bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of laser etching biomimicking configuration on the strength of metal-plastic connection
Authors: Liu Fengde , Xu Xiaoni , Liu Jiaming , Fan Haiqi , Huang Genzhe , Zhang Hong 
Published: May 2022

Abstract
This study uses a laser to etch biomimicking locking patterns on the surface of 304 stainless steel to strengthen the connection between metal-plastic products. Under heat and pressure from the device, the plastic melts into the pattern and coalesces it, while the burrs formed from the etching process lock the joint of the metal-plastic. Three biomimicking configurations, honeycomb, leaf vein, and dragonfly head-and-neck hair interlocking, are studied. As shear strength determines the connection strength, we simulate the tensile-shearing process of stainless steel and plastic connectors of the three biomimicking configurations on ABAQUS, and predict the effects of the configurations on their connection strength. Experiments show that the plastic and metal are effectively connected at a heating temperature of 400 °C and a pressure of 70 kN. When the burr rate is 7.66% and the coverage rate is 29.4 ± 0.5%, the three biomimicking connectors break at the plastic base material, and the dragonfly head-and-neck hair interlocking configuration can withstand a shear force of 942 ± 9.23 N.
Cleaning of nitrogen-containing carbon contamination by atmospheric pressure plasma jet
Authors: YANG Li , WANG Sishu , WU Andong , CHEN Bo , CHEN Jianjun , WANG Hongbin , CHEN Shuwei , WEI Jianjun , ZHANG Kun , YE Zongbiao , GOU Fujun 
Published: May 2022

Abstract
Atmospheric pressure plasma jet (APPJ) was used to clean nitrogen-containing carbon films (C–N) fabricated by plasma-assisted chemical vapor deposition method employing the plasma surface interaction linear device at Sichuan University (SCU-PSI). The properties of the contaminated films on the surface of pristine and He-plasma pre-irradiated tungsten matrix, such as morphology, crystalline structure, element composition and chemical structure were characterized by scanning electron microscopy, grazing incidence x-ray diffraction and x-ray photoelectron spectroscopy. The experimental results revealed that the removal of C–N film with a thickness of tens of microns can be realized through APPJ cleaning regardless of the morphology of the substrates. Similar removal rates of 16.82 and 13.78 μm min−1 were obtained for C–N films deposited on a smooth pristine W surface and rough fuzz-covered W surface, respectively. This is a remarkable improvement in comparison to the traditional cleaning method. However, slight surface oxidation was found after APPJ cleaning, but the degree of oxidation was acceptable with an oxidation depth increase of only 3.15 nm. Optical emission spectroscopy analysis and mass spectrometry analysis showed that C–N contamination was mainly removed through chemical reaction with reactive oxygen species during APPJ treatment using air as the working gas. These results make APPJ cleaning a potentially effective method for the rapid removal of C–N films from the wall surfaces of fusion devices.
KLFDAPC: a supervised machine learning approach for spatial genetic structure analysis
Authors: Qin Xinghu , Chiang Charleston W K , Gaggiotti Oscar E 
Published: May 2022

Abstract
Geographic patterns of human genetic variation provide important insights into human evolution and disease. A commonly used tool to detect and describe them is principal component analysis (PCA) or the supervised linear discriminant analysis of principal components (DAPC). However, genetic features produced from both approaches could fail to correctly characterize population structure for complex scenarios involving admixture. In this study, we introduce Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC), a supervised non-linear approach for inferring individual geographic genetic structure that could rectify the limitations of these approaches by preserving the multimodal space of samples. We tested the power of KLFDAPC to infer population structure and to predict individual geographic origin using neural networks. Simulation results showed that KLFDAPC has higher discriminatory power than PCA and DAPC. The application of our method to empirical European and East Asian genome-wide genetic datasets indicated that the first two reduced features of KLFDAPC correctly recapitulated the geography of individuals and significantly improved the accuracy of predicting individual geographic origin when compared to PCA and DAPC. Therefore, KLFDAPC can be useful for geographic ancestry inference, design of genome scans and correction for spatial stratification in GWAS that link genes to adaptation or disease susceptibility.
DeepSCP: utilizing deep learning to boost single-cell proteome coverage
Authors: Wang Bing , Wang Yue , Chen Yu , Gao Mengmeng , Ren Jie , Guo Yueshuai , Situ Chenghao , Qi Yaling , Zhu Hui , Li Yan , Guo Xuejiang 
Published: May 2022

Abstract
Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computational methods. In this study, we present a novel framework DeepSCP, utilizing deep learning to boost SCP coverage. DeepSCP constructs a series of features of peptide-spectrum matches (PSMs) by predicting the retention time based on the multiple SCP sample sets and fragment ion intensities based on deep learning, and predicts PSM labels with an optimized-ensemble learning model. Evaluation of DeepSCP on public and in-house SCP datasets showed superior performances compared with other state-of-the-art methods. DeepSCP identified more confident peptides and proteins by controlling q-value at 0.01 using target–decoy competition method. As a convenient and low-cost computing framework, DeepSCP will help boost single-cell proteome identification and facilitate the future development and application of single-cell proteomics.
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
Authors: Gyori Benjamin M , Hoyt Charles Tapley , Steppi Albert 
Published: May 2022

Abstract

Summary
Gilda is a software tool and web service that implements a scored string matching algorithm for names and synonyms across entries in biomedical ontologies covering genes, proteins (and their families and complexes), small molecules, biological processes and diseases. Gilda integrates machine-learned disambiguation models to choose between ambiguous strings given relevant surrounding text as context, and supports species-prioritization in case of ambiguity.

Availability and implementation
The Gilda web service is available at http://grounding.indra.bio with source code, documentation and tutorials available via https://github.com/indralab/gilda.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies
Authors: Segura Joan , Rose Yana , Bittrich Sebastian , Burley Stephen K , Duarte Jose M 
Published: May 2022

AbstractMotivationMapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level.ResultsWe present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.Availability and implementationhttps://github.com/rcsb/rcsb-saguaro-3d.Supplementary informationSupplementary data are available at Bioinformatics online.
Nezzle: an interactive and programmable visualization of biological networks in Python
Authors: Lee Daewon 
Published: May 2022

AbstractSummaryHigh-quality visualization of biological networks often requires both manual curation for proper alignment and programming to map external data to the graphical components. Nezzle is a network visualization software written in Python, which provides programmable and interactive interfaces for facilitating both manual and automatic curation of the graphical components of networks to create high-quality figures.Availability and implementationNezzle is an open-source project under MIT license and is available from https://github.com/dwgoon/nezzle.Supplementary informationSupplementary data are available at Bioinformatics online.
Strategies for improving adipose-derived stem cells for tissue regeneration
Authors: Yuan Xin , Li Li , Liu Haofan , Luo Jing , Zhao Yongchao , Pan Cheng , Zhang Xue , Chen Yuwen , Gou Maling 
Published: May 2022

Abstract
Adipose-derived stem cells (ADSCs) have promising applications in tissue regeneration. Currently, there are only a few ADSC products that have been approved for clinical use. The clinical application of ADSCs still faces many challenges. Here, we review emerging strategies to improve the therapeutic efficacy of ADSCs in tissue regeneration. First, a great quantity of cells is often needed for the stem cell therapies, which requires the advanced cell expansion technologies. In addition cell-derived products are also required for the development of ‘cell-free’ therapies to overcome the drawbacks of cell-based therapies. Second, it is necessary to strengthen the regenerative functions of ADSCs, including viability, differentiation and paracrine ability, for the tissue repair and regeneration required for different physiological and pathophysiological conditions. Third, poor delivery efficiency also restricts the therapeutic effect of ADSCs. Effective methods to improve cell delivery include alleviating harsh microenvironments, enhancing targeting ability and prolonging cell retention. Moreover, we also point out some critical issues about the sources, effectiveness and safety of ADSCs. With these advanced strategies to improve the therapeutic efficacy of ADSCs, ADSC-based treatment holds great promise for clinical applications in tissue regeneration.
Two stages of speech envelope tracking in human auditory cortex modulated by speech intelligibility
Authors: Xu Na , Zhao Baotian , Luo Lu , Zhang Kai , Shao Xiaoqiu , Luan Guoming , Wang Qian , Hu Wenhan , Wang Qun 
Published: May 2022

AbstractThe envelope is essential for speech perception. Recent studies have shown that cortical activity can track the acoustic envelope. However, whether the tracking strength reflects the extent of speech intelligibility processing remains controversial. Here, using stereo-electroencephalogram technology, we directly recorded the activity in human auditory cortex while subjects listened to either natural or noise-vocoded speech. These 2 stimuli have approximately identical envelopes, but the noise-vocoded speech does not have speech intelligibility. According to the tracking lags, we revealed 2 stages of envelope tracking: an early high-γ (60–140 Hz) power stage that preferred the noise-vocoded speech and a late θ (4–8 Hz) phase stage that preferred the natural speech. Furthermore, the decoding performance of high-γ power was better in primary auditory cortex than in nonprimary auditory cortex, consistent with its short tracking delay, while θ phase showed better decoding performance in right auditory cortex. In addition, high-γ responses with sustained temporal profiles in nonprimary auditory cortex were dominant in both envelope tracking and decoding. In sum, we suggested a functional dissociation between high-γ power and θ phase: the former reflects fast and automatic processing of brief acoustic features, while the latter correlates to slow build-up processing facilitated by speech intelligibility.
Mortality prediction of retinal vessel diameters and function in a long-term follow-up of haemodialysis patients
Authors: Günthner Roman , Streese Lukas , Angermann Susanne , Lorenz Georg , Braunisch Matthias C , Matschkal Julia , Hausinger Renate , Stadler David , Haller Bernhard , Heemann Uwe , Kotliar Konstantin , Hanssen Henner , Schmaderer Christoph 
Published: May 2022

Abstract

Aim
Retinal vessel diameters are candidate biomarkers of mortality prediction in large population-based studies. We aimed to investigate the predictive value of retinal vessel diameters and flicker-induced retinal arteriolar and venular dilation on all-cause mortality in long-term follow-up of haemodialysis patients.

Methods and results
Retinal vessel diameters as well as maximum arteriolar (aMax) and venular dilation (vMax) were investigated in 275 and 214 haemodialysis patients, respectively. Patients were observed in a long-term follow-up for a median period of 73 months. About 36% (76/214) and 41% (113/275) of patients died. Arteriolar and venular diameters were 175 ± 19 and 208 ± 20 µm, respectively. Median aMax and vMax were 1.6 (0.3–3.3) and 3.2 (2.0–5.1)%. Patients within the lowest tertile of vMax showed lower 5-year survival rates compared with the highest tertile (50.6 vs. 82.1%) and also exhibited a higher incidence of infection-related deaths (21.7 vs. 4.0%). Univariate hazard ratio (HR) per standard deviation increase of vMax for all-cause mortality was 0.69 (0.54–0.88) and was even more pronounced for infection-related mortality [HR 0.53 (0.33–0.83)]. Regarding all-cause mortality, multivariate adjustment for eight non-retinal mortality predictors including interleukin-6 did not attenuate the HR relevantly [0.73 (0.54–0.98)]. Arteriolar and venular diameters did not predict all-cause nor cardiovascular and infection-related mortality.

Conclusions
Long-term follow-up of patients on haemodialysis demonstrated the potential of retinal venular dilation capacity for mortality prediction, which was most pronounced for infection-related mortality. In the same cohort, retinal arteriolar and venular diameters showed no predictive value for hard endpoints. Retinal venular dilation but not arteriolar and venular diameters is a valuable diagnostic biomarker for risk prediction in patients with end-stage renal disease and should be considered for monitoring of critically ill patients.
Daily ambulatory remote monitoring system for drug escalation in chronic heart failure with reduced ejection fraction: pilot phase of DAVID-HF study
Authors: Wong Chun Ka , Un Ka Chun , Zhou Mi , Cheng Yangyang , Lau Yuk Ming , Shea Puigi Catherine , Lui Hin Wai , Zuo Ming Liang , Yin Li Xue , Chan Esther W , Wong Ian C K , Sin Simon Wai Ching , Yeung Pauline Pui Ning , Chen Hao , Wibowo Sandi , Wei Tong Li Nikki , Lee Sze Ming , Chow Augustine , Tong Raymond Cheuk Fung , Hai Jojo , Tam Frankie Chor Cheung , Siu Chung Wah 
Published: May 2022

Abstract

Aims
Underutilization of guideline-directed heart failure with reduced ejection fraction (HFrEF) medications contributes to poor outcomes.

Methods and results
A pilot study to evaluate the safety and efficacy of a home-based remote monitoring system for HFrEF management was performed. The system included wearable armband monitors paired with the smartphone application. An HFrEF medication titration algorithm was used to adjust medication daily. The primary endpoint was HFrEF medication utilization at 120 days. Twenty patients (60.5 ± 8.2 years, men: 85%) with HFrEF were recruited. All received angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB)/angiotensin receptor-neprilysin inhibitor (ARNI) at recruitment; 45% received ≥50% maximal targeted dose (MTD) with % MTD of 44.4 ± 31.7%. At baseline, 90 and 70% received beta-adrenergic blocker and mineralocorticoid receptor antagonist (MRA), 35% received ≥50% MTD beta-adrenergic blocker with % MTD of 34.1 ± 29.6%, and 25% received ≥50% MTD MRA with % MTD of 25.0 ± 19.9%. At 120 days, 70% received ≥50% MTD ACEI/ARB/ARNI (P = 0.110) with % MTD increased to 64.4 ± 33.5% (P = 0.060). The proportion receiving ≥50% MTD ARNI increased from 15 to 55% (P = 0.089) with % MTD ARNI increased from 20.6 ± 30.9 to 53.1 ± 39.5% (P = 0.006*). More patients received ≥50% MTD MRA (65 vs. 25%, P = 0.011*) with % MTD MRA increased from 25.0 ± 19.9 to 46.2 ± 28.8% (P = 0.009*). Ninety-five per cent of patients had reduced NT-proBNP with the percentage reduction of 26.7 ± 19.7%.

Conclusion
Heart failure with reduced ejection fraction medication escalation with remote monitoring appeared feasible.
Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants
Authors: Owen Christopher , Wright-Foulkes Dorothy , Alvarez Prisila , Delgado Haidy , Durance Eva C , Wells George F , Poretsky Rachel , Shrestha Abhilasha 
Published: May 2022

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of &gt;0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (P &gt; .05).
Rapid detection of fluoroquinolone residues in aquatic products based on a gold-labeled microwell immunochromatographic assay
Authors: Xiao Jiaxu , Yang Hongfei , Qin Liangni , Liang Jixiang , Li Long , Fan Xiaohui , Peng Dapeng 
Published: May 2022

Abstract

Objectives
Fluoroquinolones (FQs) are widely used in aquaculture, and their residues have caused many problems threatening human health. Here, this study aims to develop a colloidal gold immunochromatographic strip based on gold-labeled microwells to screen the residues of FQs on site.

Materials and methods
The Protein A Magarose Beads affinity chromatography method was adopted to purify the ascites against FQs. By using a strategy of heterologous coating antigen, different coating antigens are applied to detect FQs. The gold-labeled microwell immunochromatographic assay was used to improve the sensitivity of the test strip by the advanced reaction of antigen and antibody.

Results
The antibodies were verified to be of high purity up to 99%, and the titer reached 1:1 024 000. The combination (enoxacin-OVA and the antibody) detected the 4 banned FQs (pefloxacin, PEF; norfloxacin, NOR; lomefloxacin, LOM; ofloxacin, OFL) with the 50% inhibiting concentration (IC50) values ranging from 1.3 to 2.1 ng/mL and cross-reactions ranging from 67.3% to 106.1%. The analysis of spiked crucian carp, silver carp, grass carp, and shrimp samples showed that the limit of detection for PEF, NOR, LOM, and OFL was 4 μg/kg. A comparative study with liquid chromatography tandem mass spectrometry (LC-MS/MS) demonstrated that the assay provided an effective screening tool for the rapid detection of FQs residues.

Conclusions
The results indicated that the test strip can realize full coverage recognition of the 4 banned FQs and has good accuracy, specificity, reproducibility, and stability; therefore, they are more suitable for rapid detection of FQs in aquatic products.
Elevated preoperative CA125 is associated with poor survival in patients with metastatic colorectal cancer undergoing primary tumor resection: a retrospective cohort study
Authors: Huang Jun-Hua , Liu Hua-Shan , Hu Tuo , Zhang Zong-Jin , He Xiao-Wen , Mo Tai-Wei , Wen Xiao-Feng , Lan Ping , Lian Lei , Wu Xian-Rui 
Published: May 2022

Abstract

Background
The impact of the preoperative carbohydrate antigen 125 (CA125) level on the survival of metastatic colorectal cancer (CRC) patients undergoing primary tumor resection (PTR) remains uncertain. The aim of this study was to assess the prognostic value in overall survival (OS) and cancer-specific survival (CSS) between patients with and without an elevated preoperative CA125 level.

Methods
All metastatic CRC patients receiving PTR between 2007 and 2017 at the Sixth Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) were retrospectively included. OS and CSS rates were compared between patients with and without elevated preoperative CA125 levels.

Results
Among 326 patients examined, 46 (14.1%) exhibited elevated preoperative CA125 levels and the remaining 280 (85.9%) had normal preoperative CA125 levels. Patients with elevated preoperative CA125 levels had lower body mass index, lower preoperative albumin level, lower proportion of preoperative chemotherapy, higher carcinoembryonic antigen and carbohydrate antigen 19–9 (CA19–9) levels, poorer differentiation, and more malignant histopathological type than patients with normal preoperative CA125 levels. In addition, patients with elevated preoperative CA125 levels exhibited more advanced pathological T and N stages, more peritoneal metastasis, and more vessel invasion than patients with normal preoperative CA125 levels. Moreover, the primary tumor was more likely to be located at the colon rather than at the rectum in patients with elevated CA125 levels. Both OS and CSS rates in patients with elevated preoperative CA125 levels were significantly lower than those in patients with normal preoperative CA125 levels. Multivariate Cox regression analysis revealed that an elevated preoperative CA125 level was significantly associated with poor prognosis in metastatic CRC patients undergoing PTR. The hazard ratio (HR) in OS was 2.36 (95% confidence interval [CI], 1.67–3.33, P &lt; 0.001) and the HR in CSS was 2.50 (95% CI, 1.77–3.55, P &lt; 0.001). The survival analysis stratified by peritoneal metastasis also demonstrated that patients with elevated preoperative CA125 levels had lower OS and CSS rates regardless of peritoneal metastasis.

Conclusion
Based on an analysis of metastatic CRC patients undergoing PTR, an elevated preoperative CA125 level was associated with poor prognosis, which should be taken into consideration in clinical practice.