bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between plasma vitamin D level and heart valves calcification in acute coronary syndrome and non acute coronary syndrome patients
Authors: Feldman Viktor , Laish-Farkash Avishag , Yosefy Chaim 
Published: September 2020

Background
There is conflicting data regarding the association between low levels of plasma vitamin D and ischemic heart disease. We aimed to investigate the relationship between plasma vitamin D levels and heart valve calcification in hospitalized patients with ischemic heart disease versus non-ischemic heart disease controls.

Methods
A prospective case-control study comprising two age and gender-matched groups. The study group included consecutive patients hospitalized due to acute coronary syndrome; the control group included consecutive non-ischemic heart disease patients hospitalized for noncardiac causes. Blood samples for 25-hydroxyvitamin D level were drawn. An echocardiogram was performed during the first 3 days of hospitalization and reviewed for presence and degree of valvular calcification.

Results
Forty patients with acute coronary syndrome and 40 controls (age 58 ± 11 years, 64% male in both groups) were included. Mean plasma 25-hydroxyvitamin D vitamin level in the entire cohort was 24.5 ± 8 ng/ml. Valve calcification rates were similar in acute coronary syndrome versus non-acute coronary syndrome group (28 vs. 21 had valvular calcification; 18 vs. 12 had aortic valve calcification; 21 vs. 14 had mitral valve calcification, respectively; P = NS for all). We found no significant relationship between vitamin D level and valvular calcification, aortic valve calcification, or mitral valve calcification rate or degree in the entire cohort and in each group alone (P = NS for all). There was a negative correlation between 25-hydroxyvitamin D levels and age in the acute coronary syndrome group (r = −0.399, P = 0.012).

Conclusions
We did not find a significant relationship between plasma vitamin D levels and the rate or degree of calcification of either aortic/mitral/both valves in hospitalized patients with or without ischemic heart disease.
Ramlibacter pinisoli sp. nov., a novel bacterial species isolated from pine garden soil
Authors: Akter Shahina , N. A. M. Kihong , Lee Sun-Young , Moon Sung-Kwon , Choi Changsun , Balusamy Sri Renukadevi , Siddiqi Muhammad Zubair , Ashrafudoulla Md. , Rahman Md. Shahedur , Huq Md. Amdadul 
Published: September 2020

A Gram-stain-negative, aerobic, non-motile and rod- or coccoid-shaped novel bacterial strain, designated MAH-25T, was isolated from soil sampled in a pine garden. The colonies were observed to be light pink-coloured, smooth, spherical and 1–2 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-25T was found to be able to grow at 15–35 °C, at pH 5.0–8.0 and at 0–2.0 % NaCl. Cell growth occurred on Reasoner's 2A agar and nutrient agar. The strain was found to be positive in both oxidase and catalase tests. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus

Ramlibacter

and closely related to

Ramlibacter solisilvae

5-10T (98.0 % similarity),

Ramlibacter henchirensis

TMB834T (97.7 %),

Ramlibacter tataouinensis

TTB310T (97.6 %) and

Ramlibacter rhizophilus

YS3.2.7T (97.3 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-25T and the four closely related type strains were in the range of 78.8–81.3 % and 22.3–24.1 %, respectively. The novel strain MAH-25T has a draft genome size of 5 505 957 bp (11 contigs), annotated with 5210 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content was determined to be 70.3 mol%. The predominant isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were identified as C16 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of DNA–DNA hybridization, genotypic analysis, chemotaxonomic and physiological data, strain MAH-25T represents a novel species within the genus

Ramlibacter

, for which the name Ramlibacter pinisoli sp. nov. is proposed, with MAH-25T (=KACC 19839T=CGMCC1.13660T) as the type strain.
Use of causal claims in observational studies: a research on research study
Authors: Parra Camila Olarte , Bertizzolo Lorenzo , Schroter Sara , Dechartres Agnès , Goetghebeur Els 
Published: September 2020

AbstractObjectiveTo evaluate the consistency of causal statements in the abstracts of observational studies published in The BMJ.DesignResearch on research study.Data sourceAll cohort or longitudinal studies describing an exposure-outcome relationship published in The BMJ during 2018. We also had access to the submitted papers and reviewer reports.Main outcome measures:Proportion of published research papers with ‘inconsistent’ use of causal language in the abstract. Papers where language was consistently causal or non-causal were classified as ‘consistently causal’ or ‘consistently not causal’, respectively; those where causality may be inferred were classified as ‘suggests causal’. For the ‘inconsistent’ papers, we then compared the published and submitted version.ResultsOf 151 published research papers, 60 described eligible studies. Of these 60, we classified the causal language used as ‘consistently causal’ (13%), ‘suggests causal’ (35%), ‘inconsistent’ (20%) and ‘consistently not causal’(32%). The majority of the ‘Inconsistent’ papers (92%) were already inconsistent on submission. The inconsistencies found in both submitted and published versions was mainly due to mismatches between objectives and conclusions. One section might be carefully phrased in terms of association while the other presented causal language. When identifying only an association, some authors jumped to recommending acting on the findings as if motivated by the evidence presented.ConclusionFurther guidance is necessary for authors on what constitutes a causal statement and how to justify or discuss assumptions involved. Based on screening these abstracts, we provide a list of expressions beyond the obvious ‘cause’ word which may inspire a useful more comprehensive compendium on causal language.Strengths and limitations of this studyWe present examples of ambiguous causal statements in published abstracts of observational studies in a high impact journalWe focused on the abstract where clear messages are especially important, as many readers just read the abstract of a studyThe focus on the abstract may miss further discussion on the validity of underlying assumptions justifying causal inference in the setting studied.The prevalence and nature of the problems found is a call for better instruction on and consideration of causal language throughout the editorial process in clinical and epidemiological research.We provide a list of words and study elements that could point in the direction of causality or otherwise, which may inspire a more comprehensive compendium.
Craniofacial features of 3q29 deletion syndrome: application of next generation phenotyping technology
Authors: Mak Bryan , Russo Rossana Sanchez , Gambello Michael J. , Black Emily , Leslie Elizabeth , Murphy Melissa M. ,   The Emory 3q29 Project, Mulle Jennifer 
Published: September 2020

AbstractIntroduction3q29 deletion syndrome (3q29del) is a recurrent deletion syndrome associated with neuropsychiatric disorders and congenital anomalies. Dysmorphic facial features have been described but not systematically characterized. This study aims to detail the 3q29del craniofacial phenotype and use a machine learning approach to categorize individuals with 3q29del through analysis of 2D photos.MethodsDetailed dysmorphology exam and 2D facial photos were ascertained from 31 individuals with 3q29del. Photos were used to train the next generation phenotyping platform Face2Gene (FDNA, Inc, Boston, MA) to distinguish 3q29del cases from controls, using a proprietary algorithm. Area under the curve of receiver operating characteristic curves (AUC-ROC) were used to determine the capacity of Face2Gene to identify 3q29del cases against controls.ResultsIn this cohort, the most common observed craniofacial features were prominent forehead (48.4%), prominent nose tip (35.5%), and thin upper lip vermillion (25.8%). The FDNA technology showed an ability to distinguish cases from controls with an AUC-ROC value of 0.873 (p = 0.006).ConclusionThis study found a recognizable facial pattern in 3q29del, as observed by trained clinical geneticists and next generation phenotyping technology. These results expand the potential application of automated technology such as FDNA in identifying rare genetic syndromes, even when facial dysmorphology is subtle.
Clinical efficacy of external beam radiotherapy complementing incomplete transarterial chemoembolization for hepatocellular carcinoma
Authors: Park Sunmin , Yoon Won Sup , Jang Mi Hee , Rim Chai Hong 
Published: September 2020

AbstractPurposeExternal beam radiotherapy (EBRT) has been commonly applied as salvage or a combination locoregional modality after transarterial chemoembolization (TACE) for hepatocellular carcinomas (HCCs). This study reports oncologic outcomes and feasibility after application of the two modalities in our center.MethodsForty consecutive patients who underwent EBRT due to incomplete responses of TACE were evaluated. Fourteen patients (35.0%) received stereotactic body radiotherapy (SBRT) and the remaining patients received conventionally fractionated radiotherapy (RT). A majority of patients who underwent SBRT received doses of 27 to 48 Gy in 3–4 fractions (median *EQD2: 57.0 Gy). Conventionally fractionated RT was performed with a median EQD2 of 47.8 Gy.ResultsThe median follow-up duration was 14.4 months (range: 2.6–83.0 months). A majority (77.5%) of patients were regarded as having Child-Pugh grade A. The median tumor size was 3.4 cm (range: 0.8–20.1 cm). Ten patients (25.0%) had thrombosis at a main portal branch. The 1- and 2-year overall survival (OS) and progression-free survival (PFS) rates were 82.2% and 42.1% and 55.8% and 32.1%, respectively. The local control rates were 89.1% and 89.1% at 1 and 2 years, respectively. The albumin level was a significant factor affecting OS (p = 0.002), and the BCLC stage significantly affected PFS (p = 0.001). Intrahepatic, out-of-field recurrence was the main cause of disease progression (60.0%), and distant metastasis developed in 12 patients (30.0%) during follow-up. Non-classic radiation-induced liver disease was seen in five (12.5%) patients, and two (5%) patients experienced grade ≥ 3 hepatic toxicities.ConclusionsEBRT after incomplete TACE was feasible and yielded favorable oncologic outcomes. However, disease progression related to intrahepatic failure remained a hindrance.*EQD2: Equivalent dose in 2 Gy per fraction radiotherapy
Exponential distribution of large excess death rates in Europe during the COVID-19 outbreak in the spring of 2020
Authors: Martín-Olalla José María 
Published: September 2020

Excess death rates E during the spring of 2020 are computed in N = 540 level 3 European territorial units for statistics —NUTS3 in Belgium (40), France (96), Italy (110), Netherlands (44), Spain (50), Sweden(21) and United Kingdom (179)— from 2020 provisional week deaths, the population numbers for 2020, and observations in previous years (reference or baseline), all of them obtained from Eurostat web page.Excess death rates are classified in three tiers. Largest 27 excess death rates (tier 1, E > 1721× 10−6) were distributed exponentially with empirical complementary cumulative distribution function (empirical survival function) S following S ∝ 2−E/ε with ε1 = 958(42) × 10−6. Tier 2 (the next 52 largest excess death rates, E < 1142 × 10−6 also distributed exponentially with ε2 = 379.5(89) ×10−6. Tier 3 (smallest 460 excess death rates) were distributed normally.The results suggests that when, within some regions, the outbreak is above a threshold, interaction with neighbouring region become less relevant and the outcomes —excess death rates— become exponentially distributed as it happens with independent events.
Role of treatments for diabetes and hyperlipidaemia in risk and mortality of primary and secondary brain tumours
Authors: Robinson Jamie W , Martin Richard M , Ozawa Mio , Elwenspoek Martha M C , Redaniel Maria Theresa , Kurian Kathreena M , Ben-Shlomo Yoav 
Published: September 2020

AbstractBackgroundIn vivo and observational studies suggest anti-hyperlipidaemic and -diabetic medications (fibrates and glitazones respectively) may have a role in primary prevention and progression of brain tumours by targeting PPAR-α and -γ, respectively.MethodsWe conducted a case-control and clinical cohort study within the UK Clinical Practice Research Datalink. We identified adults (aged 18 years+) with primary or secondary brain tumours diagnosed between 2000-2016 prescribed either fibrates or glitazones and identified four controls based on age, sex and drug exposure duration. Multivariable logistic regression analysis estimated an association between drug exposure and brain tumour status. Cox’s survival models were used to look at risk of mortality.Results1,916 cases were prescribed a fibrate and 445 cases a glitazone. Our analyses showed little evidence of an association between fibrates and either risk or mortality of brain tumours (adjusted odds ratio for ever exposed PPAR-α 0.98, 95% CI: 0.77, 1.23; adjusted hazard ratio for ever exposed 0.91; 95% CI: 0.76, 1.09). We observed a reduced risk with a per-year increase in exposure duration for glitazones (adjusted odds ratio 0.88, 95% CI: 0.81, 0.96, P=0.002) but no major mortality benefit (adjusted hazard ratio 0.99, 95% CI: 0.80, 1.23).ConclusionsOur results suggest longer duration exposure to glitazones is associated with a reduced risk of primary and secondary brain tumours but no large effect on mortality. We failed to find any strong evidence of a protective effect on risk or mortality for fibrate exposure. Further studies are required for replication and to provide more precise effect estimates.Key PointsRepurposing existing drugs that target PPAR-α and -γ receptors may have a role in prevention and progression of brain tumours.We observed a reduced risk between duration of glitazones and both primary and secondary brain tumours but no major reduction on mortalityWe observed no major reduction of risk or mortality with fibratesFuture studies need to be undertaken to ensure replication and obtain more precise estimatesImportance of StudyThe incidence of brain tumours appears to be increasing with a growing impact on years of life lost. Therapeutic options are limited, either for primary prevention or to prevent mortality of disease once developed. We investigated whether two commonly prescribed families of drugs (fibrates and glitazones) could offer potential drug-repurposing options in reducing brain tumour incidence or progression as informed by previous in vivo and observational studies. Our analyses suggest that glitazones are associated with a decreased brain tumour risk. These results can help guide future research into drug re-repurposing for brain tumour treatment.
Efficacy and Safety of Guduchi Ghan Vati in the Management of Asymptomatic COVID-19 Infection: An Open Label Feasibility Study
Authors: Kumar Abhimanyu , Prasad Govind , Srivastav Sanjay , Gautam Vinod Kumar , Sharma Neha 
Published: September 2020

AbstractBackgroundGuduchi Ghan Vati (aqueous extract of Tinospora cordifolia) is an essential herbal plant in Indian traditional medicine (Ayurveda) that is well documented as an immunomodulator and antimicrobial agent. A recent in silico study found the therapeutic efficacy of Guduchi against SARS-CoV-2. Based on available evidence, we conducted a feasibility study of the safety and efficacy of Guduchi Ghan Vati in asymptomatic patients with covid-19.Patients and methodsAn open label, feasibility trial was conducted on 46 patients in the hospital setting. A single-arm study with no control group and blinding was executed in Jodhpur, Rajasthan, India. All patients orally received 2 tablets (1000 mg) twice daily for 2 weeks. Clinical parameters were collected at baseline, day 3, day 7 and day 14. Patients were continuously monitored for side effects and adverse reactions during the study period..ResultsOut of 46 asymptomatic patients included in the study, 40 completed the 14-day follow-up period. None developed any Covid-19 symptoms after admission to the hospital. On day 3 post-treatment, viral clearance was reported in 16 (32.5%) patients. By the end of D-7, 38 (95%) patients had viral load disappearance. Follow-up at D-14 showed that all participants tested negative.ConclusionIn adult patients with asymptomatic Covid-19, Gudhuchi Ghan Vati could be effective. Randomized controlled trials with larger sample sizes in patients with Covid-19 are urgently needed to confirm the definite benefit with Ayurveda.
Validation and clinical evaluation of a SARS-CoV-2 Surrogate Virus Neutralization Test (sVNT)
Authors: Meyer Benjamin , Reimerink Johan , Torriani Giulia , Brouwer Fion , Godeke Gert-Jan , Yerly Sabine , Hoogerwerf Marieke , Vuilleumier Nicolas , Kaiser Laurent , Eckerle Isabella , Reusken Chantal 
Published: September 2020

AbstractTo understand SARS-CoV-2 immunity after natural infection or vaccination, functional assays such as virus neutralizing assays are needed. So far, assays to determine SARS-CoV-2 neutralizing antibodies rely on cell-culture based infection assays either using wild type SARS-CoV-2 or pseudotyped viruses. Such assays are labour-intensive, require appropriate biosafety facilities and are difficult to standardize.Recently, a new surrogate virus neutralisation assay (sVNT) was described that uses the principle of an ELISA to measure the neutralization capacity of anti-SARS-CoV-2 antibodies directed against the receptor binding domain.Here, we performed an independent evaluation of the robustness, specificity and sensitivity on an extensive panel of sera from 269 PCR-confirmed COVID-19 cases and 259 unmatched samples collected before 2020 and compared it to cell-based neutralization assays. We found a high specificity of 99.2 (95%CI: 96.9-99.9) and overall sensitivity of 80.3 (95%CI: 74.9-84.8) for the sVNT. Clinical sensitivity increased between early (< 14 days post symptom onset or post diagnosis, dpos/dpd) and late sera (>14 dpos/dpd) from 75.0 (64.7-83.2) to 83.1 (76.5-88.1). Also, higher severity was associated with an increase in clinical sensitivity. Upon comparison with cell-based neutralisation assays we determined an analytical sensitivity of 74.3 (56.4-86.9) and 98.2 (89.4-99.9) for titres ≥10 to < 40 and ≥40 to < 160, respectively. Only samples with a titre ≥160 were always positive in the sVNT.In conclusion, the sVNT can be used as an additional assay to determine the immune status of COVID-19 infected of vaccinated individuals but its value needs to be assessed for the specific context of use.
Effect of calcium intake on iron absorption and hematologic status: A systematic review and dose-response meta-analysis of randomized trials and case-cross-over studies
Authors: Abioye Ajibola Ibraheem , Okuneye Taofik A , Odesanya Abdul-Majeed O , Adisa Olufunmilola , Abioye Asanat I , Soipe Ayorinde I , Ismail Kamal A , Yang JaeWon F , Fasehun Luther-King , Omotayo Moshood O. 
Published: September 2020

AbstractBackgroundThe interaction between dietary (and supplementary) divalent ions has been a long- standing issue in human nutrition research. Developing optimal calcium and iron supplementation recommendation needs detailed knowledge of the potential trade-offs between: a) the clinical effects of concurrent intake on iron absorption and hematological indices, and b) the potentially negative effects of separated ingestion on adherence to either or both iron and calcium supplements. Human clinical studies have examined the effects of calcium intake on iron status, but there are no meta-analyses or recent reviews summarizing the findings.ObjectiveWe aimed to summarize the literature on the effect of calcium consumption from meals and supplements on iron indices in humans, and quantify the pooled effects.DesignPeer-reviewed randomized and case-cross-over studies were included in this review.ResultThe negative effect of calcium intake was statistically significant in short-term iron absorption studies but the effect magnitude was low (weighted mean difference (WMD) = -5.57%, (95% CI: -7.09, -4.04)). The effect of calcium on iron status was mixed. There was a quadratic dose-response relationship between calcium intake and serum ferritin concentration. Higher daily calcium intake was associated with a modest reduction in serum ferritin concentration. There was, however, no reduction in hemoglobin concentration (WMD = 1.22g/L, 95% CI: 0.37, 2.07).ConclusionThe existing body of studies is insufficient to make recommendations with high confidence due to heterogeneity in design, limitations of ferritin as an iron biomarker and lack of intake studies in pregnant women. Prescribing separation of prenatal calcium and iron supplements in free living individuals is unlikely to affect the anemia burden. There is a need for effectiveness trials comparing the effects of prescribing separated intake to concurrent intake, with functional end-points as primary outcomes, and adherence to each supplement as intermediate outcomes.
An Interpretable Deep Learning Model for Early Prediction of Sepsis in the Emergency Department
Authors: Zhang Dongdong , Yin Changchang , Hunold Katherine M. , Jiang Xiaoqian , Caterino Jeffrey M. , Zhang Ping 
Published: September 2020

AbstractBackgroundSepsis, a life-threatening illness caused by the body’s response to an infection, is the leading cause of death worldwide and has become a global epidemiological burden. Early prediction of sepsis increases the likelihood of survival for septic patients.MethodsThe 2019 DII National Data Science Challenge enabled participating teams to develop models for early prediction of sepsis onset with de-identified electronic health records of over 100,000 unique patients. Our task is to predict sepsis onset 4 hours before its diagnosis using basic administrative and demographics, time-series vital, lab, nutrition as features. An LSTM-based model with event embedding and time encoding is proposed to model time-series prediction. We utilized the attention mechanism and global max pooling techniques to enable interpretation for the proposed deep learning model.ResultsWe evaluated the performance of the proposed model on 2 use cases of sepsis onset prediction which achieved AUC scores of 0.940 and 0.845, respectively. Our team, BuckeyeAI achieved an average AUC of 0.892 and the official rank is #2 out of 30 participants.ConclusionsOur model outperformed collapsed models (i.e., logistic regression, random forest, and LightGBM). The proposed LSTM-based model handles irregular time intervals by incorporating time encoding and is interpretable thanks to the attention mechanism and global max pooling techniques.AvailabilityThe code for this paper is available at: https://github.com/yinchangchang/DII-Challenge.