bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Angiotensin Receptor Blockers (ARBs) on In-Hospital Outcomes of Patients With Hypertension and Confirmed or Clinically Suspected COVID-19
Authors: Soleimani Abbas , Kazemian Sina , Karbalai Saleh Shahrokh , Aminorroaya Arya , Shajari Zahra , Hadadi Azar , Talebpour Mohammad , Sadeghian Hakimeh , Payandemehr Pooya , Sotoodehnia Mehran , Bahreini Maryam , Najmeddin Farhad , Heidarzadeh Ali , Zivari Ensieh , Ashraf Haleh
Published: September 2020

BACKGROUND

There is an ongoing controversy about harms and benefits of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) in hypertensive patients with coronavirus disease 2019 (COVID-19). Given the unresolved debate, we investigated the association of ARBs with in-hospital outcomes of these patients.

METHODS

In this retrospective observational study, we studied patients with COVID-19 who referred to Sina Hospital in Tehran, Iran, from 20 February to 29 May 2020. Patients with either positive real-time reverse-transcriptase polymerase-chain-reaction test of swab specimens, or high clinical suspicion according to the World Health Organization’s interim guidance were included. We followed-up patients for incurring death, severe COVID-19, and in-hospital complications.

RESULTS

We evaluated 681 patients with COVID-19 of whom 37 patients were excluded due to incomplete medical records and 8 patients who used ACEIs which left 636 patients in the analysis. In this cohort, 108 (17.0%) patients expired and 407 (64.0%) patients incurred severe COVID-19. Of 254 (39.9%) patients with hypertension, 122 (48.0%) patients were receiving an ARB. After adjustment for possible confounders, we found no independent association between taking ARBs and in-hospital outcomes except for acute kidney injury (AKI), in patients with confirmed or clinically suspected COVID-19, either hypertensive or not-hypertensive. We found that discontinuation of ARBs during hospitalization was associated with a greater risk of mortality, invasive ventilation, and AKI (all P ˂ 0.002).

CONCLUSIONS

We found that taking ARBs by patients with hypertension and confirmed or clinically suspected COVID-19 is not associated with poorer in-hospital outcomes after adjustment for possible confounders.
Haemosporidian parasites of Neotropical birds: Causes and consequences of infection
Authors: Ellis Vincenzo A , Fecchio Alan , Ricklefs Robert E
Published: September 2020

Haemosporidian parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are among the best studied parasites of Neotropical birds. Here, we describe variation in haemosporidian prevalence (i.e. the proportion of infected individuals in a sampled population) in Neotropical birds. We review correlates of haemosporidian prevalence (including several avian life-history traits, climate, and season) and the population and evolutionary consequences of infection for Neotropical birds. We find that prevalence varies among avian taxonomic families, genera, and even among species within the same genus, suggesting that prevalence reflects multiple factors, some of which (e.g., avian incubation period) are associated with avian family-level variation in prevalence while others (e.g., avian abundance) are associated with variation in prevalence among closely related host species. We find few correlates of prevalence that have been consistently demonstrated across studies. Prevalence in populations of many Neotropical birds has been estimated by microscopic examination of blood smears, which affords limited opportunity for comparison with data generated by molecular methods. However, at one site in the Brazilian Cerrado for which we have data, prevalence determined by microscopy does not correlate with prevalence determined by molecular methods for Plasmodium, but the 2 data types are positively correlated for Haemoproteus. Haemosporidians have been hypothesized to play a role in avian sexual selection, and we find the prevalence of Haemoproteus to be lower in polygynous species than in socially monogamous species in the Neotropics, confirming a pattern shown previously among Nearctic birds.
Drug–drug interaction prediction with Wasserstein Adversarial Autoencoder-based knowledge graph embeddings
Authors: Dai Yuanfei , Guo Chenhao , Guo Wenzhong , Eickhoff Carsten
Published: September 2020

An interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug–drug interactions (DDIs) is one of the key tasks in public health and drug development. Recently, several knowledge graph (KG) embedding approaches have received increasing attention in the DDI domain due to their capability of projecting drugs and interactions into a low-dimensional feature space for predicting links and classifying triplets. However, existing methods only apply a uniformly random mode to construct negative samples. As a consequence, these samples are often too simplistic to train an effective model. In this paper, we propose a new KG embedding framework by introducing adversarial autoencoders (AAEs) based on Wasserstein distances and Gumbel-Softmax relaxation for DDI tasks. In our framework, the autoencoder is employed to generate high-quality negative samples and the hidden vector of the autoencoder is regarded as a plausible drug candidate. Afterwards, the discriminator learns the embeddings of drugs and interactions based on both positive and negative triplets. Meanwhile, in order to solve vanishing gradient problems on the discrete representation—an inherent flaw in traditional generative models—we utilize the Gumbel-Softmax relaxation and the Wasserstein distance to train the embedding model steadily. We empirically evaluate our method on two tasks: link prediction and DDI classification. The experimental results show that our framework can attain significant improvements and noticeably outperform competitive baselines. Supplementary information: Supplementary data and code are available at https://github.com/dyf0631/AAE_FOR_KG.
Maternal high fat diet-induced obesity affects trophoblast differentiation and placental function in mice†
Authors: Kretschmer Tobias , Turnwald Eva-Maria , Janoschek Ruth , Zentis Peter , Bae-Gartz Inga , Beers Tim , Handwerk Marion , Wohlfarth Maria , Ghilav Mojgan , Bloch Wilhelm , Hucklenbruch-Rother Eva , Dötsch Jörg , Appel Sarah
Published: September 2020

Evidence suggests that maternal obesity (MO) can aggravate placental function causing severe pathologies during the perinatal window. However, molecular changes and mechanisms of placental dysfunction remain largely unknown. This work aimed to decipher structural and molecular alterations of the placental transfer zone associated with MO. To this end, mice were fed a high fat diet (HFD) to induce obesity before mating, and pregnant dams were sacrificed at E15.5 to receive placentas for molecular, histological, and ultrastructural analysis and to assess unidirectional materno-fetal transfer capacity. Laser-capture microdissection was used to collect specifically placental cells of the labyrinth zone for proteomics profiling. Using BeWo cells, fatty acid-mediated mechanisms of adherens junction stability, cell layer permeability, and lipid accumulation were deciphered. Proteomics profiling revealed downregulation of cell adhesion markers in the labyrinth zone of obese dams, and disturbed syncytial fusion and detachment of the basement membrane (BM) within this zone was observed, next to an increase in materno-fetal transfer in vivo across the placenta. We found that fetuses of obese dams develop a growth restriction and in those placentas, labyrinth zone volume-fraction was significantly reduced. Linoleic acid was shown to mediate beta-catenin level and increase cell layer permeability in vitro. Thus, MO causes fetal growth restriction, molecular and structural changes in the transfer zone leading to impaired trophoblast differentiation, BM disruption, and placental dysfunction despite increased materno-fetal transfer capacity. These adverse effects are probably mediated by fatty acids found in HFD demonstrating the need for obesity treatment to mitigate placental dysfunction and prevent offspring pathologies.
Dissecting Common and Unique Effects of Anti-α4β7 and Anti-Tumor Necrosis Factor Treatment in Ulcerative Colitis
Authors: Veny Marisol , Garrido-Trigo Alba , Corraliza Ana M , Masamunt Maria C , Bassolas-Molina Helena , Esteller Miriam , Arroyes Montserrat , Tristán Eva , Fernández-Clotet Agnès , Ordás Ingrid , Ricart Elena , Esteve Maria , Panés Julian , Salas Azucena
Published: September 2020

Background and Aims

Vedolizumab is an anti-α4β7 antibody approved for the treatment of ulcerative colitis [UC]. Although it is assumed that vedolizumab blocks intestinal homing of lymphocytes, its effects on different intestinal cell populations are not fully stablished. In order to establish the unique mechanisms of action of vedolizumab in UC patients, we compared its effects to those induced by anti-tumour necrosis factor [TNF].

Methods

Patients with active UC [endoscopic Mayo score >1] starting vedolizumab [n = 33] or anti-TNF [n = 45] and controls [n = 22] were included. Colon biopsies [at weeks 0, 14 and 46] and blood samples [at weeks 0, 2, 6, 14, 30 and 46] were used for cell phenotyping, transcriptional analysis [qPCR], and to measure receptor occupancy.

Results

Vedolizumab, in contrast to anti-TNF, significantly reduced the proportion of α4β7+ cells within intestinal T subsets while preserving the percentage of α4β7+ plasma cells. The marked decrease in α4β7 did not change the percentage of colonic αEβ7+ cells [at 46 weeks]. Both vedolizumab and anti-TNF significantly downregulated inflammation-related genes in the colon of responders [Mayo score < 2]. Moreover, both treatments significantly decreased the percentage of intestinal, but not blood, total lymphocytes [T and plasma cells], as well as the proportion of α4β1+ cells within intestinal T lymphocytes.

Conclusions

Our data show that while vedolizumab and anti-TNF block two unrelated targets, they induce remarkably similar effects. On the other hand, vedolizumab’s unique mechanism of action relies on blocking intestinal trafficking of α4β7 T cells, despite effectively binding to B and plasma cells that express α4β7.
Week 6 Calprotectin Best Predicts Likelihood of Long-term Endoscopic Healing in Crohn’s Disease: A Post-hoc Analysis of the UNITI/IM-UNITI Trials
Authors: Narula Neeraj , Wong Emily C L , Dulai Parambir S , Marshall John K , Colombel Jean-Frederic , Reinisch Walter
Published: September 2020

Objectives

There is need for biomarkers as predictors of outcome of medical treatment in Crohn’s disease. The purpose of this study was to evaluate the predictive performance of faecal calprotectin for short- and long-term clinical and endoscopic outcomes.

Methods

This post-hoc analysis of the UNITI/IM-UNITI studies [NCT01369329, NCT01369342, and NCT01369355; YODA #2019–4026] included 677 patients to evaluate the relationship of Week 6 calprotectin cut-offs and changes from baseline assessments in calprotectin for prediction of outcomes at Weeks 8, 32, and 52, using receiver operating characteristic curves with comparisons of areas under the curve [AUC]. The relationship between clinical and biomarker assessments at Week 6 and endoscopic remission [ER] at Week 52 was evaluated using multivariate logistic regression models adjusted for confounders.

Results

A Week 6 calprotectin <250 mg/kg demonstrated a significant ability to predict Week 52 ER (AUC 0.709, 95% confidence interval [CI] 0.566–0.852, p = 0.014) with fair accuracy, and performed better than other calprotectin cut-offs and deltas from baseline for prediction of Week 52 ER. When adjusted for covariates, patients with a Week 6 faecal calprotectin <250 mg/kg had 3.48 times [95% CI 1.31–9.28, p = 0.013] increased odds of Week 52 ER. No other Week 6 clinical assessment [clinical remission or clinical response] or biomarker [CRP <5 or drug level] had an association with Week 52 ER.

Conclusions

In summary, the results of this post-hoc analysis suggest that Week 6 calprotectin levels < 250 mg/kg can be predictive of future endoscopic healing and may be more informative than clinical symptom improvement.

Podcast

This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast
Enhancing EFL students’ participation through translanguaging
Authors: Kwihangana Felix
Published: September 2020

This study explored multilingual students’ attitudes towards translanguaging after the practice was introduced in group activities aimed at improving their English language skills and classroom engagement. A cohort of students taking a pre-sessional English course at a college of technology in Rwanda were initiated into translanguaging. They were then observed while translanguaging in group activities and interviewed later in focus groups to understand their acceptance of translanguaging as a resource for English language learning. Findings show that students engaged in translanguaging and acknowledged its benefits in their group activities. They nevertheless expressed reservations about embracing translanguaging as a formal pedagogy in their L2 classes. They were willing to opt for English-only classes regardless of their level of English language abilities. Students’ mixed feelings about translanguaging appeared to come from a perception of the English language as more relevant professionally and internationally than other local languages that constituted their multilingualism.
Prevalence, incidence, and outcomes across cardiovascular diseases in homeless individuals using national linked electronic health records
Authors: Nanjo Atsunori , Evans Hannah , Direk Kenan , Hayward Andrew C , Story Alistair , Banerjee Amitava
Published: September 2020

Aims

The risk and burden of cardiovascular disease (CVD) are higher in homeless than in housed individuals but population-based analyses are lacking. The aim of this study was to investigate prevalence, incidence and outcomes across a range of specific CVDs among homeless individuals.

Methods and results 

Using linked UK primary care electronic health records (EHRs) and validated phenotypes, we identified homeless individuals aged ≥16 years between 1998 and 2019, and age- and sex-matched housed controls in a 1:5 ratio. For 12 CVDs (stable angina; unstable angina; myocardial infarction; sudden cardiac death or cardiac arrest; unheralded coronary death; heart failure; transient ischaemic attack; ischaemic stroke; subarachnoid haemorrhage; intracerebral haemorrhage; peripheral arterial disease; abdominal aortic aneurysm), we estimated prevalence, incidence, and 1-year mortality post-diagnosis, comparing homeless and housed groups. We identified 8492 homeless individuals (32 134 matched housed individuals). Comorbidities and risk factors were more prevalent in homeless people, e.g. smoking: 78.1% vs. 48.3% and atrial fibrillation: 9.9% vs. 8.6%, P < 0.001. CVD prevalence (11.6% vs. 6.5%), incidence (14.7 vs. 8.1 per 1000 person-years), and 1-year mortality risk [adjusted hazard ratio 1.64, 95% confidence interval (CI) 1.29–2.08, P < 0.001] were higher, and onset was earlier (difference 4.6, 95% CI 2.8–6.3 years, P < 0.001), in homeless, compared with housed people. Homeless individuals had higher CVD incidence in all three arterial territories than housed people.

Conclusion 

CVD in homeless individuals has high prevalence, incidence, and 1-year mortality risk post-diagnosis with earlier onset, and high burden of risk factors. Inclusion health and social care strategies should reflect this high preventable and treatable burden, which is increasingly important in the current COVID-19 context.
Development and preliminary validation of the competency model for rural general practitioner in China
Authors: Wei Yun , Liu Yanli , Zhao Xuexue , Jin Guanghui , Zhao Yali , Lu Xiaoqin
Published: September 2020

Background

There is a shortage of rural general practitioners (GPs) in China. Training programs have been initiated to meet the needs of GP workforce in the rural areas; however, there is an absence of validated tool to assess their competencies.

Objective

This study aimed to develop a competency model for rural general practitioner (CMRGP) after training in China and to examine its validity and reliability.

Methods

A multistage process was adopted to develop the CMRGP comprised literature review, panel discussion and expert consultation, and the initial version of CMRGP was reduced from 10 domains and 77 items to 7 domains and 54 items. A pilot study was conducted among 202 rural GPs for the psychometric evaluation and application of the initial version of CMRGP, in which a questionnaire on the importance of items and self-evaluation was completed by the GPs.

Results

In the pilot study, 132 completed questionnaires (65.3%) were returned. Acceptability and face validity of the CMRGP were supported by high importance scores of the items, in which 52 out of 54 items achieved score higher than 4.00 (possible score from 0 to 5). Factor analysis supported the construct validity. After the modification, the final version of CMRGP contained 6 domains and 47 items. Good reliability was supported by internal consistency reliability (Cronbach’s α was 0.98) and split-half reliability (Spearman–Brown coefficient was 0.99).

Conclusions

The CMRGP demonstrated good reliability and validity. Pilot study showed its potential for application in the rural general practice and training program.
Determinants of Fall Prevention Guideline Implementation in the Home- and Community-Based Service Setting
Authors: Juckett Lisa A , Bunger Alicia C , Jarrott Shannon E , Dabelko-Schoeny Holly I , Krok-Schoen Jessica , Poling Rachael M , Mion Lorraine C , Tucker Sharon
Published: September 2020

Background and Objectives

Home- and community-based service (HCBS) recipients often possess multiple fall risk factors, suggesting that the implementation of evidence-based fall prevention guidelines may be appropriate for the HCBS setting. The purpose of this exploratory study was to examine the determinants of fall prevention guideline implementation and the potential strategies that can support implementation in HCBS organizations.

Research Design and Methods

Semistructured interview and focus group data were collected from 26 HCBS professionals representing the home-delivered meals, personal care, and wellness programs. Qualitative codes were mapped to the Consolidated Framework for Implementation Research by means of directed content analysis. The Consolidated Criteria for Reporting Qualitative research checklist was used to report the findings of this study.

Results

We identified 7 major determinants of guideline implementation: recipient needs and resources, cosmopolitanism, external policy and incentives, networks and communication, compatibility, available resources, and knowledge/beliefs. Strategies to support guideline implementation included the involvement of recipient and caregiver feedback, building fall prevention networks, and conducting educational meetings for HCBS staff.

Discussion and Implications

Falls and fall-related injuries will continue to plague the older adult community unless innovative approaches to fall prevention are developed and adopted. The implementation of fall prevention guidelines in the HCBS setting can help mitigate fall risk among a highly vulnerable older adult population and may be facilitated through the application of multifaceted implementation strategies.
An exploration of constructs related to dissemination and implementation of an early childhood systems-level intervention
Authors: Farewell Charlotte V , Puma Jini , Bergling Emily , Webb Julie , Quinlan Jennie , Shah Puja , Maiurro Emily
Published: September 2020

Obesity and overweight in early childhood have detrimental impacts on children’s health and development. Changing policy, system and environmental features focused on physical activity and healthy eating behaviors as part of health promotion interventions can play a key role in prevention strategies in early childhood education settings. These types of changes can have broad reach and are often sustained over time, which allows for impact on children who enter the early childhood education setting year after year. However, there is currently a gap between the generation of evidence for health promotion programs and their application into practice. This study used qualitative methods to evaluate intervention-, organizational- and individual-level factors within a dissemination and implementation framework that may be related to the implementation of a health-promoting intervention in early childhood education settings. Intervention-level factors, including feasibility and adaptability, organizational-level factors, including staff and leadership engagement, and individual-level factors, including attitudes, skills and knowledge, were identified as constructs that impacted the successful implementation of the intervention. These findings provide insight into core dissemination and implementation constructs that should be targeted by obesity prevention interventions in early childhood education settings to ensure maximum impact on sustainable behavior change.
Early Life Disruption of the Microbiota Affects Organ Development and Cytokine Gene Expression in Threespine Stickleback
Authors: Kirschman Lucas J , Khadjinova Anastasia , Ireland Kelly , Milligan-Myhre Kathryn C
Published: September 2020

Synopsis

The microbiota that inhabits vertebrates exerts strong effects on host physiology and can be crucial to the development of a normal phenotype. This includes development of the immune system, somatic growth and maintenance, and morphogenesis. However, the genetic background of the host can also affect these life history traits. To this end, we investigated the effects of the microbiota on growth, development, and immune gene expression on two populations of threespine stickleback (Gasterosteus aculeatus), one anadromous and one freshwater. We tested the hypotheses that microbial colonization and the genetic background of the host would affect survival, cytokine gene expression, growth, and development. We raised in vitro crosses of stickleback larvae with and without conventional microbiota. We then exposed all these treatments to Vibrio anguillarum, a potential fish pathogen, in a full factorial design. We found stickleback raised without conventional microbiota had smaller swim bladders relative to those raised with conventional microbiota. Stickleback raised with conventional microbiota exhibited small increases in cytokine gene expression. We found no differences in growth or survival regardless of treatment. These results are consistent with other investigations that show microbiota disruption, in early life, can alter host organ and tissue development and immune responses
Basic Cohomology of Canonical Holomorphic Foliations on Complex Moment-Angle Manifolds
Authors: Ishida Hiroaki , Krutowski Roman , Panov Taras
Published: September 2020

We describe the basic cohomology ring of the canonical holomorphic foliation on a moment-angle manifold, LVMB-manifold, or any complex manifold with a maximal holomorphic torus action. Namely, we show that the basic cohomology has a description similar to the cohomology ring of a complete simplicial toric variety due to Danilov and Jurkiewicz. This settles a question of Battaglia and Zaffran, who previously computed the basic Betti numbers for the canonical holomorphic foliation in the case of a shellable fan. Our proof uses an Eilenberg–Moore spectral sequence argument; the key ingredient is the formality of the Cartan model for the torus action on a moment-angle manifold. We develop the concept of transverse equivalence as an important tool for studying smooth and holomorphic foliated manifolds. For an arbitrary complex manifold with a maximal torus action, we show that it is transverse equivalent to a moment-angle manifold and therefore has the same basic cohomology.
Promises under Pressure: Statements of Reassurance in US Alliances
Authors: Blankenship Brian
Published: September 2020

The United States frequently reassures allies of its protection by stationing troops abroad, visiting allied countries, and making public statements. Yet the causes of reassurance in asymmetric alliances—those between a great power patron and its weaker allies—are understudied in the academic literature. Indeed, many scholars argue that reassurance can be counterproductive as it invites allies to free ride or provoke their adversaries, knowing that they have their patron's support. Despite the drawbacks, I argue that the United States use reassurance to discourage their allies from seeking outside options and reducing their dependence on the alliance. Patrons such as the United States thus face a dilemma wherein they trade-off between withholding reassurance for short-term leverage and using reassurance to preserve their long-term influence. I test the theory using a new cross-national dataset of US. statements of reassurance from 1950 to 2010, and the results provide stronger support for my hypotheses than for the competing explanations of deterrence, strength from desperation, and shared preferences. The findings have implications for understanding how great powers manage their alliances, and suggest a pathway through which weaker states can shape great powers’ foreign commitments.
Assessment of commercial companion animal kefir products for label accuracy of microbial composition and quantity
Authors: Metras Breanna N , Holle Maxwell J , Parker Valerie J , Miller Michael J , Swanson Kelly S
Published: September 2020

Kefir is a fermented beverage containing yeast and bacteria produced by the fermentation of water or milk with kefir grains. Lack of regulation for probiotic-containing fermented food sold for companion dogs and cats creates the potential for misreporting on viable microbial counts, taxonomy, and label claims. In this study, the microbiota of six companion animal kefir products were measured quantitatively using standard plating techniques. Microbial composition of these products was also characterized by using high-resolution, long-read amplicon sequencing of the 16S rRNA gene. Five products (83%) listed specific microorganisms, and four products (66%) guaranteed colony forming units (CFU)/g on their label. To enumerate viable lactic acid bacteria (LAB), two lots of each homogenized product were plated upon opening and following 14 d on deMan Rogosa and Sharpe (MRS) agar and incubated under anaerobic and aerobic conditions. Results from point of opening revealed that all commercial kefir products with a guaranteed CFU/g overstated the number of microorganisms present by at least 1 log, with only one product exceeding 1 × 109 CFU/g. Sequencing results demonstrated that none of the labels claiming specific bacterial genera and species on their labels were correct, and all products contained at least three additional bacterial species above the minimum detectable threshold (0.001% relative abundance) that were not disclosed by the manufacturer. In addition to the incorrect viable CFU and bacterial taxonomies, several of the product labels and websites contained a wide range of health claims, none of which are supported by the companion animal literature. Our results demonstrate a low level of accuracy in the labeling of commercial kefir products intended for use in dogs and cats. Regulatory agencies, veterinarians, pet food professionals, and pet owners must scrutinize these products and demand a higher level of accuracy and quality in the future.
Feasibility and reliability of a German guideline for farm’s self-monitoring in sows and piglets
Authors: Friedrich Lena , Krieter Joachim , Kemper Nicole , Czycholl Irena
Published: September 2020

The present study’s aim was to test a German guideline for farm’s self-monitoring in sows and piglets for its feasibility as well as its interobserver and test–retest reliability. The study was performed between September 2016 and April 2018 on 13 farrowing farms in Northern Germany. Contrary to the guideline, the testing was not carried out by the farmers themselves but by 2 observers with experience in pigs representing common farmers. For the interobserver reliability study, the observers performed 20 joint farm visits independently assessing the same animals. For the test–retest reliability study, each farm was visited 5 times by 1 observer (day 0, day 3, week 7, month 5, month 10). Farm visit 1 (day 0) was used as reference and compared with the remaining farm visits. The reliability was evaluated using Spearman’s rank correlation coefficient (RS), intraclass correlation coefficient (ICC), and limits of agreement (LoA). As results, the guideline’s feasibility was limited. The indicators’ reliability also presented divergent results: All indicators in piglets revealed acceptable to good interobserver reliability (RS 0.64 to 0.77 ICC 0.33 to 0.48 LoA between the intervals −0.02 to 0.13 and −0.02 to 0.00). Contrarily, interobserver reliability was low for indicators in sows (e.g., claw alterations: RS −0.41 ICC 0.00 LoA −0.97 to 0.68). Overall acceptable test–retest reliability could be assigned to all indicators although no exact agreement existed but only the pursuit of trends is indicated. On the basis of the present results, the guideline in its present form cannot be recommended for farms’ self-monitoring. Given the restricted applicability, it should be reconsidered whether it might not be more appropriate to use scientifically tested and generally accepted animal welfare assessment systems such as the Welfare Quality animal welfare assessment protocols, although their application is also time-consuming.
Implant placement in the removable mandibular advancement device for completely edentulous patients: a finite element study
Authors: Park Jieun , Ahn Su-Jin , Lee Hyeonjong , Noh Gunwoo
Published: September 2020

Few studies have examined the biomechanical effects of dental implant placement in the implant-supported mandibular advancement device (MAD) for the treatment of obstructive sleep apnea in completely edentulous patients. This biomechanical study aimed to evaluate the stability of the implant-supported MAD for different numbers and positions of dental implants. A 3D edentulous maxillofacial model with the one-piece MAD was considered for various numbers and positions of implants. On each mandible and maxilla, one, two, four, or six implants were placed symmetrically in various positions. Total 42 implant placements were considered. A static finite element analysis was performed under the mandibular posterior restorative force for 40% protrusion. The maximum and minimum principal stresses on the cortical and cancellous bones and the von Mises stresses on the implant were measured. When four implants were placed on each maxilla and mandible, the maximum average stress on the cancellous bone was reduced by up to approximately three times compared with the cases of placing two implants on each maxilla and mandible. The placement of at least four implants on each maxilla and mandible improved MAD stability. It is noteworthy that the mandibular implants should be arranged adjacently to avoid stress concentration in the second molar.
Nigeria’s Federal High Court relies on physical evidence and shipping documents to invalidate registered designs
Authors: Okorie Chijioke
Published: September 2020

Federal High Court, Lagos, Nigeria, West African Cotton Company Limited and Hozelock Exel, FHC/L/CP/1240/2013, 14 February 2020
A Prognostic Predictive System Based on Deep Learning for Locoregionally Advanced Nasopharyngeal Carcinoma
Authors: Qiang Mengyun , Li Chaofeng , Sun Yuyao , Sun Ying , Ke Liangru , Xie Chuanmiao , Zhang Tao , Zou Yujian , Qiu Wenze , Gao Mingyong , Li Yingxue , Li Xiang , Zhan Zejiang , Liu Kuiyuan , Chen Xi , Liang Chixiong , Chen Qiuyan , Mai Haiqiang , Xie Guotong , Guo Xiang , Lv Xing
Published: September 2020

Background

Images from magnetic resonance imaging (MRI) are crucial unstructured data for prognostic evaluation in nasopharyngeal carcinoma (NPC). We developed and validated a prognostic system based on the MRI features and clinical data of locoregionally advanced NPC (LA-NPC) patients to distinguish low-risk patients with LA-NPC for whom concurrent chemoradiotherapy (CCRT) is sufficient.

Methods

This multicenter, retrospective study included 3444 patients with LA-NPC from January 1, 2010, to January 31, 2017. A 3-dimensional convolutional neural network was used to learn the image features from pretreatment MRI images. An eXtreme Gradient Boosting model was trained with the MRI features and clinical data to assign an overall score to each patient. Comprehensive evaluations were implemented to assess the performance of the predictive system. We applied the overall score to distinguish high-risk patients from low-risk patients. The clinical benefit of induction chemotherapy (IC) was analyzed in each risk group by survival curves.

Results

We constructed a prognostic system displaying a concordance index of 0.776 (95% confidence interval [CI] = 0.746 to 0.806) for the internal validation cohort and 0.757 (95% CI = 0.695 to 0.819), 0.719 (95% CI = 0.650 to 0.789), and 0.746 (95% CI = 0.699 to 0.793) for the 3 external validation cohorts, which presented a statistically significant improvement compared with the conventional TNM staging system. In the high-risk group, patients who received induction chemotherapy plus CCRT had better outcomes than patients who received CCRT alone, whereas there was no statistically significant difference in the low-risk group.

Conclusions

The proposed framework can capture more complex and heterogeneous information to predict the prognosis of patients with LA-NPC and potentially contribute to clinical decision making.
Dissecting cholesterol and phytosterol biosynthesis via mutants and inhibitors
Authors: De Vriese Kjell , Pollier Jacob , Goossens Alain , Beeckman Tom , Vanneste Steffen
Published: September 2020

Plants stand out among eukaryotes due to the large variety of sterols and sterol derivatives that they can produce. These metabolites not only serve as critical determinants of membrane structures, but also act as signaling molecules, as growth-regulating hormones, or as modulators of enzyme activities. Therefore, it is critical to understand the wiring of the biosynthetic pathways by which plants generate these distinct sterols, to allow their manipulation and to dissect their precise physiological roles. Here, we review the complexity and variation of the biosynthetic routes of the most abundant phytosterols and cholesterol in the green lineage and how different enzymes in these pathways are conserved and diverged from humans, yeast, and even bacteria. Many enzymatic steps show a deep evolutionary conservation, while others are executed by completely different enzymes. This has important implications for the use and specificity of available human and yeast sterol biosynthesis inhibitors in plants, and argues for the development of plant-tailored inhibitors of sterol biosynthesis.
Concentrations of dark haloes emerge from their merger histories
Authors: Wang Kuan , Mao Yao-Yuan , Zentner Andrew R , Lange Johannes U , van den Bosch Frank C , Wechsler Risa H
Published: September 2020

The concentration parameter is a key characteristic of a dark matter halo that conveniently connects the halo’s present-day structure with its assembly history. Using ‘Dark Sky’, a suite of cosmological N-body simulations, we investigate how halo concentration evolves with time and emerges from the mass assembly history. We also explore the origin of the scatter in the relation between concentration and assembly history. We show that the evolution of halo concentration has two primary modes: (1) smooth increase due to pseudo-evolution; and (2) intense responses to physical merger events. Merger events induce lasting and substantial changes in halo structures, and we observe a universal response in the concentration parameter. We argue that merger events are a major contributor to the uncertainty in halo concentration at fixed halo mass and formation time. In fact, even haloes that are typically classified as having quiescent formation histories experience multiple minor mergers. These minor mergers drive small deviations from pseudo-evolution, which cause fluctuations in the concentration parameters and result in effectively irreducible scatter in the relation between concentration and assembly history. Hence, caution should be taken when using present-day halo concentration parameter as a proxy for the halo assembly history, especially if the recent merger history is unknown.
The post-common-envelope binary central star of the planetary nebula ETHOS 1
Authors: Munday James , Jones David , García-Rojas Jorge , Boffin Henri M J , Miszalski Brent , Corradi Romano L M , Rodríguez-Gil Pablo , Rubio-Díez María del Mar , Santander-García Miguel , Sowicka Paulina
Published: September 2020

We present a detailed study of the binary central star of the planetary nebula ETHOS 1 (PN G068.1+11.0). Simultaneous modelling of light and radial velocity curves reveals the binary to comprise a hot and massive pre-white dwarf with an M-type main-sequence companion. A good fit to the observations was found with a companion that follows expected mass–temperature–radius relationships for low-mass stars, indicating that despite being highly irradiated, it is consistent with not being significantly hotter or larger than a typical star of the same mass. Previous modelling indicated that ETHOS 1 may comprise the first case where the orbital plane of the central binary does not lie perpendicular to the nebular symmetry axis, at odds with the expectation that the common envelope is ejected in the orbital plane. We find no evidence for such a discrepancy, deriving a binary inclination in agreement with that of the nebula as determined by spatio-kinematic modelling. This makes ETHOS 1 the ninth post-common-envelope planetary nebula in which the binary orbital and nebular symmetry axes have been shown to be aligned, with as yet no known counter-examples. The probability of finding such a correlation by chance is now less than 0.000 02 per cent.
Experimental energy levels of 12C14N through marvel analysis
Authors: Syme Anna-Maree , McKemmish Laura K
Published: September 2020

The cyano radical (CN) is a key molecule across many different factions of astronomy and chemistry. Accurate, empirical rovibronic energy levels with uncertainties are determined for eight doublet states of CN using the marvel (Measured Active Rotational-Vibrational Energy Levels) algorithm. 40 333 transitions were validated from 22 different published sources to generate 8083 spin-rovibronic energy levels. The empirical energy levels obtained from the marvel analysis are compared to current energy levels from the mollist line list. The mollist transition frequencies are updated with marvel energy level data which brings the frequencies obtained through experimental data up to 77.3 per cent from the original 11.3 per cent, with 92.6 per cent of the transitions with intensities over 10−23 cm molecule−1 at 1000 K now known from experimental data. At 2000 K, 100.0 per cent of the partition function is recovered using only marvel energy levels, while 98.2 per cent is still recovered at 5000 K.
The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the BAO and growth rate of structure of the luminous red galaxy sample from the anisotropic correlation function between redshifts 0.6 and 1
Authors: Bautista Julian E , Paviot Romain , Vargas Magaña Mariana , de la Torre Sylvain , Fromenteau Sebastien , Gil-Marín Hector , Ross Ashley J , Burtin Etienne , Dawson Kyle S , Hou Jiamin , Kneib Jean-Paul , de Mattia Arnaud , Percival Will J , Rossi Graziano , Tojeiro Rita , Zhao Cheng , Zhao Gong-Bo , Alam Shadab , Brownstein Joel , Chapman Michael J , Choi Peter D , Chuang Chia-Hsun , Escoffier Stéphanie , de la Macorra Axel , du Mas des Bourboux Hélion , Mohammad Faizan G , Moon Jeongin , Müller Eva-Maria , Nadathur Seshadri , Newman Jeffrey A , Schneider Donald , Seo Hee-Jong , Wang Yuting
Published: September 2020

We present the cosmological analysis of the configuration-space anisotropic clustering in the completed Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey (eBOSS) Data Release 16 galaxy sample. This sample consists of luminous red galaxies (LRGs) spanning the redshift range 0.6 < $z$ < 1, at an effective redshift of $z$eff  = 0.698. It combines 174 816 eBOSS and 202 642 BOSS LRGs. We extract and model the baryon acoustic oscillation (BAO) and redshift-space distortion (RSD) features from the galaxy two-point correlation function to infer geometrical and dynamical cosmological constraints. The adopted methodology is extensively tested on a set of realistic simulations. The correlations between the inferred parameters from the BAO and full-shape correlation function analyses are estimated. This allows us to derive joint constraints on the three cosmological parameter combinations: DM($z$)/rd, DH($z$)/rd, and fσ8($z$), where DM is the comoving angular diameter distance, DH is the Hubble distance, rd is the comoving BAO scale, f is the linear growth rate of structure, and σ8 is the amplitude of linear matter perturbations. After combining the results with those from the parallel power spectrum analysis of Gil-Marin et al., we obtain the constraints: DM/rd = 17.65 ± 0.30, DH/rd = 19.77 ± 0.47, and fσ8 = 0.473 ± 0.044. These measurements are consistent with a flat Lambda cold dark matter model with standard gravity.
Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex
Authors: Zhang Ziguo , Bellini Dom , Barford David
Published: September 2020

Kinetochores are large multi-subunit complexes that attach centromeric chromatin to microtubules of the mitotic spindle, enabling sister chromatid segregation in mitosis. The inner kinetochore constitutive centromere associated network (CCAN) complex assembles onto the centromere-specific Cenp-A nucleosome (Cenp-ANuc), thereby coupling the centromere to the microtubule-binding outer kinetochore. CCAN is a conserved 14–16 subunit complex composed of discrete modules. Here, we determined the crystal structure of the Saccharomyces cerevisiae Cenp-HIKHead-TW sub-module, revealing how Cenp-HIK and Cenp-TW interact at the conserved Cenp-HIKHead–Cenp-TW interface. A major interface is formed by the C-terminal anti-parallel α-helices of the histone fold extension (HFE) of the Cenp-T histone fold domain (HFD) combining with α-helix H3 of Cenp-K to create a compact three α-helical bundle. We fitted the Cenp-HIKHead-TW sub-module to the previously determined cryo-EM map of the S. cerevisiae CCAN–Cenp-ANuc complex. This showed that the HEAT repeat domain of Cenp-IHead and C-terminal HFD of Cenp-T of the Cenp-HIKHead-TW sub-module interact with the nucleosome DNA gyre at a site close to the Cenp-ANuc dyad axis. Our structure provides a framework for understanding how Cenp-T links centromeric Cenp-ANuc to the outer kinetochore through its HFD and N-terminal Ndc80-binding motif, respectively.
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis
Authors: Chen Kunqi , Song Bowen , Tang Yujiao , Wei Zhen , Xu Qingru , Su Jionglong , de Magalhães João Pedro , Rigden Daniel J , Meng Jia
Published: September 2020

Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge. Recent studies suggest that RNA modifications play versatile roles in essential biological mechanisms, and are closely related to the progression of various diseases including multiple cancers. To comprehensively unveil the association between disease-associated variants and their epitranscriptome disturbance, we built RMDisease, a database of genetic variants that can affect RNA modifications. By integrating the prediction results of 18 different RNA modification prediction tools and also 303,426 experimentally-validated RNA modification sites, RMDisease identified a total of 202,307 human SNPs that may affect (add or remove) sites of eight types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G and Nm). These include 4,289 disease-associated variants that may imply disease pathogenesis functioning at the epitranscriptome layer. These SNPs were further annotated with essential information such as post-transcriptional regulations (sites for miRNA binding, interaction with RNA-binding proteins and alternative splicing) revealing putative regulatory circuits. A convenient graphical user interface was constructed to support the query, exploration and download of the relevant information. RMDisease should make a useful resource for studying the epitranscriptome impact of genetic variants via multiple RNA modifications with emphasis on their potential disease relevance. RMDisease is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/rmd.
cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function
Authors: Huang Yan , Wang Jing , Zhao Yue , Wang Huafeng , Liu Tianyuan , Li Yuhe , Cui Tianyu , Li Weiyi , Feng Yige , Luo Jiaxin , Gong Jiaqi , Ning Lin , Zhang Yong , Wang Dong , Zhang Yang
Published: September 2020

RNA endowed with both protein-coding and noncoding functions is referred to as ‘dual-function RNA’, ‘binary functional RNA (bifunctional RNA)’ or ‘cncRNA (coding and noncoding RNA)’. Recently, an increasing number of cncRNAs have been identified, including both translated ncRNAs (ncRNAs with coding functions) and untranslated mRNAs (mRNAs with noncoding functions). However, an appropriate database for storing and organizing cncRNAs is still lacking. Here, we developed cncRNAdb, a manually curated database of experimentally supported cncRNAs, which aims to provide a resource for efficient manipulation, browsing and analysis of cncRNAs. The current version of cncRNAdb documents about 2600 manually curated entries of cncRNA functions with experimental evidence, involving more than 2,000 RNAs (including over 1300 translated ncRNAs and over 600 untranslated mRNAs) across over 20 species. In summary, we believe that cncRNAdb will help elucidate the functions and mechanisms of cncRNAs and develop new prediction methods. The database is available at http://www.rna-society.org/cncrnadb/.