bluuebunny/crossref_metadata_2025_split huggingface dataset:
MloDisDB: a manually curated database of the relations between membraneless organelles and diseases
Authors: Hou Chao , Xie Haotai , Fu Yang , Ma Yao , Li Tingting 
Published: September 2020

AbstractCells are compartmentalized by numerous membrane-bounded organelles and membraneless organelles (MLOs) to ensure temporal and spatial regulation of various biological processes. A number of MLOs, such as nucleoli, nuclear speckles and stress granules, exist as liquid droplets within the cells and arise from the condensation of proteins and RNAs via liquid–liquid phase separation (LLPS). By concentrating certain proteins and RNAs, MLOs accelerate biochemical reactions and protect cells during stress, and dysfunction of MLOs is associated with various pathological processes. With the development in this field, more and more relations between the MLOs and diseases have been described; however, these results have not been made available in a centralized resource. Herein, we build MloDisDB, a database which aims to gather the relations between MLOs and diseases from dispersed literature. In addition, the relations between LLPS and diseases were included as well. Currently, MloDisDB contains 771 curated entries from 607 publications; each entry in MloDisDB contains detailed information about the MLO, the disease and the functional factor in the relation. Furthermore, an efficient and user-friendly interface for users to search, browse and download all entries was provided. MloDisDB is the first comprehensive database of the relations between MLOs and diseases so far, and the database is freely accessible at http://mlodis.phasep.pro/.
Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework
Authors: Wei Leyi , He Wenjia , Malik Adeel , Su Ran , Cui Lizhen , Manavalan Balachandran 
Published: September 2020

AbstractOrigins of replication sites (ORIs), which refers to the initiative locations of genomic DNA replication, play essential roles in DNA replication process. Detection of ORIs’ distribution in genome scale is one of key steps to in-depth understanding their regulation mechanisms. In this study, we presented a novel machine learning-based approach called Stack-ORI encompassing 10 cell-specific prediction models for identifying ORIs from four different eukaryotic species (Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana). For each cell-specific model, we employed 12 feature encoding schemes that cover nucleic acid composition, position-specific and physicochemical properties information. The optimal feature set was identified from each encoding individually and developed their respective baseline models using the eXtreme Gradient Boosting (XGBoost) classifier. Subsequently, the predicted scores of 12 baseline models are integrated as a novel feature vector to train XGBoost and develop the final model. Extensive experimental results show that Stack-ORI achieves significantly better performance as compared with their baseline models on both training and independent datasets. Interestingly, Stack-ORI consistently outperforms existing predictor in all cell-specific models, not only on training but also on independent test. Moreover, our novel approach provides necessary interpretations that help understanding model success by leveraging the powerful SHapley Additive exPlanation algorithm, thus underlining the most important feature encoding schemes significant for predicting cell-specific ORIs.
Serum Antibody Profile of a Patient With Coronavirus Disease 2019 Reinfection
Authors: To Kelvin Kai-Wang , Hung Ivan Fan-Ngai , Chan Kwok-Hung , Yuan Shuofeng , To Wing-Kin , Tsang Dominic Ngai-Chong , Cheng Vincent Chi-Chung , Chen Zhiwei , Kok Kin-Hang , Yuen Kwok-Yung 
Published: September 2020

Abstract
We recently reported a patient with coronavirus disease 2019 reinfection. Here, we show that serum neutralizing antibodies could be detected during the first episode but not at the presentation of the second episode. During reinfection, neutralizing antibodies and high avidity immunoglobulin G were found within 8 days after hospitalization, whereas immunoglobulin M response was absent.
Metabolic Response in Patients With Post-treatment Lyme Disease Symptoms/Syndrome
Authors: Fitzgerald Bryna L , Graham Barbara , Delorey Mark J , Pegalajar-Jurado Adoracion , Islam M Nurul , Wormser Gary P , Aucott John N , Rebman Alison W , Soloski Mark J , Belisle John T , Molins Claudia R 
Published: September 2020

Abstract

Background
Post-treatment Lyme disease symptoms/syndrome (PTLDS) occurs in approximately 10% of patients with Lyme disease following antibiotic treatment. Biomarkers or specific clinical symptoms to identify patients with PTLDS do not currently exist and the PTLDS classification is based on the report of persistent, subjective symptoms for ≥6 months following antibiotic treatment for Lyme disease.

Methods
Untargeted liquid chromatography–mass spectrometry metabolomics was used to determine longitudinal metabolic responses and biosignatures in PTLDS and clinically cured non-PTLDS Lyme patients. Evaluation of biosignatures included (1) defining altered classes of metabolites, (2) elastic net regularization to define metabolites that most strongly defined PTLDS and non-PTLDS patients at different time points, (3) changes in the longitudinal abundance of metabolites, and (4) linear discriminant analysis to evaluate robustness in a second patient cohort.

Results
This study determined that observable metabolic differences exist between PTLDS and non-PTLDS patients at multiple time points. The metabolites with differential abundance included those from glycerophospholipid, bile acid, and acylcarnitine metabolism. Distinct longitudinal patterns of metabolite abundance indicated a greater metabolic variability in PTLDS versus non-PTLDS patients. Small numbers of metabolites (6 to 40) could be used to define PTLDS versus non-PTLDS patients at defined time points, and the findings were validated in a second cohort of PTLDS and non-PTLDS patients.

Conclusions
These data provide evidence that an objective metabolite-based measurement can distinguish patients with PTLDS and help understand the underlying biochemistry of PTLDS.
Durability of Response to Fecal Microbiota Transplantation After Exposure to Risk Factors for Recurrence in Patients With Clostridioides difficile Infection
Authors: Saha Srishti , Mara Kristin , Pardi Darrell S , Khanna Sahil 
Published: September 2020

Abstract

Background
Fecal microbiota transplantation (FMT) is highly effective for preventing recurrent Clostridioides difficile infection (CDI). Durability (no recurrence despite additional risk factor exposure) of FMT protection is largely unknown. We studied the durability of FMT in patients with recurrent CDI.

Methods
We conducted a retrospective study of adults undergoing FMT for recurrent CDI. Data collected included demographics, CDI risk factors (comorbidities, healthcare exposure, non-CDI antibiotic use, acid suppressant medications), and future CDI episodes. Durable response to FMT was defined as lack of CDI episodes within 1 year post-FMT despite risk factor exposure.

Results
Overall, 460 patients were included (median age, 57 years [18–94]; 65.2% female). Comorbidities included chronic liver disease, 12.8% (n = 59); cancer, 11.7% (n = 54); chronic kidney disease, 3.9% (n = 18); and inflammatory bowel disease, 21.9% (n = 101). Overall, 31.3% (n = 144) received antibiotics, 21.7% (n = 100) received acid suppressants, and 76.8% (n = 350) had healthcare exposure after FMT. Of 374 patients with risk factor exposure, 78.1% (95% confidence interval [CI], 72.7%–84.0%) had durable response to FMT at 1 year. On multivariable analysis, antibiotic use was independently associated with decreased durability of FMT (hazard ratio, 0.27; 95% CI, .15–.49; P &lt; .001).

Conclusions
The majority of patients had a durable response to FMT despite exposure to CDI risk factors. Antibiotic exposure after FMT independently predicted loss of durability of FMT. Larger studies are needed to define predictors of durable response in patients with and without exposure to antibiotics.
Early Impact of Social Distancing in Response to Coronavirus Disease 2019 on Hospitalizations for Acute Bronchiolitis in Infants in Brazil
Authors: Friedrich Frederico , Ongaratto Renata , Scotta Marcelo C , Veras Tiago N , Stein Renato T , Lumertz Magali Santos , Jones Marcus Herbert , Comaru Talitha , Pinto Leonardo Araújo 
Published: September 2020

Abstract

Background
Interventions to tackle the coronavirus disease 2019 (COVID-19) pandemic may affect the burden of other respiratory diseases. Considering the repercussions of these unique social experiences to infant health, this study aims to assess the early impact of social distancing due to the COVID-19 pandemic in hospital admissions for acute bronchiolitis.

Methods
Data from hospitalizations of acute bronchiolitis in infants &lt;1 year of age were obtained from the Department of Informatics of the Brazilian Public Health database for the period between 2016 and 2020. These data were also analyzed by macroregions of Brazil (North, Northeast, Southeast, South, and Midwest). To evaluate the effect of social distancing strategy on the incidence of acute bronchiolitis, the absolute and relative reductions were calculated by analyzing the yearly subsets of 2016 vs 2020, 2017 vs 2020, 2018 vs 2020, and 2019 vs 2020.

Results
There was a significant reduction in all comparisons, ranging from −78% (incidence rate ratio [IRR], 0.22 [95% confidence interval {CI}, .20–.24]) in 2016 vs 2020 to −85% (IRR, 0.15 [95% CI, .13–.16]) in 2019 vs 2020, for the data from Brazil. For analyses by macroregions, the reduction varied from −58% (IRR, 0.41 [95% CI, .37–.45]) in the Midwest in 2016 vs 2020 to −93% (IRR, 0.07 [95% CI, .06–.08]) in the South in 2019 vs 2020.

Conclusions
There was a significant reduction in hospitalization for acute bronchiolitis in children &lt;1 year old in Brazil, on the order of &gt;70% for most analysis. Our data suggest an important impact of social distancing on reducing the transmission of viruses related to acute bronchiolitis. Such knowledge may guide strategies for prevention of viral spread.
Predictors at Admission of Mechanical Ventilation and Death in an Observational Cohort of Adults Hospitalized With Coronavirus Disease 2019
Authors: Jackson Brendan R , Gold Jeremy A W , Natarajan Pavithra , Rossow John , Neblett Fanfair Robyn , da Silva Juliana , Wong Karen K , Browning Sean D , Bamrah Morris Sapna , Rogers-Brown Jessica , Hernandez-Romieu Alfonso C , Szablewski Christine M , Oosmanally Nadine , Tobin-D’Angelo Melissa , Drenzek Cherie , Murphy David J , Hollberg Julie , Blum James M , Jansen Robert , Wright David W , Sewell William M , Owens Jack D , Lefkove Benjamin , Brown Frank W , Burton Deron C , Uyeki Timothy M , Bialek Stephanie R , Patel Priti R , Bruce Beau B 
Published: September 2020

Abstract

Background
Coronavirus disease (COVID-19) can cause severe illness and death. Predictors of poor outcome collected on hospital admission may inform clinical and public health decisions.

Methods
We conducted a retrospective observational cohort investigation of 297 adults admitted to 8 academic and community hospitals in Georgia, United States, during March 2020. Using standardized medical record abstraction, we collected data on predictors including admission demographics, underlying medical conditions, outpatient antihypertensive medications, recorded symptoms, vital signs, radiographic findings, and laboratory values. We used random forest models to calculate adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for predictors of invasive mechanical ventilation (IMV) and death.

Results
Compared with age &lt;45 years, ages 65–74 years and ≥75 years were predictors of IMV (aORs, 3.12 [95% CI, 1.47–6.60] and 2.79 [95% CI, 1.23–6.33], respectively) and the strongest predictors for death (aORs, 12.92 [95% CI, 3.26–51.25] and 18.06 [95% CI, 4.43–73.63], respectively). Comorbidities associated with death (aORs, 2.4–3.8; P &lt; .05) included end-stage renal disease, coronary artery disease, and neurologic disorders, but not pulmonary disease, immunocompromise, or hypertension. Prehospital use vs nonuse of angiotensin receptor blockers (aOR, 2.02 [95% CI, 1.03–3.96]) and dihydropyridine calcium channel blockers (aOR, 1.91 [95% CI, 1.03–3.55]) were associated with death.

Conclusions
After adjustment for patient and clinical characteristics, older age was the strongest predictor of death, exceeding comorbidities, abnormal vital signs, and laboratory test abnormalities. That coronary artery disease, but not chronic lung disease, was associated with death among hospitalized patients warrants further investigation, as do associations between certain antihypertensive medications and death.
Causal Relationship between Plasma Adiponectin and Body Mass Index: One- and Two-Sample Bidirectional Mendelian Randomization Analyses in 460 397 Individuals
Authors: Nielsen Maria Booth , Çolak Yunus , Benn Marianne , Nordestgaard Børge Grønne 
Published: September 2020

AbstractBackgroundAdiponectin is a protein hormone produced by adipocytes that may play an important role in obesity. However, the causal interrelation between plasma adiponectin and body mass index (BMI) is still uncertain. We tested the hypotheses that (a) plasma adiponectin and BMI are inversely associated observationally, (b) genetically high BMI is associated with lower plasma adiponectin, and (c) genetically high plasma adiponectin is associated with lower BMI.MethodsInformation on 108 896 individuals from the Copenhagen General Population Study was used in observational and bidirectional one-sample Mendelian randomization analyses, using 5 genetic variants for BMI and 3 for adiponectin. For independent confirmation, information on 322 154 individuals from the GIANT consortium, and 29 347 individuals from the ADIPOGen consortium was used in bidirectional two-sample Mendelian randomization analysis, using 68 genetic variants for BMI and 14 for adiponectin.ResultsIn observational analyses, a 1 kg/m2 increase in BMI was associated with −0.44 µg/mL (95% confidence interval: −0.46, −0.42) in plasma adiponectin, whereas a 1 µg/mL increase in plasma adiponectin was associated with −0.11 kg/m2 (−0.12, −0.11) in BMI. In causal genetic analyses, no associations were observed between BMI and plasma adiponectin and vice versa. In one-sample Mendelian randomization analyses, a 1 kg/m2 genetically determined increase in BMI was associated with −0.13 µg/mL (−0.53, 0.28) in plasma adiponectin, whereas a 1 µg/mL genetically determined increase in plasma adiponectin was associated with 0.01 kg/m2 (−0.05, 0.07) in BMI. Corresponding estimates in the two-sample Mendelian randomization analyses were 0.03 µg/mL (−0.02, 0.07) and 0.03 kg/m2(−0.02, 0.07), respectively.ConclusionsObservationally, plasma adiponectin and BMI are inversely associated. In contrast, genetically high plasma adiponectin is unlikely to influence BMI, and genetically high BMI is unlikely to influence plasma adiponectin.
Evaluation of postoperative outcomes of valve reoperation: a retrospective study
Authors: Tatsuishi Wataru , Kumamaru Hiraku , Nakano Kiyoharu , Miyata Hiroaki , Motomura Noboru 
Published: September 2020

Abstract

OBJECTIVES
The aim of this study was to compare the incidence of operative death and postoperative complications between primary and reoperation valve surgeries and to identify independent risk factors for these events among valve-reoperation patients.

METHODS
Between 2013 and 2015, 54 269 patients who underwent valve surgery were retrospectively analyzed using the Japan Cardiovascular Surgery Database. They were divided into the primary (group P; n = 49 833) and reoperation (group R; n = 4436) surgery groups. Among the reoperation patients, we conducted multivariable logistic regression analyses to identify risk factors for the incidences of operative mortality and postoperative complications. Then, we also conducted propensity score matched analyses to compare the incidences of these 2 outcomes for primary versus reoperation procedures separately for patients with and without infective endocarditis (IE).

RESULTS
Incidences of postoperative mortality (4.6% vs 9.1%; P &lt; 0.001) and any complications (36.6% vs 41.4%; P &lt; 0.001) were higher in the reoperation group. For patients undergoing reoperation, strong risk factors for operative mortality included urgency status, ejection fraction &lt;30%, IE, dialysis, chronic kidney disease, New York Heart Association class 3/4, concomitant coronary artery bypass grafting and aorta procedure, tricuspid valve surgery only, multivalve surgery and age. In the propensity score matched cohort, the relative odds of operative mortality were 1.53 (95% confidence interval: 1.26–1.86, P &lt; 0.001) among patients with IE and were 1.58 (95% confidence interval: 1.18–2.13, P &lt; 0.002) among those without.

CONCLUSIONS
Outcomes for reoperation were significantly worse than those for primary surgery. At the primary operation, the risk of reoperation should be considered and when considering the indications for reoperation, the preoperative state, surgical timing and intervention method should be considered.
Factors related to maxillary expander loss due to anchoring deciduous molars exfoliation during treatment in the mixed dentition phase
Authors: Quinzi Vincenzo , Federici Canova Fabio , Rizzo Fiorella Alessandra , Marzo Giuseppe , Rosa Marco , Primozic Jasmina 
Published: September 2020

Summary

Objectives
The aim was to identify factors associated with maxillary expander loss due to anchoring deciduous molars exfoliation and assess the diagnostic accuracy of the upper second premolar cusp position as a prognostic factor for the exfoliation of its corresponding deciduous molar.

Materials/methods
Ninety-two subjects aged 8.4 ± 1.1 years, treated with a Haas or hyrax expander, and using the same expansion protocol and deciduous teeth as anchorage were included. The position of the upper second premolar cusp, according to the half pulp chamber (HPC) line of the ipsilateral upper first permanent molar, was assessed on pre-treatment panoramic radiographs.

Results
A significant association between anchoring deciduous molar exfoliation and the position of the upper second premolar cusp according to the HPC line (P = 0.002; odds ratio = 5.7) was seen, while there was no association with gender, age, treatment duration, and type of expander. The median survival time for an anchoring deciduous molar, when the underlying premolar cusp was touching/crossing the HPC line, was 13.0 (11.7; 14.2) months. The upper second premolar cusp position to the HPC line showed high accuracy (at least 76.11 per cent) and substantial repeatability (at least 0.7) as a prognostic factor for the corresponding second deciduous molar exfoliation.

Limitations
Applicability in the mixed dentition phase with fully erupted upper first permanent molars.

Conclusions
The probability of a second deciduous molar to be successfully used as maxillary expander anchorage for at least 16 months is above 94 per cent; when at baseline, the corresponding premolar cusp is apical to the HPC line.
Newly introducedCardiniumendosymbiont reduces microbial diversity in the rice brown planthopperNilaparvata lugens
Authors: Li Tong-Pu , Zha Si-Si , Zhou Chun-Ying , Gong Jun-Tao , Zhu Yu-Xi , Zhang Xu , Xi Zhiyong , Hong Xiao-Yue 
Published: September 2020

ABSTRACTSymbiotic microorganisms in invertebrates play vital roles in host ecology and evolution. Cardinium, a common intracellular symbiont, is transinfected into the important agricultural pest Nilaparvata lugens (rice brown planthopper) to regulate its reproduction, but how this impacts its microbial community is unknown. Here, we characterized the bacterial microbiota from N. lugens, with or without Cardinium, at different developmental stages and in various adult tissues using 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing. Upon infection with Cardinium, we found that microbial diversity in the different developmental stages of N. lugens (especially females), and in female midguts and male testes, was lower than that in the uninfected control. There was a negative correlation between Cardinium and most related genera and between Bacteroidetes and Proteobacteria. Although the microbial structure varied during Cardinium infection, Acinetobacter spp. were a core microbiome genus. The Cardinium infection enhanced the relative density of midgut-associated Acinetobacter spp., with both bacteria exhibiting tissue-specific tropism. In addition, this infection caused the changes of main microbial functions in N. lugens. These results offer insights into the effects of alien (i.e. newly introduced from other organism) Cardinium infection on N. lugens-associated microbiotas, aiding in the development of transinfected endosymbionts for pest control.
Conceptualizing Food Insecurity Among Older Adults: Development of a Summary Indicator in the National Health and Aging Trends Study
Authors: Tucher Emma L , Keeney Tamra , Cohen Alicia J , Thomas Kali S 
Published: September 2020

Abstract

Objectives
Measurement of food insecurity in older adults is focused on financial barriers to food access. Given that older adults are particularly susceptible to additional access-related barriers including functional limitations and lack of social support, the objective of this study was to construct a summary indicator of food insecurity incorporating these domains.

Methods
We used nationally representative survey data from Round 5 of the National Health and Aging Trends Study (NHATS; n = 7,070). We constructed a summary indicator of food insecurity using factors within the following three domains: functional, social support, and financial limitations. First, we identified the prevalence of food insecurity among the sample as defined by the new summary indicator. Then, we estimated unadjusted and adjusted logistic regression models to assess the association between the expanded measure of food insecurity and biopsychosocial factors.

Results
In 2015, 4.3% (95% confidence interval [CI] 3.75–4.94) of community-dwelling older adults, approximately 1,673,775 million people, were characterized as having food insecurity. Multivariable-adjusted regression models identified that being homebound (odds ratio [OR] 3.49, 95% CI 2.03, 6.00), frail (OR 9.50, 95% CI 4.92–18.37), and experiencing community disability (OR 5.19, 95% CI 3.90–6.90) was associated with food insecurity.

Discussion
Food insecurity among older adults is broader than lacking adequate financial resources to obtain food; it is also associated with social and functional limitations. A more comprehensive conceptualization will aid future study on the impact of food insecurity on health status, utilization, and outcomes to inform senior nutrition program targeting and services.