bluuebunny/crossref_metadata_2025_split huggingface dataset:
Information Retrieval in Food Science Research II: Accounting for Relevance When Evaluating Database Performance
Authors: Urhan Tuba Karaarslan , Rempel Hannah Gascho , Meunier‐Goddik Lisbeth , Penner Michael H. 
Published: September 2019

AbstractThe impetus for this study is the limited amount of information on performance characteristics of food science–encompassing online bibliographic databases. Database usage is an important element in modern research because a comprehensive understanding of current knowledge is essential for effective, unbiased hypothesis formulation and testing. Six databases commonly recommended by academic libraries for information retrieval in the food sciences (Academic Search Premier [ASP], Agricultural Online Access [AGRICOLA], CAB Direct, Food Science and Technology Abstracts [FSTA], PubMed, and Web of Science [WoS]) were compared in a case study based on the research topic “in vitro bile acid binding properties of dietary lignin.” A complex string of search terms was used for citation retrieval, and predetermined inclusion/exclusion criteria were used to determine the relevancy of retrieved articles. Searching WoS and CAB Direct returned the greatest number of relevant articles, followed closely by FSTA, PubMed, and AGRICOLA. FSTA and AGRICOLA returned the highest ratios of relevant‐to‐irrelevant articles, followed closely by CAB Direct. None of the databases, when used alone, recovered all of the relevant articles identified in the study; WoS indexed the highest percentage of relevant articles identified (WoS = 10; total = 19). WoS also had the highest number of relevant articles that were unique to any one database. The thoroughness of searching the complete group of databases was tested by comparison of retrieved citations with those found in relevant review articles, revealing the need for testing overall inclusivity.Practical ApplicationComprehensive online information retrieval is the most efficient means of accessing current knowledge. Awareness of current knowledge is essential for effective, unbiased decision making in private sector and academic/government‐based research endeavors. Thus, online database usage is an essential element of modern food science research. This paper provides tangible examples of the performance characteristics of online bibliographic databases commonly recommended for information retrieval in the food sciences. The paper is written so as to aid the reader in making decisions with respect to database usage for the recovery of topic‐relevant peer‐reviewed articles germane to their area of research.
Psychometric evaluation of the Chinese version of the Fonseca anamnestic index for temporomandibular disorders
Authors: Zhang Min‐juan , Yap Adrian U‐Jin , Lei Jie , Fu Kai‐Yuan 
Published: September 2019

AbstractBackgroundThe Fonseca anamnestic index (FAI) offers a simple, low‐cost, patient‐reported method for screening temporomandibular disorders (TMDs).ObjectivesThis study described the development of the Chinese version of the FAI (FAI‐C) and examined its reliability and validity when compared to the Diagnostic Criteria for Temporomandibular Disorders (DC/TMD).MethodsThe FAI‐C was created by translation and cross‐cultural adaptation of the English instrument following international guidelines. Psychometric evaluation of the FAI‐C was carried out on a sample of 613 patients with TMDs and 57 controls. Reliability of the FAI‐C was determined by means of internal consistency and test‐retest methods while validity was ascertained by criterion‐related validity. Criterion validity was examined via Cohen's kappa, sensitivity and specificity when compared with DC/TMD Axis I diagnoses.ResultsCronbach's alpha value (internal consistency) for total FAI‐C score was 0.669, and intra‐class correlation coefficient (ICC) value (test‐retest reliability) was 0.823. For criterion validity, kappa coefficient value was 0.633 while sensitivity and specificity was 95.9% and 71.9%, respectively.ConclusionThe Chinese version of the FAI demonstrated acceptable reliability and good validity. The FAI‐C could thus be used as an instrument for screening TMDs in Chinese literate populations.
Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing
Authors: Wan Jun‐Nan , Guo Yan‐Ping , Rao Guang‐Yuan 
Published: September 2019

AbstractAllopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species could lead to the origin of different taxa has received little attention. Here we used a new progenitor‐specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, Achillea alpina L. and Achillea wilsoniana Heimerl ex Hand.‐Mazz., through allotetraploidy from the same diploid progenitor species pair, Achillea acuminata (Ledeb.) Sch. Bip. and Achillea asiatica Serg. Based on the sequences of 17 nuclear genes from 21 wild populations of the four Achillea species investigated, a clear view of genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, A. acuminata, and ancestors belonging to those two groups contributed to the two tetraploid species. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study indicates that independent allopolyploidization events between the same Achillea parental species have generated two genetically and ecologically distinct taxa.
Can earlier BCG vaccination reduce early infant mortality? Study protocol for a cluster randomised trial in Guinea-Bissau
Authors: Thysen Sanne M , Jensen Aksel Karl Georg , Rodrigues Amabelia , Borges Igualdino da Silva , Aaby Peter , Benn Christine , Fisker Ane 
Published: September 2019

IntroductionThe BCG vaccine is designed to protect against tuberculosis, but the vaccine may have broader effects. In 2014, the Strategic Advisory Group of Experts on Immunization reviewed the literature on non-specific effects of BCG, and concluded that the evidence was consistent with beneficial non-specific effects and requested further randomised trials.Methods and analysesWithin the Bandim Health Project’s urban and rural health and demographic surveillance systems, we will conduct a cluster-randomised trial in six suburban districts and 55 rural villages. Infants are enrolled at a home visit before 72 hours of life. In intervention clusters, children are vaccinated with BCG and oral polio vaccine (OPV). In control clusters, the caregivers are informed about vaccination opportunities. Using Cox-proportional hazards models, we will test whether BCG and OPV provided at a single home visit can reduce early infant mortality up to 60 days.The trial was initiated with a pilot study in Biombo region in June 2015. The trial was scaled up to full study including Oio and Cacheu regions in July 2016. The trial was expanded to include the urban study area in July 2017.Ethics and disseminationBCG vaccination is delayed in many low-income settings. WHO-recommended home visits are resource demanding and vaccines are not part of the recommendation. Utilising the home visits to provide BCG and OPV may provide countries with a further incentive to introduce a single home visit. In countries, where home visits are already in place, vaccines can easily be added to reduce early infant mortality. The trial is approved by the Guinean Ethical Committee (Reference number: 0016/CNES/INASA/2015) and the Danish Ethics Committee has given its consultative approval. The results of the trial will be published in international peer-reviewed journals.Trial registration numberNCT02504203; Pre-results.
Rationale and population-based prospective cohort protocol for the disadvantaged populations at risk of decline in eGFR (CO-DEGREE)
Authors: Gonzalez-Quiroz Marvin , Nitsch Dorothea , Hamilton Sophie , O'Callaghan Gordo Cristina , Saran Rajiv , Glaser Jason , Correa-Rotter Ricardo , Jakobsson Kristina , Singh Ajay , Gunawardena Nalika , Levin Adeera , Remuzzi Giuseppe , Caplin Ben , Pearce Neil 
Published: September 2019

IntroductionA recently recognised form of chronic kidney disease (CKD) of unknown origin (CKDu) is afflicting communities, mostly in rural areas in several regions of the world. Prevalence studies are being conducted in a number of countries, using a standardised protocol, to estimate the distribution of estimated glomerular filtration rate (eGFR), and thus identify communities with a high prevalence of reduced glomerular filtration rate (GFR). In this paper, we propose a standardised minimum protocol for cohort studies in high-risk communities aimed at investigating the incidence of, and risk factors for, early kidney dysfunction.Methods and analysisThis generic cohort protocol provides the information to establish a prospective population-based cohort study in low-income settings with a high prevalence of CKDu. This involves a baseline survey that included key elements from the DEGREE survey (eg, using the previously published DEGREE methodology) of a population-representative sample, and subsequent follow-up visits in young adults (without a pre-existing diagnosis of CKD (eGFR<60 mL/min/1.73m2), proteinuria or risk factors for CKD at baseline) over several years. Each visit involves a core questionnaire, and collection and storage of biological samples. Local capacity to measure serum creatinine will be required so that immediate feedback on kidney function can be provided to participants. After completion of follow-up, repeat measures of creatinine should be conducted in a central laboratory, using reference standards traceable to isotope dilution mass spectrometry (IDMS) quality control material to quantify the main outcome of eGFR decline over time, alongside a description of the early evolution of disease and risk factors for eGFR decline.Ethics and disseminationEthical approval will be obtained by local researchers, and participants will provide informed consent before the study commences. Participants will typically receive feedback and advice on their laboratory results, and referral to a local health system where appropriate.
Cohort profile: the clinical ‘Psoriasis in Adolescents’ (PIA) cohort in Denmark
Authors: Blegvad Christoffer , Andersen Anne-Marie Nybo , Groot Jonathan , Zachariae Claus , Skov Lone 
Published: September 2019

PurposePsoriasis is a chronic inflammatory skin disease that frequently debuts in childhood and adolescence. We wished to determine environmental and genetic risk factors for the development of psoriasis in children and adolescents, as well as to investigate debut type, trigger factors, course of disease, nature and influence of stress related to both child and family and risk factors for comorbidity. The ‘Psoriasis in Adolescents’ (PIA) cohort will provide data on the relationship between psoriasis and, respectively, genetic disposition, early-life exposures, quality of life and comorbidity.ParticipantsThe PIA cohort is nested in the large general population Danish National Birth Cohort (DNBC). We invited 390 adolescents with psoriasis and corresponding maternally predisposed and non-predisposed controls. Participants underwent an interview and a clinical examination consisting of a skin inspection and physical measurements including blood sampling and microbiological swabs. Additionally, four self-administered questionnaires on physical and mental health were completed.Findings to dateThe final PIA cohort consists of 81 adolescents with psoriasis, 110 parentally predisposed and 124 non-predisposed psoriasis-free adolescents. The validity of the maternally reported psoriasis status from the DNBC was found to be low on clinical examination (47.5%). In contrast, the self-reported psoriasis status of the DNBC mothers was clinically confirmed in 80.8% of the cases.Future plansThe PIA cohort offers the possibility of assessing the clinical characteristics, course of psoriasis and development of comorbidities in adolescents with clinically confirmed disease from a general population. Comparison with predisposed and non-predisposed controls is possible and genetic analyses are scheduled. We plan to invite the participants for a follow-up in 5–10 years. Furthermore, we plan to include newly diagnosed adolescents with psoriasis from the 18-year DNBC follow-up. All information is linkable on the individual level with data from the DNBC and nationwide registries in Denmark.
Sirtuin6 (SIRT6) Promotes the EMT of Hepatocellular Carcinoma by Stimulating Autophagic Degradation of E-Cadherin
Authors: Han Li Li , Jia Lijun , Wu Fei , Huang Chen 
Published: September 2019

Abstract

EMT is a pivotal mechanism involved in tumor metastasis, which is the leading cause of poor prognosis for hepatocellular carcinoma (HCC). Sirtuin family members function as NAD+-dependent deacetylases that are essential for tumor metastasis and epithelial–mesenchymal transition (EMT). However, no causal association has been established between Sirtuin6 (SIRT6) and HCC metastasis. SIRT6 expression pattern and its association with HCC metastasis were investigated by informatic analysis, and verified by qRT-PCR and immunochemistry in HCC tissues. Transwell assay, qRT-PCR, and immunofluorescence assay were utilized to assess the effects of SIRT6 on metastasis and E-cadherin expression in vitro and in vivo. Immunoprecipitation assay was performed to observe whether SIRT6 deacetylated Beclin-1 in HCC cells. Immunofluorescence assay and inhibitor treatment rescue experiments were used to clarify the mechanism by which SIRT6 facilitated EMT and metastasis. SIRT6 upregulation was quite prevalent in HCC tissues and closely correlated with worse overall survival, disease-relapse free survival, and HCC metastasis. Furthermore, SIRT6 promoted HCC cell migration, invasion, and EMT. Mechanistically, we found that SIRT6 deacetylated Beclin-1 in HCC cells and this event led to the promotion of the autophagic degradation of E-cadherin. Noticeably, E-cadherin degradation and invasion, migration induced by SIRT6 overexpression could be rescued by dual mutation of Beclin-1 (inhibition of acetylation), CQ (autophagy inhibitor), and knockdown of Atg7. In addition, SIRT6 promoted N-cadherin and Vimentin expression via deacetylating FOXO3a in HCC. These results established a relationship between SIRT6 and HCC EMT and further elucidated the mechanisms underlying HCC metastasis, helping provide a promising approach for the treatment of HCC.

Implications:
Inhibiting SIRT6 represents a potential therapeutic approach to suppress HCC metastasis partially through reduction of autophagic degradation of E-cadherin.
Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells
Authors: Murakami Shino , Li Rui , Nagari Anusha , Chae Minho , Camacho Cristel V. , Kraus W. Lee 
Published: September 2019

Abstract

The bromodomain family member proteins (BRD; BET proteins) are key coregulators for estrogen receptor alpha (ERα)-mediated transcriptional enhancers. The use of BRD-selective inhibitors has gained much attention as a potential treatment for various solid tumors, including ER-positive breast cancers. However, the roles of individual BET family members have largely remained unexplored. Here, we describe the role of BRDs in estrogen (E2)-dependent gene expression in ERα-positive breast cancer cells. We observed that chemical inhibition of BET family proteins with JQ1 impairs E2-regulated gene expression and growth in breast cancer cells. In addition, RNAi-mediated depletion of each BET family member (BRDs 2, 3, and 4) revealed partially redundant roles at ERα enhancers and for target gene transcription. Furthermore, we found a unique role of BRD3 as a molecular sensor of total BET family protein levels and activity through compensatory control of its own protein levels. Finally, we observed that BRD3 is recruited to a subset of ERα-binding sites (ERBS) that are enriched for active enhancer features, located in clusters of ERBSs likely functioning as “super enhancers,” and associated with highly E2-responsive genes. Collectively, our results illustrate a critical and specific role for BET family members in ERα-dependent gene transcription.

Implications:
BRD3 is recruited to and controls the activity of a subset ERα transcriptional enhancers, providing a therapeutic opportunity to target BRD3 with BET inhibitors in ERα-positive breast cancers.
Inherited Thrombophilia and the Risk of Arterial Ischemic Stroke: A Systematic Review and Meta‐Analysis
Authors: Chiasakul Thita , De Jesus Elizabeth , Tong Jiayi , Chen Yong , Crowther Mark , Garcia David , Chai‐Adisaksopha Chatree , Messé Steven R. , Cuker Adam 
Published: September 2019

Background
Inherited thrombophilias are well‐established predisposing factors for venous thromboembolism, but their role in arterial thrombosis, such as arterial ischemic stroke, remains uncertain. We aimed to evaluate the association between inherited thrombophilia (factor V Leiden, prothrombin G20210A mutation, protein C deficiency, protein S deficiency, and antithrombin deficiency) and risk of arterial ischemic stroke in adults.

Methods and Results

We searched PubMed,
EMBASE
, and Cochrane Library Databases from inception to December 31, 2018. We included case‐control or cohort studies of adults reporting the prevalence of inherited thrombophilias in those with arterial ischemic stroke and subjects without arterial ischemic stroke. Two reviewers (T.C., E.D.) independently searched the literature and extracted data. Pooled odds ratios (
OR
s) and 95%
CI
s were calculated using random‐effects model. We identified 68 eligible studies, which collectively enrolled 11 916 stroke patients and 96 057 controls. The number of studies reporting factor V Leiden, prothrombin G20210A mutation, protein C deficiency, protein S deficiency, and antithrombin deficiency were 56, 45, 15, 17, and 12, respectively. Compared with controls, patients with arterial ischemic stroke were significantly more likely to have the following inherited thrombophilias: factor V Leiden (
OR
, 1.25; 95%
CI
, 1.08–1.44; I
2
=0%), prothrombin G20210A mutation (
OR
, 1.48; 95%
CI
, 1.22–1.80; I
2
=0%), protein C deficiency (
OR
, 2.13; 95%
CI
, 1.16–3.90; I
2
=0%), and protein S deficiency (
OR
, 2.26; 95%
CI
, 1.34–3.80; I
2
=8.8%). Statistical significance was not reached for antithrombin deficiency (
OR
, 1.25; 95%
CI
, 0.58–2.67; I
2
=8.8%).

Conclusions
Inherited thrombophilias (factor V Leiden, prothrombin G20210A mutation, protein C deficiency, and protein S deficiency) are associated with an increased risk of arterial ischemic stroke in adults. The implications of these findings with respect to clinical management of patients with ischemic stroke require further investigation.
Plasma Androgen Receptor Copy Number Status at Emergence of Metastatic Castration-Resistant Prostate Cancer: A Pooled Multicohort Analysis
Authors: Jayaram Anuradha , Wingate Anna , Wetterskog Daniel , Conteduca Vincenza , Khalaf Daniel , Sharabiani Mansour Taghavi Azar , Calabrò Fabio , Barwell Lorraine , Feyerabend Susan , Grande Enrique , Martinez-Carrasco Alberto , Font Albert , Berruti Alfredo , Sternberg Cora N. , Jones Rob , Lefresne Florence , Lahaye Marjolein , Thomas Shibu , Joshi Shilpy , Shen Dong , Ricci Deborah , Gormley Michael , Merseburger Axel S. , Tombal Bertrand , Annala Matti , Chi Kim N. , De Giorgi Ugo , Gonzalez-Billalabeitia Enrique , Wyatt Alexander W. , Attard Gerhardt 
Published: September 2019

PURPOSE Increases in androgen receptor ( AR) copy number (CN) can be detected in plasma DNA when patients develop metastatic castration-resistant prostate cancer. We aim to evaluate the association between AR CN as a continuous variable and clinical outcome. PATIENTS AND METHODS PCR2023 was an international, multi-institution, open-label, phase II study of abiraterone acetate plus prednisolone (AAP) or abiraterone acetate plus dexamethasone that included plasma AR assessment as a predefined exploratory secondary end point. Plasma AR CN data (ClinicalTrials.gov identifier: NCT01867710 ) from this study (n = 133) were pooled with data from the following three other cohorts: cohort A, which was treated with either AAP or enzalutamide (n = 73); the PREMIERE trial (ClinicalTrials.gov identifier: NCT02288936 ) of biomarkers for enzalutamide (n = 94); and a phase II trial from British Columbia (ClinicalTrials.gov identifier: NCT02125357 ) that randomly assigned men to either AAP or enzalutamide (n = 201). The primary outcome measures for the biomarker analysis were overall survival and progression-free survival. RESULTS Using multivariable fractional polynomials analysis using Cox regression models, a nonlinear relationship between plasma AR CN and outcome was identified for overall survival, where initially for small incremental gains in CN there was a large added hazard ratio that plateaued at higher CN. The CN cut point associated with the highest local hazard ratio was 1.92. A similar nonlinear association was observed with progression-free survival. In an exploratory analysis of PCR2023, the time from start of long-term androgen-deprivation therapy to start of AAP or abiraterone acetate plus dexamethasone was significantly shorter in patients with plasma AR CN of 1.92 or greater than patients with plasma AR CN of less than 1.92 (43 v 130 weeks, respectively; P = .005). This was confirmed in cohort A ( P = .003), the PREMIERE cohort ( P = .03), and the British Colombia cohort ( P = .003). CONCLUSION Patients with metastatic castration-resistant prostate cancer can be dichotomized by a plasma AR CN cut point of 1.92. Plasma AR CN value of 1.92 or greater identifies aggressive disease that is poorly responsive to AR targeting and is associated with a prior short response to primary androgen-deprivation therapy.
Comparison of human population receptive field estimates between scanners and the effect of temporal filtering
Authors: Morgan Catherine , Schwarzkopf D. Samuel 
Published: September 2019

Background: Population receptive field (pRF) analysis with functional magnetic resonance imaging (fMRI) is an increasingly popular method for mapping visual field representations and estimating the spatial selectivity of voxels in human visual cortex. However, the multitude of experimental setups and processing methods used makes comparisons of results between studies difficult. Methods: Here, we compared pRF maps acquired in the same three individuals using comparable scanning parameters on a 1.5 and a 3 Tesla scanner located in two different countries. We also tested the effect of low-pass filtering of the time series on pRF estimates. Results: As expected, the signal-to-noise ratio for the 3 Tesla data was superior; critically, however, estimates of pRF size and cortical magnification did not reveal any systematic differences between the sites. Unsurprisingly, low-pass filtering enhanced goodness-of-fit, presumably by removing high-frequency noise. However, there was no substantial increase in the number of voxels containing meaningful retinotopic signals after low-pass filtering. Importantly, filtering also increased estimates of pRF size in the early visual areas which could substantially skew interpretations of spatial tuning properties. Conclusion: Our results therefore suggest that pRF estimates are generally comparable between scanners of different field strengths, but temporal filtering should be used with caution.