to assume new responsibilities for natural resource management. By the end of World War I, Congress exercised some form of control over western irrigation, flood control, and range and mineral policies. Yet Progressive Era national policymakers were also deeply interested in wetlands drainage. In the early 1900s they launched an abortive movement to nationalize drainage in the hopes of creating new farms, improving public health, and relieving urban congestion. The failure of the movement illustrates that centralization, which scholars identify as a primary theme of Progressive Era conservation, was neither inevitable nor inexorable. Ironically, the growth of the embryonic administrative and regulatory state sometimes precluded the development of centralized natural resource programs by pitting different natural resource agencies, local communities, and constituent groups against one another in a bitter and irreconcilable feud over power and funding.
Nanosecond pulsed single longitudinal mode diamond Raman laser in the 1.6 µm spectral region
Authors: Ma Houjie , Wei Xin , Zhao Hui , Zhang Minglong , Zhou Haiqiong , Zhu Siqi , Yin Hao , Li Zhen , Chen Zhenqiang , Shen Yu , Zong Nan , Zhang Shenjin , Dai Shibo
Published: March 2022

We demonstrate the first nanosecond pulsed single longitudinal mode (SLM) intracavity-pumped diamond Raman laser, to the best of our knowledge. The eye-safe coherent source at 1634 nm, which was converted from the actively Q-switched 1342 nm Nd:YVO4 laser, yielded 4.35 W of multimode average output power with a pulse duration of 6 ns and peak power of 29 kW. By exploiting the spatial hole burning free gain mechanism in the Raman media, stable SLM operation was observed at low output power (0.46 W) for the free-running case. Furthermore, by incorporating an etalon in the fundamental standing-wave cavity, the spectral linewidth of the fundamental field was suppressed substantially below the diamond Raman gain linewidth and slightly less than the free spectral range of the mm-scale Raman resonator. Thereby, a much higher SLM output power of 1.63 W was obtained with a pulse duration of ∼9 ns and a spectral linewidth of ∼77 MHz.
Heterogeneous integrated phase modulator based on two-dimensional layered materials
Authors: Chen Hao , Zhao Zexing , Zhang Ziming , Wang Guoqing , Li Jiatong , Shang Zhenyuan , Zhang Mengyu , Guo Kai , Yang Junbo , Yan Peiguang
Published: March 2022

Silicon nitride, with ultralow propagation loss and a wide transparency window, offers an exciting platform to explore integrated photonic devices for various emerging applications. It is appealing to combine the intrinsic optical properties of two-dimensional layered materials with high-quality optical waveguides and resonators to achieve functional devices in a single chip. Here we demonstrate a micro-ring resonator-based phase modulator integrated with few-layer

MoS

2

. The ionic liquid is employed directly on the surface of

MoS

2

to form a capacitor configuration. The effective index of the composite

MoS

2

–
SiN

waveguide can be modulated via adjusting bias voltages to achieve different charged doping induced electro-refractive responses in

MoS

2

film. The maximum effective index modulation of the composite

MoS

2

–
SiN

waveguide can be achieved to

0.45
×

10

−
3

. The phase tuning efficiency is measured to be 29.42 pm/V, corresponding to a

V

π

L

of 0.69 V·cm. Since the micro-ring resonator is designed near the critical coupling regime, the coupling condition between the bus waveguide and micro-ring resonator can also be engineered from under-coupling to over-coupling regime during the charged doping process. That can be involved as a degree of freedom for the coupling tailoring. The ability to modulate the effective index with two-dimensional materials and the robust nature of the heterostructure integrated phase modulator could be useful for engineering reliable ultra-compact and low-power-consumption integrated photonic devices.
Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities
Authors: Li Juan , Schumer Molly , Bank Claudia
Published: March 2022

Dobzhansky-Muller incompatibilities (DMIs) are a major component of reproductive isolation between species. DMIs imply negative epistasis and are exposed when two diverged populations hybridize. Mapping the locations of DMIs has largely relied on classical genetic mapping. Approaches to date are hampered by low power and the challenge of identifying DMI loci on the same chromosome, because strong initial linkage of parental haplotypes weakens statistical tests. Here, we propose new statistics to infer negative epistasis from haplotype frequencies in hybrid populations. When two divergent populations hybridize, the variance in heterozygosity at two loci decreases faster with time at DMI loci than at random pairs of loci. When two populations hybridize at near-even admixture proportions, the deviation of the observed variance from its expectation becomes negative for the DMI pair. This negative deviation enables us to detect intermediate to strong negative epistasis both within and between chromosomes. In practice, the detection window in hybrid populations depends on the demographic scenario, the recombination rate, and the strength of epistasis. When the initial proportion of the two parental populations is uneven, only strong DMIs can be detected with our method unless migration prevents parental haplotypes from being lost. We use the new statistics to infer candidate DMIs from three hybrid populations of swordtail fish. We identify numerous new DMI candidates, some of which are inferred to interact with several loci within and between chromosomes. Moreover, we discuss our results in the context of an expected enrichment in intrachromosomal over interchromosomal DMIs.
Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis
Authors: Ibarra-Chávez Rodrigo , Brady Aisling , Chen John , Penadés José R. , Haag Andreas F.
Published: March 2022

Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.
The relationship between finger length ratio, masculinity, and sexual orientation in women: A correlational study
Authors: Holmes Luke , Watts-Overall Tuesday M. , Slettevold Erlend , Gruia Dragos C. , Rieger Gerulf
Published: March 2022

Homosexual women are, on average, more masculine in their appearance and behavior than heterosexual women. We hypothesized that their masculinity was influenced by exposure to elevated levels of prenatal androgen during early development. We recruited 199 women (including 67 homosexual women) and measured their masculinity via self-report and observer ratings. Our measure of prenatal androgen exposure was the ratio of the index to ring finger (2D:4D), which is hypothesized to be lower in women exposed to elevated levels of androgens during prenatal development. Homosexual women were substantially more masculine than heterosexual women in both self-report and observer ratings. However, homosexual women neither had more male-typical finger length ratios, nor did their finger length ratios relate to their masculinity in any predicted direction. Thus, we found no evidence that increased prenatal androgen exposure influenced masculinity in homosexual women.