bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crack-free high-aspect ratio holes in glasses by top–down percussion drilling with infrared femtosecond laser GHz-bursts
Authors: Balage Pierre , Lopez John , Bonamis Guillaume , Hönninger Clemens , Manek-Hönninger Inka 
Published: December 2022

Abstract
We report novel results on top-down percussion drilling in different glasses with femtosecond laser GHz-bursts. Thanks to this particular regime of light–matter interaction, combining non-linear absorption and thermal cumulative effects, we obtained crack-free holes of aspect ratios exceeding 30 in sodalime and 70 in fused silica. The results are discussed in terms of inner wall morphology, aspect ratio and drilling speed.
Home-made pulse magnet power supply for magnetizing permanent magnets and magnetic measurements
Authors: Sakon Takuo , Kitagawa Kazunari , Miyaoku Takumi 
Published: December 2022

Abstract
In this article, we propose a home-made pulse magnetic field generation system constructed using a thyristor and large capacitance capacitors to generate high magnetic fields to investigate magnetic properties and magnetize the magnet and high-performance magnetic materials at room temperature. The proposed system produced a magnetic induction (magnetic field) μ
0
H of 15.6 T with the 33.6 mF capacitor and an excitation voltage of 600 V. Further, we designed a new power supply system and a pulse magnet using the commercially available pulse magnet and power supply. We found that the duration time of the magnetic fields (t
d) and the generated magnetic fields were three and four times larger than those for a conventional system, respectively. We also performed magnetization of a NEOMAX permanent magnet; the coercivity (Β
CJ) was 2.0 T, and the magnetization saturated at ∼4.0 T. These results suggest that we can magnetise a permanent magnet such as NEOMAX with strong magnetic fields using this system. Further, the magnetic measurements of these magnets can be performed as well. The merit of our system is that the capacitance of the capacitor bank is larger than that of other studies or general commercial power supplies. Therefore, relatively high magnetic fields with long duration time can be generated. We also performed experiments on the magnetization process (M-H) of Gd to investigate the magnetocaloric effect in high magnetic fields. The magnetic entropy change was comparable to the result of former investigation. We believe that our research can contribute to the development of permanent magnets and magnetic materials for scientific and industrial use because our system allows the generation of strong magnetic fields at room temperature.
Boost invariant polynomials for efficient jet tagging
Authors: Munoz Jose M , Batatia Ilyes , Ortner Christoph 
Published: December 2022

Abstract
Given the vast amounts of data generated by modern particle detectors, computational efficiency is essential for many data-analysis jobs in high-energy physics. We develop a new class of physically interpretable boost invariant polynomial (BIP) features for jet tagging that achieves such efficiency. We show that, for both supervised and unsupervised tasks, integrating BIPs with conventional classification techniques leads to models achieving high accuracy on jet tagging benchmarks while being orders of magnitudes faster to train and evaluate than contemporary deep learning systems.
Deciding Between Contradicting Norms: Rights-Based Law vs. Duty-Based Law and Their Social Ramifications
Authors: Porat Benjamin 
Published: December 2022

Abstract
The concept of rights stands at the very center of our legal universe. An imaginary alternative legal universe might have similar legal norms to ours, except that they are centered on the concept of duty. Is there any significant difference between these two legal universes? The Hohfeldian assumption of complete correlativity between rights and duties might imply that the difference between these two universes is merely a matter of rhetoric. This Article, however, argues that a rights-based legal world would presumably be significantly different from a legal world based upon duties. For this purpose, the Article examines the way in which contradictory norms are resolved. A rights-based system decides cases of contradictory norms according to a process that is different from that used by a duty-based system. The Article is devoted to examining the roots of this difference, its significance and its social implications. Alongside the discussion of the classical and modern legal sources from the Western legal tradition, the Article contains a comparative discussion of Jewish law sources, which demonstrates a typical example of a duty-based legal system.
Nucleotide augmentation for machine learning-guided protein engineering
Authors: Minot Mason , Reddy Sai T 
Published: December 2022

Abstract

Summary
Machine learning-guided protein engineering is a rapidly advancing field. Despite major experimental and computational advances, collecting protein genotype (sequence) and phenotype (function) data remains time- and resource-intensive. As a result, the quality and quantity of training data are often a limiting factor in developing machine learning models. Data augmentation techniques have been successfully applied to the fields of computer vision and natural language processing; however, there is a lack of such augmentation techniques for biological sequence data. Towards this end, we develop nucleotide augmentation (NTA), which leverages natural nucleotide codon degeneracy to augment protein sequence data via synonymous codon substitution. As a proof of concept for protein engineering, we test several online and offline augmentation implementations to train machine learning models with benchmark datasets of protein genotype and phenotype, revealing performance gains on par and surpassing benchmark models using a fraction of the training data. NTA also enables substantial improvements for classification tasks under heavy class imbalance.

Availability and implementation
The code used in this study is publicly available at https://github.com/minotm/NTA

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets
Authors: Falola Oluwadamilare , Adam Yagoub , Ajayi Olabode , Kumuthini Judit , Adewale Suraju , Mosaku Abayomi , Samtal Chaimae , Adebayo Glory , Emmanuel Jerry , Tchamga Milaine S S , Erondu Udochukwu , Nehemiah Adebayo , Rasaq Suraj , Ajayi Mary , Akanle Bola , Oladipo Olaleye , Isewon Itunuoluwa , Adebiyi Marion , Oyelade Jelili , Adebiyi Ezekiel 
Published: December 2022

Abstract

Motivation
Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into research insights and clinical benefits such as the effectiveness of strategies for disease screening, treatment and prevention. However, the setup of pGWAS (pGWAS) tools can be quite complicated, and it mostly requires big data. The challenge however is, scientists are required to have sufficient experience with several of these technically complex and complicated tools in order to complete the pGWAS analysis.

Results
We present SysBiolPGWAS, a pGWAS web application that provides a comprehensive functionality for biologists and non-bioinformaticians to conduct several pGWAS analyses to overcome the above challenges. It provides unique functionalities for analysis involving multi-omics datasets and visualization using various bioinformatics tools. SysBiolPGWAS provides access to individual pGWAS tools and a novel custom pGWAS pipeline that integrates several individual pGWAS tools and data. The SysBiolPGWAS app was developed to be a one-stop shop for pGWAS analysis. It targets researchers in the area of the human genome and performs its analysis mainly in the autosomal chromosomes.

Availability and implementation
SysBiolPGWAS web app was developed using JavaScript/TypeScript web frameworks and is available at: https://spgwas.waslitbre.org/. All codes are available in this GitHub repository https://github.com/covenant-university-bioinformatics.
Optimal bail-out and complication management strategies in protected high-risk percutaneous coronary intervention with the Impella
Authors: Sinning Jan-Malte , Ibrahim Karim , Schröder Jörg , Sef Davorin , Burzotta Francesco 
Published: December 2022

Abstract
Despite the routine use of percutaneous mechanical circulatory support (pMCS) with the Impella heart pump, vascular and bleeding complications may occur during removal with or without pre-closure. To safely close the large-bore access (LBA), post-hoc selection of the appropriate treatment of vascular complications is critical to patient recovery and survival. Femoral artery access is typically utilized for LBA, and percutaneous axillary artery access is a common alternative, especially in the instance of severe peripheral artery disease. Optimization of patient outcomes and efficiency of pMCS can be achieved with adequate arterial access using state-of-the-art techniques. Impella removal techniques with or without pre-closure will be addressed as well as the management of large-bore femoral access complications. In addition, treatment strategies to manage patient deterioration during a protected high-risk percutaneous coronary intervention will be provided.
Organic and inorganic nutrients modulate taxonomic diversity and trophic strategies of small eukaryotes in oligotrophic oceans
Authors: Villiot Naomi , Maas Amy E , Poulton Alex J , Blanco-Bercial Leocadio 
Published: December 2022

AbstractAs the oligotrophic gyres expand due to global warming, exacerbating resource limitation impacts on primary producers, predicting changes to microbial assemblages and productivity requires knowledge of the community response to nutrient availability. This study examines how organic and inorganic nutrients influence the taxonomic and trophic composition (18S metabarcoding) of small eukaryotic plankton communities (&lt; 200 µm) within the euphotic zone of the oligotrophic Sargasso Sea. The study was conducted by means of field sampling of natural microbial communities and laboratory incubation of these communities under different nutrient regimes. Dissimilarity in community composition increased along a depth gradient, with a homogeneous protist community within the mixed layer and distinct microbial assemblages at different depths below the deep chlorophyll maximum. A nutrient enrichment assay revealed the potential of natural microbial communities to rapidly shift in composition in response to nutrient addition. Results highlighted the importance of inorganic phosphorus availability, largely understudied compared to nitrogen, in constraining microbial diversity. Dissolved organic matter addition led to a loss of diversity, benefiting a limited number of phagotrophic and mixotrophic taxa. Nutrient history of the community sets the physiological responsiveness of the eukaryotic community to changing nutrient regimes and needs to be considered in future studies.
Watching Living Cells in Action in the Exocrine Pancreas: The Palade Prize Lecture
Authors: Petersen Ole H 
Published: December 2022

Abstract
George Palade’s pioneering electron microscopical studies of the pancreatic acinar cell revealed the intracellular secretory pathway from the rough endoplasmic reticulum at the base of the cell to the zymogen granules in the apical region. Palade also described for the first time the final stage of exocytotic enzyme secretion into the acinar lumen. The contemporary studies of the mechanism by which secretion is acutely controlled, and how the pancreas is destroyed in the disease acute pancreatitis, rely on monitoring molecular events in the various identified pancreatic cell types in the living pancreas. These studies have been carried out with the help of high-resolution fluorescence recordings, often in conjunction with patch clamp current measurements. In such studies we have gained much detailed information about the regulatory events in the exocrine pancreas in health as well as disease, and new therapeutic opportunities have been revealed.
Nomogram for predicting overall survival time of patients with stage IV colorectal cancer
Authors: Lv Min-Yi , Chen Xi-Jie , Chen Jun-Guo , Zhang Bin , Lin Yan-Yun , Huang Tian-Ze , He De-Gao , Wang Kai , Chi Zeng-Jie , Hu Jian-Cong , He Xiao-Sheng 
Published: December 2022

Abstract

Background
Prognosis varies among stage IV colorectal cancer (CRC). Our study aimed to build a robust prognostic nomogram for predicting overall survival (OS) of patients with stage IV CRC in order to provide evidence for individualized treatment.

Method
We collected the information of 16,283 patients with stage IV CRC in the Surveillance, Epidemiology, and End Results (SEER) database and then randomized these patients in a ratio of 7:3 into a training cohort and an internal validation cohort. In addition, 501 patients in the Sixth Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) database were selected and used as an external validation cohort. Univariate and multivariate Cox analyses were used to screen out significant variables for nomogram establishment. The nomogram model was assessed using time-dependent receiver-operating characteristic curve (time-dependent ROC), concordance index (C-index), calibration curve, and decision curve analysis. Survival curves were plotted using the Kaplan–Meier method.

Result
The C-index of the nomogram for OS in the training, internal validation, and external validation cohorts were 0.737, 0.727, and 0.655, respectively. ROC analysis and calibration curves pronounced robust discriminative ability of the model. Further, we divided the patients into a high-risk group and a low-risk group according to the nomogram. Corresponding Kaplan–Meier curves showed that the prediction of the nomogram was consistent with the actual practice. Additionally, model comparisons and decision curve analysis proved that the nomogram for predicting prognosis was significantly superior to the tumor-node-metastasis (TNM) staging system.

Conclusions
We constructed a nomogram to predict OS of the stage IV CRC and externally validate its generalization, which was superior to the TNM staging system.
Abdominal trachelectomy in a case of cervical myoma as a fertility sparing surgery
Authors: Gari Abdulrahim , Alrajhi Balqes F 
Published: December 2022

Abstract
Cervical leiomyoma is considered a rare pathology with limited treatment options especially if preserving fertility is a concern. Traditional fertility-preserving surgery such as myomectomy has been the mainstay of management if it is possible (Ferrari F, Forte S, Valenti G, Ardighieri L, Barra F, Esposito V, et al. Current treatment options for cervical leiomyomas: a systematic review of literature. Medicina (Kaunas) 2021;57:1–15). Trachelectomy was described as fertility-preserving surgery in patients with early-stage cervical cancer. However, recent studies manage patients with trachelectomy for benign pathology and suggest that; it as an alternative option that otherwise will be treated as hysterectomy (Ferrari F, Forte S, Valenti G, Ardighieri L, Barra F, Esposito V, et al. Current treatment options for cervical leiomyomas: a systematic review of literature. Medicina (Kaunas) 2021;57:1–15). A 33-year-old female, Para 3, referred to a gynecology clinic with a history of heavy menstrual flow, pelvic pain and pressure symptoms. She is known case of fibroid uterus however after having done pelvic MRI with contrast it confirmed the diagnosis of cervical myoma, measured 10 cm × 10 cm, which is intraoperatively managed by trachelectomy as a fertility preservation surgery. The surgery was complicated by ureterovaginal fistula, which was managed with a DJ stent conservatively. Cervical myoma is a rare pathology, and trachelectomy should be considered as an option for a woman who wants to preserve her fertility. Complication and obstetrical outcome should be discussed with the patient; hence, more studies are needed to address the management of cervical myoma, surgical complications and outcome of this procedure, especially in a benign condition.
Context-dependent variation in innovation as a function of urbanization in a songbird
Authors: Weaver Melinda , McGraw Kevin J 
Published: December 2022

Abstract
Recent human-induced transformations to the environment are significantly impacting wild animal populations. Whereas some animals thrive due to these changes, others are being extinguished. Many studies have attempted to identify behavioural traits (e.g. personality, diet versatility, cognition) that allow some animals to succeed in human-dominated landscapes, but few have studied multiple traits or environmental contexts concurrently, despite the fact that different environments may require different types of behavioural performance. We presented house finches (Haemorhous mexicanus) captured from urban, suburban, and rural sites with two different environmental problems to solve (escaping from a confinement and finding food in multiple feeding structures) and measured the success and speed of solving the challenge as well as activity levels and stress behaviours of the birds. We found that urban birds were better at solving the escape challenge, but there was no difference in finding a hidden food source. In addition, we found that birds who solved the escape challenge were more active than those who did not solve this problem, although we observed no such behavioural difference in the food challenge. These results indicate that, because problem-solving challenges can vary across environments, certain types of innovation may be prioritized over others in urban-dwelling species.
Estimated excretion and clearance of uric acid as optimal surrogate indices for daily urinary uric acid excretion
Authors: Tsutani Hiroshi , Otsuki Nozomi , Mitsuke Yasuhiko , Ueda Takanori 
Published: December 2022

ABSTRACT

Objectives
Daily uric acid excretion (Eua) is an essential index for patients with gout/hyperuricaemia. We identified alternative indices most correlated with 24-hour uric acid clearance (Cua 24 h) and 24-hour Eua (Eua 24 h) using data from the reference interval of urinary clearance and excretion of urate study.

Methods
The subjects were indoor workers aged 20–65 years who met the Clinical and Laboratory Standards Institute Guidelines C28-A3c. Alternative indices using spot urine were urine uric acid creatinine ratio, Cua—creatinine clearance ratio (Cua/Ccr), Eua—CCr ratio (Eua/Ccr), estimated Cua (eCua), and estimated Eua (eEua). eCua and eEua are the values obtained by multiplying Cua/Ccr and Eua/Ccr with the estimated glomerular filtration rate.

Results
The final number of subjects analysed was 739. Among the indices using spot urine, eCua and eEua showed the highest correlation with Cua 24 h and Eua 24 h, respectively. Compared with Cua 60 min and Eua 60 min obtained from 60-min urine collection, eCua and eEua showed lower root means squared error, lower bias, and significantly higher accuracy of within 30% and within 15%.

Conclusions
The newly proposed eCua and eEua may be appropriate from a practical perspective.
Nation-wide cohort study of remission induction therapy using rituximab in Japanese patients with antineutrophil cytoplasmic antibody–associated vasculitis: Effectiveness and safety in the first 6 months
Authors: Nagasaka Kenji , Amano Koichi , Dobashi Hiroaki , Nagafuchi Hiroko , Sada Ken-Ei , Komagata Yoshinori , Yamamura Masahiro , Kato Masaru , Endo Tomomi , Nakaya Izaya , Takeuchi Tsutomu , Murakawa Yohko , Sugihara Takahiko , Saito Masaya , Hayashi Taichi , Furuta Shunsuke , Tamura Naoto , Karasawa Kazunori , Banno Shogo , Endo Shuichiro , Majima Masako , Kaname Shinya , Arimura Yoshiriro , Harigai Masayoshi 
Published: December 2022

ABSTRACT

Objectives
The aim of this article is to evaluate the effectiveness and safety of rituximab (RTX) for microscopic polyangiitis and granulomatosis with polyangiitis in Japan.

Methods
In this prospective observational study, all patients with microscopic polyangiitis and granulomatosis with polyangiitis administered RTX were enrolled at each institution. During the observation period of 2 years, data up to 6 months were analysed. Cox proportional hazards analysis was used to assess the factors associated with an outcome.

Results
Of the 75 patients who received RTX for remission induction therapy, 53 achieved remission by the sixth month and 50 were in remission at the sixth month. During therapy, 39 serious adverse events were observed in 24 patients, 21 serious infections in 16 patients, and 9 patients died. No factors were associated with remission; however, there was a significant difference between patients with and without remission in serious adverse events (22.6% vs. 54.5%), serious infections (11.3% vs. 45.4%), and death (1.9% vs. 36.4%). The hazard ratio (95% confidence interval) for serious infection was 3.49 (1.29–9.74) for patients aged ≥ 75 years and 3.53 (1.31–9.53) for pulmonary complications. Four patients maintained remission for 6 months.

Conclusions
The effectiveness and safety of RTX for microscopic polyangiitis and granulomatosis with polyangiitis for up to 6 months was demonstrated.
Discovery of novel thyrointegrin αvβ3 antagonist fb-PMT (NP751) in the management of human glioblastoma multiforme
Authors: Godugu Kavitha , Hay Bruce A , Glinsky Gennadi V , Mousa Shaker A 
Published: December 2022

AbstractBackgroundThyrointegrin αvβ3 receptors are unique molecular cancer therapeutic targets because of their overexpression on cancer and rapidly dividing blood vessel cells compared and quiescent on normal cells. A macromolecule, TriAzole Tetraiodothyroacetic acid (TAT) conjugated to polyethylene glycol with a lipophilic 4-fluorobenyl group (fb-PMT and NP751), interacts with high affinity (0.21 nM) and specificity with the thyrointegrin αvβ3 receptors on the cell surface without nuclear translocation in contrast to the non-polymer conjugated TAT.MethodsThe following in vitro assays were carried out to evaluate NP751 including binding affinity to different integrins, transthyretin (TTR)-binding affinity, glioblastoma multiforme (GBM) cell adhesion, proliferation assays, nuclear translocations, chorioallantoic membrane model of angiogenesis, and microarray for molecular mechanisms. Additionally, in vivo studies were carried out to evaluate the anticancer efficacy of NP751, its biodistribution, and brain GBM tumor versus plasma levels kinetics.ResultsNP751 demonstrated a broad spectrum of antiangiogenesis and anticancer efficacy in experimental models of angiogenesis and xenografts of human GBM cells. Tumor growth and cancer cells’ viability were markedly decreased (by &gt; 90%; P &lt; .001) in fb-PMT-treated U87-luc or 3 different primary human GBM xenograft-bearing mice based on tumor in vivo imaging system (IVIS) imaging and histopathological examination, without relapse upon treatment discontinuation. Additionally, it effectively transports across the blood-brain barrier via its high-affinity binding to plasma TTR with high retention in brain tumors. NP751-induced effects on gene expression support the model of molecular interference at multiple key pathways essential for GBM tumor progression and vascularization.Conclusionsfb-PMT is a potent thyrointegrin αvβ3 antagonist with potential impact on GBM tumor progression.