bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term results of definitive chemoradiotherapy for unresectable locally advanced esophageal squamous cell carcinoma
Authors: Ochi Masanori , Murakami Yuji , Nishibuchi Ikuno , Kubo Katsumaro , Imano Nobuki , Takeuchi Yuki , Kimura Tomoki , Hamai Yoichi , Emi Manabu , Okada Morihito , Nagata Yasushi 
Published: November 2020

Abstract

Purpose
The present study aimed to evaluate the long-term results of definitive chemoradiotherapy (CRT) for unresectable locally advanced esophageal squamous cell carcinoma (LA-ESCC).

Materials and methods
We analyzed eighty patients with unresectable LA-ESCC, who underwent definitive CRT between 2001 and 2014. The 5-year overall survival (OS), cause-specific survival (CSS), and progression-free survival (PFS) rates were calculated, and we investigated the prognostic factors and adverse events.

Results
The median age was 66 years (range, 41–83 years). Histologically, all patients had squamous cell carcinoma. The most common tumor site was the middle thoracic esophagus in 43 (54%) patients. According to the eighth edition of the Union for International Cancer Control TNM classification, sixty-six patients (83%) had T4 disease, 59 (74%) had regional lymph node (LN) metastases, and 35 (44%) had distant LN metastases beyond the regional LN (M1 LYM) disease. Forty-five (56%) and 35 (44%) patients belong to clinical stages IVA and IVB, respectively. The median follow-up period for survivors was 86 months. The 5-year OS, CSS, and PFS rates were 20.2%, 25.7%, and 18.4%, respectively. On univariate analysis, only the performance status score was significantly associated with better overall survival (p = 0.026). Grade 3 or higher late adverse events were observed in 12 (15%) patients, and these included cardiopulmonary adverse events in 6 (8%) patients. Treatment-related death occurred in 3 (4%) patients.

Conclusion
We showed the long-term results of definitive CRT for unresectable LA-ESCC. The survivals are still poor and new treatment strategies need to be developed.
External stoma diversion: a palliative measure for peristomal wound healing in resource-limited settings
Authors: Davis Rachel W , Sherif Youmna A , Morrison Catherine Anne 
Published: November 2020

Abstract
The provision of intestinal stoma care is challenging in austere settings due to limitations in surgical and wound care access as well as the high cost and sparsity of ostomy supplies. As a result, many surgical patients suffer from ostomy-related complications such as peristomal wounds and are unable to find relief for these complications from standard treatments and measures. This article describes the external stoma diversion, a cost-effective palliative surgical procedure that assists in the healing of peristomal wounds in resource-limited settings.
The B chromosome ofSorghum purpureosericeumreveals the first pieces of its sequence
Authors: Karafiátová Miroslava , Bednářová Martina , Said Mahmoud , Čížková Jana , Holušová Kateřina , Blavet Nicolas , Bartoš Jan 
Published: November 2020

AbstractMore than a century has passed since the B chromosomes were first discovered. Today we know much of their variability, morphology, and transmission to plant progeny. With the advent of modern technologies, B chromosome research has accelerated, and some of their persistent mysteries have since been uncovered. Building on this momentum, here we extend current knowledge of B chromosomes in Sorghum purpureosericeum to the sequence level. To do this, we estimated the B chromosome size at 421 Mb, sequenced DNA from flow-sorted haploid pollen nuclei of both B-positive (B+) and B-negative (B0) plants, and performed a repeat analysis on the Illumina raw sequence data. This analysis revealed nine putative B-specific clusters, which were then used to develop B chromosome-specific markers. Additionally, cluster SpuCL4 was identified and verified to be a centromeric repeat. We also uncovered two repetitive clusters (SpuCL168 and SpuCL115), which hybridized exclusively on the B chromosome under fluorescence in situ hybridization and can be considered as robust cytogenetic markers. Given that B chromosomes in Sorghum are rather unstable across all tissues, our findings could facilitate expedient identification of B+ plants and enable a wide range of studies to track this chromosome type in situ.
The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs
Authors: Alenaizan Asem , Barnett Joshua L , Hud Nicholas V , Sherrill C David , Petrov Anton S 
Published: November 2020

AbstractThe helical structures of DNA and RNA were originally revealed by experimental data. Likewise, the development of programs for modeling these natural polymers was guided by known structures. These nucleic acid polymers represent only two members of a potentially vast class of polymers with similar structural features, but that differ from DNA and RNA in the backbone or nucleobases. Xeno nucleic acids (XNAs) incorporate alternative backbones that affect the conformational, chemical, and thermodynamic properties of XNAs. Given the vast chemical space of possible XNAs, computational modeling of alternative nucleic acids can accelerate the search for plausible nucleic acid analogs and guide their rational design. Additionally, a tool for the modeling of nucleic acids could help reveal what nucleic acid polymers may have existed before RNA in the early evolution of life. To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA.
Validation of human microRNA target pathways enables evaluation of target prediction tools
Authors: Kern Fabian , Krammes Lena , Danz Karin , Diener Caroline , Kehl Tim , Küchler Oliver , Fehlmann Tobias , Kahraman Mustafa , Rheinheimer Stefanie , Aparicio-Puerta Ernesto , Wagner Sylvia , Ludwig Nicole , Backes Christina , Lenhof Hans-Peter , von Briesen Hagen , Hart Martin , Keller Andreas , Meese Eckart 
Published: November 2020

Abstract
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution
Authors: Kang Hyun Je , Cheon Na Young , Park Hyun , Jeong Gyu Won , Ye Byeong Jin , Yoo Eun Jin , Lee Jun Ho , Hur Jin-Hoe , Lee Eun-A , Kim Hongtae , Lee Kyoo-young , Choi Soo Youn , Lee-Kwon Whaseon , Myung Kyungjae , Lee Ja Yil , Kwon Hyug Moo 
Published: November 2020

Abstract
R-loops are three-stranded, RNA–DNA hybrid, nucleic acid structures produced due to inappropriate processing of newly transcribed RNA or transcription-replication collision (TRC). Although R-loops are important for many cellular processes, their accumulation causes genomic instability and malignant diseases, so these structures are tightly regulated. It was recently reported that R-loop accumulation is resolved by methyltransferase-like 3 (METTL3)-mediated m6A RNA methylation under physiological conditions. However, it remains unclear how R-loops in the genome are recognized and induce resolution signals. Here, we demonstrate that tonicity-responsive enhancer binding protein (TonEBP) recognizes R-loops generated by DNA damaging agents such as ultraviolet (UV) or camptothecin (CPT). Single-molecule imaging and biochemical assays reveal that TonEBP preferentially binds a R-loop via both 3D collision and 1D diffusion along DNA in vitro. In addition, we find that TonEBP recruits METTL3 to R-loops through the Rel homology domain (RHD) for m6A RNA methylation. We also show that TonEBP recruits RNaseH1 to R-loops through a METTL3 interaction. Consistent with this, TonEBP or METTL3 depletion increases R-loops and reduces cell survival in the presence of UV or CPT. Collectively, our results reveal an R-loop resolution pathway by TonEBP and m6A RNA methylation by METTL3 and provide new insights into R-loop resolution processes.
How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH
Authors: Kappenberger Jeannette , Koelmel Wolfgang , Schoenwetter Elisabeth , Scheuer Tobias , Woerner Julia , Kuper Jochen , Kisker Caroline 
Published: November 2020

AbstractThe superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. The ATPase activity of XPB is required in both processes. We investigated the interaction network that regulates XPB via the p52 and p8 subunits with functional mutagenesis based on our crystal structure of the p52/p8 complex and current cryo-EM structures. Importantly, we show that XPB’s ATPase can be activated either by DNA or by the interaction with the p52/p8 proteins. Intriguingly, we observe that the ATPase activation by p52/p8 is significantly weaker than the activation by DNA and when both p52/p8 and DNA are present, p52/p8 dominates the maximum activation. We therefore define p52/p8 as the master regulator of XPB acting as an activator and speed limiter at the same time. A correlative analysis of the ATPase and translocase activities of XPB shows that XPB only acts as a translocase within the context of complete core TFIIH and that XPA increases the processivity of the translocase complex without altering XPB’s ATPase activity. Our data define an intricate network that tightly controls the activity of XPB during transcription and nucleotide excision repair.
Plasma exchange for the management of ANCA-associated vasculitis: the con position
Authors: Specks Ulrich , Fussner Lynn A , Cartin-Ceba Rodrigo , Casal Moura Marta , Zand Ladan , Fervenza Fernando C 
Published: November 2020

AbstractAdvances in the diagnosis and treatment of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis have led to continued improvement in survival and prognosis over the course of the last 4 decades. Nevertheless, the most acute and severe disease manifestations, including severe kidney disease and alveolar hemorrhage, continue to be associated with increased early mortality from disease activity or treatment complications as well as risk for the development of end-stage kidney disease (ESKD), which in turn directly affects the overall prognosis of ANCA-associated vasculitis. Plasma exchange (PLEX) has long been proposed and used for these most severe disease manifestations under the assumption that its effects are swift and supported by our understanding of the pathogenic role of ANCA. Yet convincing evidence of a beneficial effect of PLEX in ANCA-associated vasculitis has been lacking, as early studies and small trials have generated conflicting results. The controversy regarding PLEX has been accentuated recently as the largest randomized controlled trial ever conducted in ANCA-associated vasculitis, the Plasma Exchange and Glucocorticoids in Severe ANCA-associated Vasculitis trial, which was specifically designed to evaluate the efficacy of PLEX in patients with severe renal disease or alveolar hemorrhage, failed to show a difference in the combined primary outcome measure of death or ESKD in patients who received PLEX versus those who did not. In light of these disappointing results, we herein review the currently available data on PLEX for ANCA-associated vasculitis and explain why we believe that these data no longer support the use of PLEX in ANCA-associated vasculitis.
Three-Month Pulmonary Function and Radiological Outcomes in COVID-19 Survivors: A Longitudinal Patient Cohort Study
Authors: Liao Xuejiao , Wang Ying , He Ziyi , Yun Yongxing , Hu Ming , Ma Zhenghua , Huang Ling , Cai Qingxian , Xu Lin , Hao Yuantao , Liu Lei 
Published: November 2020

Abstract

Background
This study aimed to investigate pulmonary function and radiological outcomes in a group of coronavirus disease 2019 (COVID-19) survivors.

Methods
One hundred seventy-two COVID-19 survivors in a follow-up clinic in a referral hospital underwent high-resolution computed tomography (CT) of the thorax and pulmonary function at 3 months after hospital discharge.

Results
The median duration from hospital discharge to radiological and pulmonary function test (interquartile range) was 90 (88–95) days. Abnormal pulmonary function was found in 11 (6.40%) patients, and abnormal small airway function (FEF25-75%) in 12 (6.98%). Six (3.49%) patients had obstructive ventilation impairment, and 6 (3.49%) had restrictive ventilatory impairment. No significant differences in lung function parameters were observed between the nonsevere and severe groups. Of 142 COVID-19 patients who underwent CT scan, 122 (85.91%) showed residual CT abnormalities and 52 (36.62%) showed chronic and fibrotic changes. The ground-glass opacities absorption in the lungs of severe cases was less satisfactory than that of nonsevere patients. The severe patients had higher CT scores than the nonsevere cases (2.00 vs 0.00; P &lt; .001)

Conclusions
Of the COVID-19 survivors in our study, 6.40% still presented pulmonary function abnormality 3 months after discharge, which did not vary by disease severity during hospitalization; 85.91% of patients had abnormalities on chest CT, with fibrous stripes and ground-glass opacities being the most common patterns.
The Externalities of Corruption: Evidence from Entrepreneurial Firms in China*
Authors: Giannetti Mariassunta , Liao Guanmin , You Jiaxing , Yu Xiaoyun 
Published: November 2020

Abstract
Exploiting China’s anti-corruption campaign, we show that following a decrease in corruption, firm performance improves. Small and young firms benefit more. We identify the channels through which corruption hampers firm performance. Following the anti-corruption campaign, the allocation of capital and labor becomes more efficient. Firms operating in ex ante more corrupt environments experience larger productivity gains, higher growth of sales, and lower cost of debt than other firms. Taken together, our results suggest that corruption is an inefficient equilibrium for an economy because it creates negative externalities.
Medicating Anaesthesiology: Pharmaceutical Change, Specialisation and Healthcare Reform in Post-War Britain
Authors: Mueller Lucas M 
Published: November 2020

Summary
This article examines how chemists, pharmacologists and anaesthetists developed the anaesthetic drug halothane and assessed the clinical use of the drug in the UK in the 1950s. I argue that halothane became seen as a superior drug not because of properties inherent in the new molecule CF3-CHClBr, but because anaesthetists used it to build a professional identity during a period of significant change in British medicine. The recently established National Health Service called for increasing the number of anaesthetists and other specialist hospital consultants. In this context, the specialist knowledge, novel technologies and new practices necessary for the safe usage of halothane enabled anaesthetists to forge a profession. The history of this process shows how professionalisation, pharmaceutical change and healthcare reform have interacted to shape knowledge transfer between laboratory and hospital with consequences for experimental ethics and patient safety.
Impact of storage conditions on protein oxidation of rendered by-product meals1
Authors: Frame Carl A , Huff-Lonergan Elisabeth J , Rossoni Serao Mariana C 
Published: November 2020

AbstractRendered products used in animal feed and pet food undergo extreme temperatures during manufacturing and may be stored up to 2 yr. No information is available on protein oxidation in these products. The objective of this study was to determine the extent to which typical antioxidant inclusion at different storage conditions may limit protein oxidation in typical rendered protein meals. Two experiments were conducted on 14 rendered products stored at either 45 °C for 7 or 14 d, or at 20 °C for 3 or 6 mo to determine the extent to which time, temperature, and antioxidants affect protein oxidation. Results from this study show that fish meal and chicken blood meal are susceptible to protein oxidation during storage at 45 °C (P = 0.05; 0.03) as well as during storage at 20 °C (P = 0.01; 0.04). Natural antioxidants were effective at limiting carbonyl formation in fish meal during short-term storage at 45 °C, whereas ethoxyquin was effective at limiting the extent of protein oxidation in fish meal stored long term at 20 °C.
Molecular Barcoding Reveals the Genus Streptomyces as Associated Root Endophytes of Apple (Malus domestica) Plants Grown in Soils Affected by Apple Replant Disease
Authors: Mahnkopp-Dirks Felix , Radl Viviane , Kublik Susanne , Gschwendtner Silvia , Schloter Michael , Winkelmann Traud 
Published: November 2020

Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now, the etiology has been poorly understood; however, soil (micro)biota are known to be involved. Because endophytes often colonize plants via the rhizosphere, this study aimed at comparing the bacterial endophytic root microbiome in plants growing in ARD-affected and unaffected soils from three different sites based on greenhouse biotests using a molecular barcoding approach. The initial endophytic microbiome of the starting material (in vitro propagated plants of the apple rootstock M26) did not significantly affect the overall richness and diversity of the endophytic community in plants after 8 weeks of growth in the respective soils but some genera of the initial microbiome managed to establish in apple roots. Proteobacteria was the dominant phylum in all samples. No differences in diversity or number of amplicon sequence variants (ASVs) between plants grown in ARD soil and unaffected soil was observed. However, several ASVs of high abundance uniquely found in plants grown in ARD-affected soils were Streptomyces spp. In soil from all three sites, these Streptomyces spp. were negatively correlated with plant growth parameters. Future inoculation experiments using selected Streptomyces isolates have to prove whether bacteria from this genus are opportunists or part of the ARD complex. For the first time, the bacterial endophytic community of apple roots grown in ARD-affected soils was characterized, which will help us to understand the etiology of ARD and develop countermeasures. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Association between gastrointestinal symptoms and depression among older adults in Taiwan: A cross-sectional study
Authors: Huang Mao-Hsuan , Wang Yen-Po , Wu Po-Shan , Chan Yee-Lam E. , Cheng Chih-Ming , Yang Cheng-Hung , Tsai Shih-Jen , Lu Ching-Liang , Tsai Chia-Fen 
Published: November 2020

Background:
Older adults with depression more frequently experience somatic and gastrointestinal (GI) problems compared with people without depression and younger adults with depression. However, whether GI symptoms are predictive of elevated rates of depression among older adults is unclear.

Methods:
We enrolled 106 older adults (>60 years old); 69 had late-life depression (LLD), and 37 were controls. All participants gave ratings on the Gastrointestinal Symptom Rating Scale (GSRS) and Hamilton Depression Rating Scale. Food consumption was assessed using a food frequency questionnaire, and a Mediterranean diet score was used as a covariate.

Results:
Compared with the controls, patients with LLD reported higher levels of depressive and GI symptoms and reported more reflux, abdominal pain, and dyspepsia symptoms, and these symptoms were correlated with Hamilton Depression Rating Scale scores (GSRS total: β = 0.47; reflux: β = 1.47; abdominal pain: β = 1.98; dyspepsia: β = 1.02; all p < 0.01). After demographic variables and Mediterranean diet score were controlled for, a logistic regression analysis indicated that total GSRS score was an independent determinant of LLD (odds ratio: 1.20, 95% CI: 1.04-1.38). Moreover, a stratified analysis by depression severity indicated that higher total GSRS score may contribute to greater depression severity (odds ratio: 1.25, 95% CI: 1.04-1.52).

Conclusion:
We provide evidence that GI symptoms are associated with depressive symptoms among patients with LLD. Older people with more specific GI symptoms, such as reflux, abdominal pain, and dyspepsia, are potentially at greater risk of having LLD.
Skin Cancer, Back to Basics
Authors: Davis Kyleen E. 
Published: November 2020

ABSTRACT
Actinic keratoses (AKs) are rough, scaly papules or plaques on sun-exposed areas of the body that may progress to squamous cell carcinoma. AKs are extremely common, with the highest incidence in individuals living close to the equator. Risk factors for AKs include advanced age, fair skin, male gender, baldness in men, immunosuppression, and chronic sun exposure. Many effective therapies for individual AKs exist; however, underlying field cancerization—a mix of clinical and subclinical lesions—must be addressed for treatment to be successful. Nurses can play a pivotal role in empowering and educating their patients to make the right choices to keep their skin healthy and cancer-free for years to come.