bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Barcoding Reveals Cryptic Diversity in the Underestimated Genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the Northeastern Qinghai-Tibet Plateau
Authors: wang tai , Zhang Yanping , Yang Zhuoyu , Liu Zhe , Du Yanyan 
Published: November 2020

Abstract
Background: The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results: After careful identification and comparison of the morphology and DNA barcoding of 1,630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.Conclusions: The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
Age trajectories of disability in instrumental activities of daily living and disability-free life expectancy among middle-aged and older adults in Taiwan: an 11-year longitudinal study
Authors: Liao Wen-Ling , Chang Yu-Hung 
Published: November 2020

Abstract
Objectives: This study aims to identify the age trajectories of disability in instrumental activities of daily life (IADLs) over 11 years and their correlates, and to estimate disability-free life expectancy for identified trajectory groups in middle-aged and older adults.Methods: We included 3,118 participants aged 50 and over without IADL limitations at baseline from the Taiwan Longitudinal Study in Aging, followed across 1996-2007. We used group-based trajectory models to identify age trajectories of IADL disability, and multiple logistic regressions to examine their correlates. Sullivan method was used to compute IADL disability-free life expectancy for trajectory groups at different ages.Results: We identified two trajectories groups: 67.7% of participants classified as the late-onset group and 32.3% as the early-onset group. Female (adjusted odds ratio [aOR]: 1.93, 95% confidence interval [95% CI]: 1.54, 2.41), not being employed (aOR: 1.30, 95% CI: 1,08, 1,56), poor/fair self-rated health (aOR: 1.31, 95% CI:1.09, 1.58), hypertension (aOR: 1.32, 95% CI: 1.07, 1.63) , diabetes mellitus (aOR: 2.29, 95% CI: 1.72, 3.07), arthritis (aOR: 1.42, 95% CI: 1.11, 1.81), stroke (aOR: 2.21, 95% CI: 1.04, 4.70), and one-point increase in a 10-item depression scale (aOR: 1.04, 95% CI: 1.02, 1.06) were associated with early-onset of disability, whereas higher education (aOR: 0.59, 95% CI: 0.42, 0.81), regular exercise (aOR: 0.76, 95% CI: 0.62, 0.93), and participating voluntary or club activities (aOR: 0.78, 95% CI: 0.65, 0.93) related to the late-onset. IADL disability-free life expectancies at 65 years old in the late-onset group were 15.6 years for women and 14.4 for men, respectively, comprising 56.6% and 64.2% of their remaining life, whereas those of the early-onset group were 4.8 and 4.6 years for women and men respectively, comprising 22.5% and 27.2% of remaining life.Conclusions: Early-onset of IADLs disability may correlate to chronic conditions, and engagement in employment, exercise, and social participation were associated with a reduced risk of early disability in IADLs.
Comparison of oral glucose tolerance test and HbA1c in detection of disorders of glucose metabolism in patients with acute stroke
Authors: Matz Karl , Tuomilehto Jaakko , Teuschl Yvonne , Dachenhausen Alexandra , Brainin Michael 
Published: November 2020

Abstract
Background: Diabetes is an increasingly important risk factor for ischemic stroke and worsens stroke prognosis. Yet a large proportion of stroke patients who are eventually diabetic are undiagnosed. Therefore, it is important to have sensitive assessment of unrecognized hyperglycaemia in stroke patients. Design: Secondary outcome analysis of a randomized controlled trial focussing on parameters of glucose metabolism and detection of diabetes and prediabetes in patients with acute ischemic stroke (AIS). Methods: A total of 130 consecutively admitted patients with AIS without previously known type 2 diabetes mellitus (T2DM) were screened for diabetes or prediabetes as part of secondary outcome analysis of a randomized controlled trial that tested lifestyle intervention to prevent post-stroke cognitive decline. Patients had the oral glucose tolerance test (OGTT) and glycated hemoglobin (HbA1c) measurements in the second week after stroke onset and after one year. The detection rates of diabetes and prediabetes based on the OGTT or HbA1c values were compared.Results: By any of the applied tests at the second week after stroke onset 62 of 130 patients (48%) had prediabetes or T2DM. Seventy-five patients had results from both tests available, the OGTT and HbA1c; according to the OGTT 40 (53.3%) patients had normal glucose metabolism, 33 (44%) had prediabetes, two (2.7%) T2DM. In 50 (66.7%) patients the HbA1c results were normal, 24 (32%) in the prediabetic and one (1.3%) in the diabetic range. The detection rate for disorders of glucose metabolism was 10% higher (absolute difference; relative difference 29%) with the OGTT compared with HbA1c. After one year the detection rate for prediabetes or T2DM was 7% higher with the OGTT (26% relative difference).The study intervention led to a more favourable evolution of glycemic status after one year.Conclusion: The OGTT is a more sensitive screening tool than HbA1c for the detection of previously unrecognized glycemic disorders in patients with acute stroke with an at least a 25% relative difference in detection rate. Therefore, an OGTT should be performed in all patients with stroke with no history of diabetes.
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes
Authors: Meyer Corentin , Scalzitti Nicolas , Jeannin-Girardon Anne , Collet Pierre , Poch Olivier , Thompson Julie 
Published: November 2020

Abstract
Background: Recent advances in sequencing technologies have led to an explosion in the number of genomes available, but accurate genome annotation remains a major challenge. The prediction of protein-coding genes in eukaryotic genomes is especially problematic, due to their complex exon-intron structures. Even the best eukaryotic gene prediction algorithms can make serious errors that will significantly affect subsequent analyses. Results: We first investigated the prevalence of gene prediction errors in a large set of 176,478 proteins from ten primate proteomes available in public databases. Using the well-studied human proteins as a reference, a total of 82,305 potential errors were detected, including 44,001 deletions, 27,289 insertions and 11,015 mismatched segments where part of the correct protein sequence is replaced with an alternative erroneous sequence. We then focused on the mismatched sequence errors that cause particular problems for downstream applications. A detailed characterization allowed us to identify the potential causes for the gene misprediction in approximately half (5446) of these cases. As a proof-of-concept, we also developed a simple method which allowed us to propose improved sequences for 603 primate proteins. Conclusions: Gene prediction errors in primate proteomes affect up to 50% of the sequences. Major causes of errors include undetermined genome regions, genome sequencing or assembly issues, and limitations in the models used to represent gene exon-intron structures. Nevertheless, existing genome sequences can still be exploited to improve protein sequence quality. Perspectives of the work include the characterization of other types of gene prediction errors, as well as the development of a more comprehensive algorithm for protein sequence error correction.
Histone tail analysis reveals H3K36me2 and H4K16ac as epigenetic signatures of diffuse intrinsic pontine glioma
Authors: An Shejuan , Camarillo Jeannie , Huang Tina , Li Daphne , Morris Juliette , Zoltek Madeline , Qi Jin , Behbahani Mandana , Kelleher Neil , Nazarian Javad , Thomas Paul , Saratsis Amanda Muhs 
Published: November 2020

Abstract
Background: Diffuse intrinsic pontine glioma (DIPG) is an aggressive pediatric brainstem tumor. Most DIPGs harbor a histone H3 mutation, which alters histone post-translational modification (PTM) states and transcription. Here, we employed quantitative proteomic analysis to elucidate the impact of H3.3K27M mutation, as well as radiation and bromodomain inhibition (BRDi) with JQ1, on DIPG PTM profiles. Methods: We performed targeted mass spectroscopy on H3.3K27M mutant and wild-type tissues (n=12) and cell lines (n=7). Results: We found 29.2% and 26.4% of total H3.3K27 peptides were H3.3K27M in mutant DIPG tumor cell lines and tissue specimens, respectively. Significant differences in distinct PTMs were observed in H3.3K27M specimens, including at H3K27, H3K36, and H4K16 amino acid residues. In addition, H3.3K27me1 and H4K16ac were the most significantly distinct modifications in H3.3K27M mutant tumors relative to wild-type. Further, H3.3K36me2 was the most abundant modification co-occurring on the H3.3K27M mutant peptide in DIPG tissue, while H4K16ac was the most acetylated residue. Radiation treatment caused changes in PTM abundance in vitro , including increased H3K9me3. BRDi with JQ1 resulted in increased mono- and di-methylation of H3.1K27, H3.3K27, H3.3K36 and H4K20 in vitro . Conclusion: Taken together, our findings provide insight into the effects of the H3K27M mutation on Histone modification states and response to treatment, and suggest H3K36me2 and H4K16ac in DIPG may represent unique tumor epigenetic signatures for targeted therapy.
One-year Outcomes of Fixed-Dosing Aflibercept Therapy for pre treated and naive polypoidal choroidal vasculopathy patient
Authors: Choo Hun Gu , Lee Jin Hae , Oh Hyun Sub , You Yong Sung , Kim Soon Hyun , Kwon Oh Woong 
Published: November 2020

Abstract
Background: Polypoidal choroidal vasculopathy (PCV) is a type of age-related macular degeneration that can cause permanent vision loss. The purpose of this paper was to report the one-year outcomes of fixed-dosing aflibercept therapy for the treatment of PCV. Methods: This was a prospective, single-arm, interventional case series study of 25 PCV patients; 12 pre-treated and 13 treatment-naïve patients. The patients were treated and monitored for 12 months. Each patient was administered with an aflibercept (2.0 mg) injection every month for the first three months (the loading phase), and thereafter, once every two months. At every follow-up visit, best-corrected visual acuity (BCVA) test, fundus examination, and optical coherence tomography for measuring the central subfield macular thickness (CSMT) were performed. Fluorescein and indocyanine green angiography were conducted at baseline and at 4 and 12 months. Results: After 12 months of aflibercept therapy, the mean BCVA of the patients significantly improved from 65.48 letters at baseline to 69.91 letters (p=0.001), and the CSMT significantly decreased from 406.92 um at baseline to 276.12 um (p<0.001). Additionally, ten patients (40%) showed complete polyp regression. The treatment-naïve patients showed a statistically significant improvement in BCVA from 66.58 letters at baseline to 76.36 letters at 12 months, and a significant decrease in CSMT, from 462 to 243 um. In the pre-treated group, there was no change in BCVA (64.46 letters), and the decrease in CSMT from 356.08 to 303.69 um was not statistically significant. Conclusions: The fixed-dosing aflibercept regimen is effective for treating patients with PCV and is more effective in treatment-naïve patients than in pre-treated patients.
Corticosteroid use in COVID-19 patients: A systematic review and meta-analysis on clinical outcomes
Authors: Paassen Judith van , Vos Jeroen S. , Hoekstra Eva M. , Neumann Katinka M.I. , Boot Pauline C. , Arbous Sesmu M. 
Published: November 2020

Abstract
Background: In the current SARS-CoV-2 pandemic, there has been worldwide debate on the use of corticosteroids in COVID-19. In the recent RECOVERY trial, evaluating the effect of dexamethasone, a reduced 28-day mortality in patients requiring oxygen therapy or mechanical ventilation was shown. Their results have led to considering amendments in guidelines or actually already recommending corticosteroids in COVID-19. However, the effectiveness and safety of corticosteroids still remain uncertain, and reliable data to further shed light on the benefit and harm are needed. Objectives: The aim of this systematic review and meta-analysis was to evaluate the effectiveness and safety of corticosteroids in COVID-19. Methods: A systematic literature search of RCTS and observational studies on adult patients was performed across Medline/PubMed, Embase, and Web of Science from 1st of December 2019 until 1 st of October 2020, according to the PRISMA guidelines. Primary outcomes were short-term mortality and viral clearance (based on RT-PCR in respiratory specimens). Secondary outcomes were: need for mechanical ventilation, other oxygen therapy, length of hospital stay and secondary infections. Results: Forty-four studies were included, covering 20.197 patients. In twenty-two studies, the effect of corticosteroid use on mortality was quantified. The overall pooled estimate (observational studies and RCTs) showed a significant reduced mortality in the corticosteroid group (OR 0.72 (95%CI 0.57-0.87). Furthermore, viral clearance time ranged from 10-29 days in the corticosteroid group and from 8-24 days in the standard of care group. Fourteen studies reported a positive effect of corticosteroids on need for and duration of mechanical ventilation. A trend towards more infections and antibiotic use was present. Conclusions: Our findings from both observational studies and RCTs confirm a beneficial effect of corticosteroids on short-term mortality and a reduction of need for mechanical ventilation. And although data in the studies were too sparse to draw any firm conclusions, there might be a signal of delayed viral clearance and an increase in secondary infections.
Body mass index and cardiovascular outcomes in patients with acute coronary syndrome by diabetes status: the obesity paradox in a Korean national cohort study
Authors: Park Se-Jun , Ha Kyoung Hwa , Kim Dae Jung 
Published: November 2020

Abstract
Background: The “obesity paradox” has not been elucidated in the long-term outcomes of acute coronary syndrome (ACS). We investigated the association between obesity and cardiovascular (CV) outcomes in ACS patients with and without diabetes.Methods: We identified 6,978 patients with ACS aged 40–79 years from the Korean National Health Insurance Service-Health Screening Cohort between 2002 and 2015. Baseline body mass index (BMI) was categorized as underweight (<18.5 kg/m2), normal weight (18.5–22.9 kg/m2), overweight (23.0–24.9 kg/m2), obese class I (25.0–29.9 kg/m2), and obese class II (≥30.0 kg/m2). The primary outcome was major adverse CV events (MACE)—CV death, myocardial infarction (MI), and stroke. The secondary outcomes were the individual components of MACE, hospitalization for heart failure (HHF), and all-cause death. Results: After adjustment for confounding variables, compared to normal-weight patients without diabetes (reference group), obese class I patients with and without diabetes had a lower risk of MACE, but only significant in patients without diabetes (with diabetes: hazard ratio [HR] 0.95, 95% confidence interval [CI] 0.78–1.14; without diabetes: HR 0.78, 95% CI 0.62–0.97). Obese class II patient with diabetes had a higher risk of MACE with no statistical significance (HR 1.14, 95% CI 0.82–1.59). Underweight patients with and without diabetes had a higher risk of MACE, but only significant in patients with diabetes (with diabetes: HR 1.79, 95% CI 1.24–2.58; without diabetes: HR 1.23, 95% CI 0.77–1.97).Conclusion: In ACS patients, obesity had a protective effect on CV outcomes, especially in patients without diabetes.
Beyond standardized mortality ratios; some uses of smoothed age-specific mortality rates on small areas studies.
Authors: Perez-Panades Jordi , Botella-Rocamora Paloma , Martinez-Beneito Miguel Angel 
Published: November 2020

Abstract
Background: Most epidemiological risk indicators strongly depend on the age composition of populations, which makes the direct comparison of raw(unstandardized) indicators misleading because of the dierent age structures of the spatial units of study. Age-standardized rates (ASR) are a common solution for overcoming this confusing effect. The main drawback of ASRs is that they depend on age-specific rates which, when working with small areas, are often based on very few, or no, observed cases for most age groups. A similar effect occurs with life expectancy at birth and many more epidemiological indicators, which makes standardized mortality ratios (SMR) the omnipresent risk indicator for small areas epidemiologic studies.Methods: To deal with this issue, a multivariate smoothing model, the M-model, is proposed in order to t the age-specic probabilities of death (PoDs)for each spatial unit, which assumes dependence between closer age groups and spatial units. This age-space dependence structure enables information to be transferred between neighboring consecutive age groups and neighboring areas, at the same time, providing more reliable age-specific PoDs estimates.Results: Three case studies are presented to illustrate the wide range of applications that smoothed age specific PoDs have in practice . The first case study shows the application of the model to a geographical study of lung cancer mortality in women. This study illustrates the convenience of considering age-space interactions in geographical studies and to explore the different spatial risk patterns shown by the different age groups. Second, the model is also applied to the study of ischaemic heart disease mortality in women in two cities at the census tract level. Smoothed age-standardized rates are derived and compared for the census tracts of both cities, illustrating some advantages of this mortality indicator over traditional SMRs. In the latest case study, the model is applied to estimate smoothed life expectancy (LE), which is the most widely used syntheticindicator for characterizing overall mortality differences when (not so small) spatial units are considered.Conclusion: Our age-space model is an appropriate and flexible proposal that provides more reliable estimates of the probabilities of death, which allow the calculation of enhanced epidemiological indicators (smoothed ASR, smoothed LE), thus providing alternatives to traditional SMR-based studies of small areas.
HER2 gene assessment in liquid biopsy of gastric and esophagogastric junction cancer patients qualified for surgery
Authors: Grenda Anna , Wojas-Krawczyk Kamila , Skoczylas Tomasz , Krawczyk Paweł , Sierocińska-Sawa Jadwiga , Wallner Grzegorz , Milanowski Janusz 
Published: November 2020

Abstract
Background Amplification of HER2 gene (ERBB2) and overexpression of HER2 protein on cancer cells are found in 10-26% of gastric cancer (GC) and esophagogastric junction cancer (EGJC). Gene copy number variation (CNV) could be detected in these patients in liquid biopsy and in cancer cells.Methods We analysed HER2 gene CNV used qPCR method in 87 sera collected from GC and EGJC patients before surgical treatment and in 40 sera obtained from healthy donors. HER2 gene CNV was also assessed in formalin-fixed paraffin-embedded (FFPE) tumor tissue. Furthermore, we assessed the number of HER2 gene copies and HER2 expression in cancer cells using the fluorescent in situ hybridization method (FISH) and immunohistochemistry (IHC).Results We found that the HER2 gene copy number in liquid biopsy was higher in GC and EGJC patients compared to healthy people (p=0.01). Moreover, EGJC patients had higher number of HER2 gene copies than healthy donors (p=0.0016). HER2 CNV examination could distinguish healthy individuals and patients with gastric or esophagogastric junction cancers with sensitivity and specificity of 58% and 98% (AUC=0.707, 95% CI: 0.593-0.821, p=0.004). We found that patients with a high copy number of the HER2 gene in the tumor tissue assessed by qPCR (but not by FISH) have significantly more often a high number of HER2 gene copies in liquid biopsy (p=0.04).Conclusions We suggested that HER2 testing in liquid biopsy could be used as an auxiliary method to analysis of HER2 status in tumor tissue in gastric or esophagogastric junction cancers.