bluuebunny/crossref_metadata_2025_split huggingface dataset:
Canine babesiosis – a disease rarely considered in the context of male infertility
Authors: Domosławska Anna , Zdunczyk Sławomir 
Published: November 2020

AbstractBackgroundLittle is known about the impact of babesiosis on semen quality and fertility in dogs.Case presentationFour cases of infertility in male dogs after infection withBabesia canisare described. In all dogs sperm quality was low. Two dogs were castrated pharmacologically or surgically. In two dogs fertility was restored after supplementation with selenium and Vitamin E. As possible causes of spermatogenesis disorders due to the treatment of infection withBabesia caniswith imidocarb, fever and disturbed testicular microcirculation are discussed.ConclusionsThese cases indicate that if males have fertility problems, question about babesiosis infection in the past should be a permanent point in the clinical interview.
Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys
Authors: Jasinska Anna J. , Dong Tien S. , Lagishetty Venu , Katzka William , Jacobs Jonathan P. , Schmitt Christopher A. , Cramer Jennifer Danzy , Ma Dongzhu , Coetzer Willem G. , Grobler J. Paul , Turner Trudy R. , Freimer Nelson , Pandrea Ivona , Apetrei Cristian 
Published: November 2020

AbstractBackgroundThe microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa.ResultsWe characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated withLactobacillusandEscherichia/ShigellaandHelicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples.ConclusionsThe vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus.
Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications
Authors: Van de Guchte Maarten , Burz Sebastian D. , Cadiou Julie , Wu Jiangbo , Mondot Stanislas , Blottière Hervé M. , Doré Joël 
Published: November 2020

Abstract

Background
Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with a possible pre-disease condition (more susceptible to disease development) of the host-microbiota ecosystem. These observations are reminiscent of the behavior of an ecosystem with alternative stable states (different stable configurations that can exist under identical external conditions), and we recently postulated that health, pre-disease and disease represent such alternative states. Here, our aim was to examine if alternative stable states indeed exist in the intestinal ecosystem.

Results
Rats were exposed to varying concentrations of DSS in order to create a wide range of mildly inflammatory conditions, in a context of diet-induced low microbiota diversity. The consequences for the intestinal microbiota were traced by 16S rRNA gene profiling over time, and inflammation of the distal colon was evaluated at sacrifice, 45 days after the last DSS treatment. The results provide the first formal experimental proof for the existence of alternative stable states in the rat intestinal ecosystem, taking both microbiota and host inflammatory status into consideration. The alternative states are host-microbiota ecosystem states rather than independent and dissociated microbiota and host states, and inflammation can prompt stable state-transition. Based on these results, we propose a conceptual model providing new insights in the interplay between host inflammatory status and microbiota status. These new insights call for innovative therapeutic strategies to cure (pre-)disease.

Conclusions
We provide proof of concept showing the existence of alternative stable states in the rat intestinal ecosystem. We further propose a model which, if validated in humans, will support innovative diagnosis, therapeutic strategy, and monitoring in the treatment of chronic inflammatory conditions. This model provides a strong rationale for the application of combinatorial therapeutic strategies, targeting host and microbiota rather than only one of the two in chronic immune-mediated diseases.
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
Authors: Liu Lei , Wang Yulin , Che You , Chen Yiqiang , Xia Yu , Luo Ruibang , Cheng Suk Hang , Zheng Chunmiao , Zhang Tong 
Published: November 2020

AbstractBackgroundGenome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward.ResultsHere, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genusCa.Brocadiareconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level.ConclusionsOur results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems.
Dysregulated bile acid receptor-mediated signaling and IL-17A induction are implicated in diet-associated hepatic health and cognitive function
Authors: Jena Prasant Kumar , Sheng Lili , Nguyen Michelle , Di Lucente Jacopo , Hu Ying , Li Yongchun , Maezawa Izumi , Jin Lee-Way , Wan Yu-Jui Yvonne 
Published: November 2020

AbstractBackgroundChronic consumption of high sugar and high fat diet associated with liver inflammation and cognitive decline. This paper tests a hypothesis that the development and resolution of diet-induced nonalcoholic fatty liver disease (NAFLD) has an impact on neuroplasticity and cognition.MethodsC57BL/6 wild-type mice were fed with either a healthy control diet (CD) or a fructose, palmitate, and cholesterol (FPC)-enriched diet since weaning. When mice were 3-months old, FPC diet-fed mice were randomly assigned to receive either FPC-enriched diet with or without 6% inulin supplementation. At 8 months of age, all three groups of mice were euthanized followed by analysis of inflammatory signaling in the liver and brain, gut microbiota, and cecal metabolites.ResultsOur data showed that FPC diet intake induced hepatic steatosis and inflammation in the liver and brain along with elevated RORγ and IL-17A signaling. Accompanied by microglia activation and reduced hippocampal long-term potentiation, FPC diet intake also reduced postsynaptic density-95 and brain derived neurotrophic factor, whereas inulin supplementation prevented diet-reduced neuroplasticity and the development of NAFLD. In the gut, FPC diet increasedCoriobacteriaceaeandErysipelotrichaceae, which are implicated in cholesterol metabolism, and the genusAllobaculum,and inulin supplementation reduced them. Furthermore, FPC diet reduced FXR and TGR5 signaling, and inulin supplementation reversed these changes. Untargeted cecal metabolomics profiling uncovered 273 metabolites, and 104 had significant changes due to FPC diet intake or inulin supplementation. Among the top 10 most affected metabolites, FPC-fed mice had marked increase of zymosterol, a cholesterol biosynthesis metabolite, and reduced 2,8-dihydroxyquinoline, which has known benefits in reducing glucose intolerance; these changes were reversible by inulin supplementation. Additionally, the abundance ofBarnesiella,Coprobacter,Clostridium XIVa, andButyrivibriowere negatively correlated with FPC diet intake and the concentration of cecal zymosterol but positively associated with inulin supplementation, suggesting their benefits.ConclusionTaken together, the presented data suggest that diet alters the gut microbiota and their metabolites, including bile acids. This will subsequently affect IL-17A signaling, resulting in systemic impacts on both hepatic metabolism and cognitive function.
The relevance of transversal competences in vocational education and training: a bibliometric analysis
Authors: Calero López Inmaculada , Rodríguez-López Beatriz 
Published: November 2020

Abstract
Vocational Education and Training (VET) programmes have included the acquisition of transversal competences in their curricula as a tool to increase employability. The number of researches has exponentially grown in the last years, emphasizing its relevance and the multiple approaches and factors involved in the learning process. The present bibliometric study aims to provide an overview of the scientific research carried out during the last 10 years and to shed some light on several relevant topics in this field. The results indicate the need to improve students’ transversal competences in order to meet the demands of the labour market, the importance of the collaboration of all the actors involved in the process (policy makers, industry and educators) and from a pedagogical point of view, the necessity of introducing new teaching approaches to implement and assess the acquisition of transversal competences. However, and despite the surge of interest in the study of transversal competences in the last decade, further empirical research is needed, especially at Vocational Education and Training level, to understand how transversal competences develop and what kind of initiatives have an impact of their acquisition.
How to foster the formation of STEM identity: studying diversity in an authentic learning environment
Authors: Singer Alison , Montgomery Georgina , Schmoll Shannon 
Published: November 2020

AbstractBackgroundSTEM identity has been shown to have a powerful role in an individual’s success in educational environments, as well as on their career goals and trajectories. Historically, however, STEM identity formation for underrepresented students has been hampered by the lack of representation of in STEM fields, which predominantly consist of white males. One educational challenge is diversifying STEM classrooms, both in terms of the students themselves and also in terms of the science and scientists they learn about.MethodsWe piloted a 4-credit History, Philosophy, and Sociology of Science course at Michigan State University. Students were tasked with creating exhibits focused on themes of diversity and inclusion in science for a real client. Using a STEM identity survey, we assessed students’ attitudes towards the sciences, issues of diversity in science, and their sense of belonging to their educational communities. We also had the students respond to various short-answer questions throughout the semester to better understand their experiences working on a collaborative authentic learning task.ResultsOur results suggest that authentic learning experiences based around ideas of diversity and inclusion can help students develop sense of belonging and positive STEM identities. Students demonstrated shifts in their self-identities as scientists, focusing more on the intersection between their gender, ethnicity, and self-perception as a scientist. Through qualitative analysis of short-answer questions, we were able to ascertain that working in groups in an authentic learning environment helped the students improve their communication and collaboration skills.ConclusionsStudents’ increased focus on gender and ethnicity suggests that they are thinking critically about how their personal identities intersect with their scientific identities. Additional research would help us better understand if the coupling of authentic learning and inclusive teaching practices have significant impacts on the formation of students’ STEM identities.
Biomechanical asymmetries persist after ACL reconstruction: results of a 2-year study
Authors: Sharafoddin-Shirazi Fatemeh , Letafatkar Amir , Hogg Jennifer , Saatchian Vahid 
Published: November 2020

Abstract

Purpose
This study was aimed to examine longitudinal (6, 12, 18, 24 months) asymmetries in double-leg landing kinetics and kinematics of subjects with and without unilateral ACLR.

Methods
Three-dimensional kinematic and kinetic parameters of 40 participants (n = 20 post-ACLR, n = 20 healthy) were collected with a motion analysis system and force plate during a drop-landing task, and asymmetry indices were compared between groups.

Results
The asymmetry index (AI) in the ACLR group compared to the healthy group decreased from six to 24 months for vertical ground reaction force (vGRF) from 100% to 6.5% and for anterior posterior ground reaction force (a-pGRF) from 155.5% to 7%. Also, the AI decreased for peak hip flexion moment from 74.5% to 17.1%, peak knee flexion moment from 79.0% to 5.8% and peak ankle dorsiflexion moment from 59.3% to 5.9%. As a further matter, the AI decreased for peak hip abduction moment from 67.8% to 5.1%, peak knee adduction moment from 55.7% to 14.8% and peak knee valgus angle from 48.7% to 23.5%.

Conclusions
Results obtained from this longitudinal study showed that ACLR patients still suffer from limb asymmetries during landing tasks, which appear to normalize by 24-monthspost-surgery. This finding can help us to better understand biomechanics of the limbs after ACLR, and design more efficient post-surgery rehabilitation programs.

Level of evidence
Level III.
Brain metastases assessment by FDG-PET/CT: can it eliminate the necessity for dedicated brain imaging?
Authors: Zidan Mamdouh A. , Hassan Radwa S. , El-Noueam Khaled I. , Zakaria Yasser M. 
Published: November 2020

Abstract

Background
Brain metastases (BM) are the most common intracranial tumors in adults outnumbering all other intracranial neoplasms. Positron emission tomography combined with computed tomography (PET/CT) is a widely used imaging modality in oncology with a unique combination of cross-sectional anatomic information provided by CT and the metabolic information provided by PET using the [18F]-2-fluoro-2-deoxy-d-glucose (FDG) as a tracer. The aim of the study is to assess the role and diagnostic performance of brain-included whole-body PET/CT in detection and evaluation of BM and when further imaging is considered necessary. The study was conducted over a period of 12 months on 420 patients suffering from extra-cranial malignancies utilizing brain-included whole-body PET/CT.

Results
Thirty patients with 71 brain lesions were detected, 18 patients (60%) had BM of unknown origin while 12 patients (40%) presented with known primary tumors. After brain-included whole-body FDG-PET/CT examination, the unknown primaries turned out to be bronchogenic carcinoma in 10 patients (33.3%), renal cell carcinoma in 2 patients (6.7%), and lymphoma in 2 patients (6.7%), yet the primary tumors remained unknown in 4 patients (13.3%). In 61 lesions (85.9%), the max SUV ranged from 0.2- < 10, while in 10 lesions (14.1%) the max SUV ranged from 10 to 20. Hypometabolic lesions were reported in 41 (57.7%) lesions, hypermetabolic in 3 lesions (4.2%), whereas 27 lesions (38.0%) showed similar FDG uptake to the corresponding contralateral brain matter. PET/CT overall sensitivity, specificity, positive and negative predictive, and accuracy values were 78.1, 92.6, 83.3, 90, and 88% respectively.

Conclusion
Brain-included whole-body FDG-PET/CT provides valuable complementary information in the evaluation of patients with suspected BM. However, the diagnostic performance of brain PET-CT carries the possibility of false-negative results with consequent false sense of security. The clinicians should learn about the possible pitfalls of PET/CT interpretation to direct patients with persistent neurological symptoms or high suspicion for BM for further dedicated CNS imaging.
Incidence, Mortality, and Survival Trends of Primary CNS Tumors in Cali, Colombia, From 1962 to 2019
Authors: Riano Ivy , Bravo Pablo , Bravo Luis Eduardo , Garcia Luz Stella , Collazos Paola , Carrascal Edwin 
Published: November 2020

PURPOSEGlobal studies have shown varying trends of CNS tumors within geographic regions. In Colombia, the epidemiologic characteristics of CNS neoplasms are not well elucidated. We aimed to provide a summary of the descriptive epidemiology of primary CNS tumors among the urban population of Cali, Colombia.METHODSWe conducted a time-trend study from 1962 to 2019 using the Population-Based Cali Cancer Registry. The age-standardized rates per 100,000 person-years were obtained by direct method using the world standard population. Results were stratified by sex, age group at diagnosis, and histologic subtype. We used Joinpoint regression analysis to detect trends and obtain annual percentage change (APC) with 95% CIs. We estimated 5-year net survival using the Pohar-Perme method.RESULTSDuring 1962 to 2016, 4,732 new cases of CNS tumors were reported. From 1985 to 2019, a total of 2,475 deaths from malignant CNS tumors were registered. A statistically significant increase in the trends of incidence (APC, 2.8; 95% CI, 2.1 to 3.5) and mortality (APC, 1.5; 95% CI, 1.1 to 2.0) rates was observed during the study. The most common malignant CNS tumor was glioblastoma (17.8% of all tumors), and the most frequent benign tumor was meningioma (17.2%). Malignancy was more common in males than in females. Unspecified malignant neoplasms represented 32% of all cases. The highest 5-year net survival was 31.4% during 2012 to 2016.CONCLUSIONOur findings demonstrate an increasing burden of primary CNS tumors for the last 60 years, with a steady rate from the early 2010s. There was an improvement of 5-year net survival for the last decade. Males had higher mortality than did females. Additional efforts are needed to fully explore the geographic, environmental, and genetic contributors of CNS malignancies within the region.
Clinical Outcome of Leiomyosarcomas With Somatic Alteration in Homologous Recombination Pathway Genes
Authors: Rosenbaum Evan , Jonsson Philip , Seier Kenneth , Qin Li-Xuan , Chi Ping , Dickson Mark , Gounder Mrinal , Kelly Ciara , Keohan Mary L. , Nacev Benjamin , Donoghue Mark T. A. , Chiang Sarah , Singer Samuel , Ladanyi Marc , Antonescu Cristina R. , Hensley Martee L. , Movva Sujana , D’Angelo Sandra P. , Tap William D. 
Published: November 2020

PURPOSE To detect alterations in DNA damage repair (DDR) genes, measure homologous recombination deficiency (HRD), and correlate these findings with clinical outcome in patients with leiomyosarcoma (LMS). PATIENTS AND METHODS Patients with LMS treated at Memorial Sloan Kettering (MSK) Cancer Center who consented to prospective targeted next-generation sequencing with MSK-IMPACT were screened for oncogenic somatic variants in one of 33 DDR genes; where feasible, an experimental HRD score was calculated from IMPACT data. Progression-free survival (PFS) and overall survival (OS) were estimated after stratifying patients by DDR gene alteration status and HRD score. RESULTS Of 211 patients with LMS, 20% had an oncogenic DDR gene alteration. Univariable analysis of PFS in 117 patients who received standard frontline chemotherapy in the metastatic setting found that an altered homologous recombination pathway gene was significantly associated with shorter PFS (hazard ratio [HR], 1.79; 95% CI, 1.04 to 3.07; P = .035). Non- BRCA homologous recombination gene alteration was associated with shorter PFS (HR, 2.61; 95% CI, 1.35 to 5.04; P = .004) compared with BRCA-altered and wild-type homologous recombination genes. Univariable analysis of OS from diagnosis in the entire cohort of 211 patients found that age, tumor size, number of metastatic sites, localized disease, and non- BRCA homologous recombination gene alteration were significantly associated with OS. On multivariable analysis, non- BRCA homologous recombination pathway gene alteration remained significant (HR, 4.91; 95% CI, 2.47 to 9.76; P < .001). High HRD score was not associated with a different PFS or OS. CONCLUSION Patients with LMS with homologous recombination pathway gene alterations have poor clinical outcomes, particularly those with non- BRCA gene alterations. HRD score calculated from a targeted exome panel did not discern disparate clinical outcomes.