bluuebunny/crossref_metadata_2025_split huggingface dataset:
From cadaveric and animal studies to the clinical reality of robotic mastectomy: a feasibility report of training program
Authors: Lee Jeea , Park Hyung Seok , Lee Dong Won , Song Seung Yong , Yu Jonghan , Ryu Jai Min , Bae Soong June , Lew Dea Hyun , Kim Seung Il , Toesca Antonio 
Published: October 2021

AbstractRobotic nipple-sparing mastectomy (RNSM) provides better cosmetic outcomes and improves the quality of life of women with breast cancer. However, this has not been widely adapted due to the lack of well-structured training programs. The present study aimed to report the establishment of cadaveric and animal skill laboratory training programs for RNSM and the participants’ perception on the training programs. We performed 24 RNSMs using 11 cadavers and one porcine model. Then, the skill laboratory characteristics were reviewed. Five trainers and 10 trainees participated in the programs. The first four cadaveric RNSMs with latissimus dorsi flaps and implants were performed using the da Vinci Si® system. We performed 14 and six RNSMs using the Xi® and SP® systems, respectively. The scores for questionnaires on the satisfaction with the training consisted of the trainees’ perceived goals in attending the course, teaching/learning environment, and teaching staff performance. The scores were excellent. Cadaveric or porcine RNSM skill laboratory training may be essential programs that can provide safe and efficient training.
Accelerated fibrin clot degradation is associated with arterial thromboembolism in patients following venous thrombosis: a cohort study
Authors: Mrozinska Sandra , Wypasek Ewa , Broniatowska Elżbieta , Undas Anetta 
Published: October 2021

AbstractSeveral lines of evidence have suggested that patients following venous thromboembolism (VTE) are at higher risk of arterial thromboembolism (ATE). Prothrombotic fibrin clot characteristics were reported in individuals with cardiovascular risk factors. We investigated whether specific fibrin clot properties measured after 3–4 months of anticoagulation characterize VTE patients with subsequent ATE. We enrolled 320 patients following VTE aged below 70 years (median age, 46). Ten patients were lost to follow-up. ATE occurred in 21 individuals after a median 54 (31–68) months during a follow-up of 87.5 months (incidence 0.94%; 95% confidence interval [CI], 0.59–1.4 per patient-year). Patients with ATE had faster fibrin clot degradation, reflected by maximum rate of D-dimer increase during plasma clot lysis induced by tissue-type plasminogen activator (D-Drate) at baseline. Clot permeability, turbidimetric variables, clot lysis time, and thrombin generation were unrelated to ATE. Univariable Cox proportional hazards analysis showed that age, diabetes, and D–Dratewere risk factors for subsequent ATE. Increased D–Drate(by 0.001 mg/L/min; hazard ratio, 1.08; 95% CI 1.02–1.14) was an independent predictor of ATE after adjustment for potential confounders. Faster fibrin clot degradation at 3 months since VTE may increase the risk of ATE among VTE patients during follow-up.
Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network
Authors: Xu Yong-Chang , ShangGuan Tian-Jun , Ding Xue-Ming , Cheung Ngaam J. 
Published: October 2021

AbstractThe amino acid sequence of a protein contains all the necessary information to specify its shape, which dictates its biological activities. However, it is challenging and expensive to experimentally determine the three-dimensional structure of proteins. The backbone torsion angles play a critical role in protein structure prediction, and accurately predicting the angles can considerably advance the tertiary structure prediction by accelerating efficient sampling of the large conformational space for low energy structures. Here we first time propose evolutionary signatures computed from protein sequence profiles, and a novel recurrent architecture, termed ESIDEN, that adopts a straightforward architecture of recurrent neural networks with a small number of learnable parameters. The ESIDEN can capture efficient information from both the classic and new features benefiting from different recurrent architectures in processing information. On the other hand, compared to widely used classic features, the new features, especially the Ramachandran basin potential, provide statistical and evolutionary information to improve prediction accuracy. On four widely used benchmark datasets, the ESIDEN significantly improves the accuracy in predicting the torsion angles by comparison to the best-so-far methods. As demonstrated in the present study, the predicted angles can be used as structural constraints to accurately infer protein tertiary structures. Moreover, the proposed features would pave the way to improve machine learning-based methods in protein folding and structure prediction, as well as function prediction. The source code and data are available at the website https://kornmann.bioch.ox.ac.uk/leri/resources/download.html.
Modulation of circadian clock by crude drug extracts used in Japanese Kampo medicine
Authors: Zhang Manhui , Kobayashi Kohei , Atsumi Haruki , Katada Yuma , Nakane Yusuke , Chen Junfeng , Nagano Ryo , Kadofusa Naoya , Nishiwaki-Ohkawa Taeko , Kon Naohiro , Hirota Tsuyoshi , Sato Ayato , Makino Toshiaki , Yoshimura Takashi 
Published: October 2021

AbstractCircadian rhythm is an approximately 24 h endogenous biological rhythm. Chronic disruption of the circadian clock leads to an increased risk of diabetes, cardiovascular disease, and cancer. Hence, it is important to develop circadian clock modulators. Natural organisms are a good source of several medicines currently in use. Crude drugs used in Japanese traditional Kampo medicine or folk medicines are an excellent source for drug discovery. Furthermore, identifying new functions for existing drugs, known as the drug repositioning approach, is a popular and powerful tool. In this study, we screened 137 crude drug extracts to act as circadian clock modulators in human U2OS cells stably expressing the clock reporter Bmal1-dLuc, and approximately 12% of these modulated the circadian rhythm. We further examined the effects of several crude drugs in Rat-1 fibroblasts stably expressing Per2-luc, explant culture of lung from Per2::Luciferase knockin mice, and zebrafish larvae in vivo. Notably, more than half of the major ingredients of these crude drugs were reported to target AKT and its relevant signaling pathways. As expected, analysis of the major ingredients targeting AKT signaling confirmed the circadian clock-modulating effects. Furthermore, activator and inhibitor of AKT, and triple knockdown of AKT isoforms by siRNA also modulated the circadian rhythm. This study, by employing the drug repositioning approach, shows that Kampo medicines are a useful source for the identification of underlying mechanisms of circadian clock modulators and could potentially be used in the treatment of circadian clock disruption.
Brain connectivity dynamics in cisgender and transmen people with gender incongruence before gender affirmative hormone treatment
Authors: Uribe Carme , Junque Carme , Gómez-Gil Esther , Díez-Cirarda María , Guillamon Antonio 
Published: October 2021

AbstractLarge-scale brain network interactions have been described between trans- and cis-gender binary identities. However, a temporal perspective of the brain's spontaneous fluctuations is missing. We investigated the functional connectivity dynamics in transmen with gender incongruence and its relationship with interoceptive awareness. We describe four states in native and meta-state spaces: (i) one state highly prevalent with sparse overall connections; (ii) a second with strong couplings mainly involving components of the salience, default, and executive control networks. Two states with global sparse connectivity but positive couplings (iii) within the sensorimotor network, and (iv) between salience network regions. Transmen had more dynamical fluidity than cismen, while cismen presented less meta-state fluidity and range dynamism than transmen and ciswomen. A positive association between attention regulation and fluidity and meta-state range dynamism was found in transmen. There exist gender differences in the temporal brain dynamism, characterized by distinct interrelations of the salience network as catalyst interacting with other networks. We offer a functional explanation from the neurodevelopmental cortical hypothesis of a gendered-self.
pCLE highlights distinctive vascular patterns in early gastric cancer and in gastric diseases with high risk of malignant complications
Authors: Fornasarig Mara , Capuano Alessandra , Maiero Stefania , Pivetta Eliana , Guarnieri Giovanni , Canzonieri Vincenzo , Zucchetto Antonella , Mongiat Maurizio , Cannizzaro Renato , Spessotto Paola 
Published: October 2021

AbstractEndoscopy is widely used to detect and diagnose precancerous lesions and gastric cancer (GC). The probe-based Confocal Laser Endomicroscopy (pCLE) is an endoscopic technique suitable for subcellular resolution and for microvasculature analyses. The aim of this study was to use pCLE to identify specific vascular patterns in high-risk and early stage GC. Mucosal architecture, vessel tortuosity, enlargements and leakage were assessed in patients with autoimmune gastritis and early gastric cancer (EGC). We were able to stratify gastritis patients by identifying distinct vascular profiles: gastritis was usually associated with increased vascularization characterized by a high number of tortuous vessels, which were also found in atrophic autoimmune disease. Leaky and tortuous vessels, distributed in a spatially irregular network, characterized the atrophic metaplastic mucosa. The mucosal vasculature of EGC patients displayed tortuous vessels, but unlike what detected in atrophic gastritis, they appeared patchy, as is in neoplastic gastric tissue. Very importantly, we detected vascular changes even in areas without lesions, supporting the contention that vascular alterations may provide a favorable microenvironment for carcinogenesis. This report confirms that pCLE is a valid endoscopic approach to improve the definition of patients with malignant lesions or at increased risk for GC by assessing vascular changes.
Influence of Turkish origin on hematology reference intervals in the German population
Authors: Mayr Franz X. , Bertram Alexander , Cario Holger , Frühwald Michael C. , Groß Hans-Jürgen , Groening Arndt , Grützner Stefanie , Gscheidmeier Thomas , Hoffmann Reinhard , Krebs Alexander , Ruf Hans-Georg , Torge Antje , Woelfle Joachim , Razum Oliver , Rauh Manfred , Metzler Markus , Zierk Jakob 
Published: October 2021

AbstractReference intervals for laboratory test results have to be appropriate for the population in which they are used to be clinically useful. While sex and age are established partitioning criteria, patients’ origin also influences laboratory test results, but is not commonly considered when creating or applying reference intervals. In the German population, stratification for ethnicity is rarely performed, and no ethnicity-specific hematology reference intervals have been reported yet. In this retrospective study, we investigated whether specific reference intervals are warranted for the numerically largest group of non-German descent, individuals originating from Turkey. To this end, we analyzed 1,314,754 test results from 167,294 patients from six German centers. Using a name-based algorithm, 1.9% of patients were identified as originating from Turkey, in line with census data and the algorithm’s sensitivity. Reference intervals and their confidence intervals were calculated using an indirect data mining approach, and Turkish and non-Turkish reference limits overlapped completely or partially in nearly all analytes, regardless of age and sex, and only 5/144 (3.5%) subgroups’ reference limits showed no overlap. We therefore conclude that the current practice of using common reference intervals is appropriate and allows correct clinical decision-making in patients originating from Turkey.
Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation
Authors: Lucas-Sánchez Marcel , Font-Porterias Neus , Calafell Francesc , Fadhlaoui-Zid Karima , Comas David 
Published: October 2021

AbstractHuman populations are genetically affected by their demographic history, which shapes the distribution of their functional genomic variation. However, the genetic impact of recent demography is debated. This issue has been studied in different populations, but never in North Africans, despite their relevant cultural and demographic diversity. In this study we address the question by analyzing new whole-exome sequences from two culturally different Tunisian populations, an isolated Amazigh population and a close non-isolated Arab-speaking population, focusing on the distribution of functional variation. Both populations present clear differences in their variant frequency distribution, in general and for putatively damaging variation. This suggests a relevant effect in the Amazigh population of genetic isolation, drift, and inbreeding, pointing to relaxed purifying selection. We also discover the enrichment in Imazighen of variation associated to specific diseases or phenotypic traits, but the scarce genetic and biomedical data in the region limits further interpretation. Our results show the genomic impact of recent demography and reveal a clear genetic differentiation probably related to culture. These findings highlight the importance of considering cultural and demographic heterogeneity within North Africa when defining population groups, and the need for more data to improve knowledge on the region’s health and disease landscape.
AA amyloid in human food chain is a possible biohazard
Authors: Rising Anna , Gherardi Paola , Chen Gefei , Johansson Jan , Oskarsson Marie E. , Westermark Gunilla T. , Westermark Per 
Published: October 2021

AbstractAA amyloidosis can be transmitted experimentally in several mammalian and avian species as well as spontaneously between captive animals, even by oral intake of amyloid seeds. Amyloid seeding can cross species boundaries, and fibrils of one kind of amyloid protein may also seed other types. Here we show that meat from Swedish and Italian cattle for consumption by humans often contains AA amyloid and that bovine AA fibrils efficiently cross-seed human amyloid β peptide, associated with Alzheimer’s disease.
Characteristic analysis of volatile avalanche diode threshold switching for bionic nerve synapse applications
Authors: Wang Yang , Zhong Zeyu , Jin Xiangliang , Peng Yan , Luo Jun 
Published: October 2021

AbstractThe combination of biological neurology and memristive theory has greatly promoted the development of neuromorphic computing. To build a large-scale artificial intelligence alert system, the exploration of bionic synapses compatible with standard processes has become an urgent problem to be solved in the next step. In response to the above application requirements, this paper proposes a volatile avalanche diode threshold switching (VADTS) that is fully compatible with standard semiconductor technology to simulate the various functions of the synapse. Technology computer-aided design device-level simulation can verify the bionic principle of VADTS. The function of VADTS's bionic synapse was verified by the experimental test platform. The results show that under the action of the excitation signal (11.25 V), the device can continuously change from a high-resistance state to a low-resistance state. When the excitation signal is lower than the threshold, VADTS presents a “no adaptation” state of nerve synapses. When the excitation signal is higher than the threshold and changes continuously, the current changes along with the amplitude of the excitation signal, similar to the “sensitization” state of the nerve synapse.
Optimizing the evaluation of gene-targeted panels for tumor mutational burden estimation
Authors: Li Yawei , Luo Yuan 
Published: October 2021

AbstractThough whole exome sequencing (WES) is the gold-standard for measuring tumor mutational burden (TMB), the development of gene-targeted panels enables cost-effective TMB estimation. With the growing number of panels in clinical trials, developing a statistical method to effectively evaluate and compare the performance of different panels is necessary. The mainstream method uses R-squared value to measure the correlation between the panel-based TMB and WES-based TMB. However, the performance of a panel is usually overestimated via R-squared value based on the long-tailed TMB distribution of the dataset. Herein, we propose angular distance, a measurement used to compute the extent of the estimated bias. Our extensive in silico analysis indicates that the R-squared value reaches a plateau after the panel size reaches 0.5 Mb, which does not adequately characterize the performance of the panels. In contrast, the angular distance is still sensitive to the changes in panel sizes when the panel size reaches 6 Mb. In particular, R-squared values between the hypermutation-included dataset and the non-hypermutation dataset differ widely across many cancer types, whereas the angular distances are highly consistent. Therefore, the angular distance is more objective and logical than R-squared value for evaluating the accuracy of TMB estimation for gene-targeted panels.
Quantification of aniline and N-methylaniline in indigo
Authors: Cordin Michael , Bechtold Thomas , Pham Tung 
Published: October 2021

AbstractAniline and N-methylaniline are common contaminants in commercially produced indigo. It is known, that commercially produced indigo contains up to 0.6% aniline and 0.4% N-methylaniline by weight and indigo dye shows a small mutagenic effect, most probably due to the presence of these contaminants. The present work describes a new and powerful analytical method to determine the concentration of these contaminants in indigo. This method is based on the transformation of water insoluble indigo into soluble leucoindigo and allows therefore the acidic extraction of the aromatic contaminants. This transformation step is essential, because the main part of these contaminants are strongly included in the indigo crystals. The amount of extracted aniline and N-methylaniline from the leucoindigo solution was quantified with high performance liquid chromatography (HPLC, combined with a photo diode array detector). A possible accumulation of the aromatic amines at the indigo crystal surface was investigated using FTIR and by adsorption studies. Therefore this method allows an accurate monitoring of these toxic by-products in the indigo dye, which is important for an economic and environmental assessment of the denim production.
The effect of solvent on reactivity of the Li2S–P2S5 system in liquid-phase synthesis of Li7P3S11 solid electrolyte
Authors: Gamo Hirotada , Nagai Atsushi , Matsuda Atsunori 
Published: October 2021

AbstractSynthesis technology for sulfide-based solid electrolytes based on liquid-phase processing has attracted significant interest in relation to achieving the optimal design for all-solid-state batteries. Herein, guidelines to solvent selection for the liquid-phase synthesis of superionic conductor Li7P3S11 are described through systematic examination. 70Li2S–30P2S5 system, a source of Li7P3S11, is treated via a wet chemical reaction using eight organic solvents with different physical and chemical properties (i.e., dielectric constant, molecule structure, and boiling point). We reveal that the solvent’s polarity, characterized by the dielectric constant, plays an important role in the formation of crystalline Li7P3S11 via wet chemical reaction. In addition, acetonitrile (ACN) solvent with a high dielectric constant was found to lead to high-purity crystalline Li7P3S11 and intrinsically high ionic conductivity. Further, solvents with a high boiling point and ring structures that cause steric hindrance were found to be unfavorable for the wet chemical synthesis of Li7P3S11 solid electrolyte. Overall, we demonstrate that ACN solvent is the most suitable for the liquid-phase synthesis of a crystalline Li7P3S11 solid electrolyte with high purity based on its dielectric constant, molecular structure, and boiling point.
Predicting miRNA–disease associations using improved random walk with restart and integrating multiple similarities
Authors: Nguyen Van Tinh , Le Thi Tu Kien , Than Khoat , Tran Dang Hung 
Published: October 2021

AbstractPredicting beneficial and valuable miRNA–disease associations (MDAs) by doing biological laboratory experiments is costly and time-consuming. Proposing a forceful and meaningful computational method for predicting MDAs is essential and captivated many computer scientists in recent years. In this paper, we proposed a new computational method to predict miRNA–disease associations using improved random walk with restart and integrating multiple similarities (RWRMMDA). We used a WKNKN algorithm as a pre-processing step to solve the problem of sparsity and incompletion of data to reduce the negative impact of a large number of missing associations. Two heterogeneous networks in disease and miRNA spaces were built by integrating multiple similarity networks, respectively, and different walk probabilities could be designated to each linked neighbor node of the disease or miRNA node in line with its degree in respective networks. Finally, an improve extended random walk with restart algorithm based on miRNA similarity-based and disease similarity-based heterogeneous networks was used to calculate miRNA–disease association prediction probabilities. The experiments showed that our proposed method achieved a momentous performance with Global LOOCV AUC (Area Under Roc Curve) and AUPR (Area Under Precision-Recall Curve) values of 0.9882 and 0.9066, respectively. And the best AUC and AUPR values under fivefold cross-validation of 0.9855 and 0.8642 which are proven by statistical tests, respectively. In comparison with other previous related methods, it outperformed than NTSHMDA, PMFMDA, IMCMDA and MCLPMDA methods in both AUC and AUPR values. In case studies of Breast Neoplasms, Carcinoma Hepatocellular and Stomach Neoplasms diseases, it inferred 1, 12 and 7 new associations out of top 40 predicted associated miRNAs for each disease, respectively. All of these new inferred associations have been confirmed in different databases or literatures.