bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting TCR sequences for unseen antigen epitopes using structural and sequence features
Authors: Zhang Hongmei , Ji Hongchen , Zhang Chengkai , Qiong Zhang
Published: January 2024

T-cell receptor (TCR) recognition of antigens is fundamental to the adaptive immune response. With the expansion of experimental techniques, a substantial database of matched TCR-antigen pairs has emerged, presenting opportunities for computational prediction models. However, the accurate forecasting of binding affinities for unseen antigen-TCR pairs remains a major challenge. Here, we present Convolutional-Self-Attention TCR (CATCR), a novel framework tailored to enhance the prediction of epitope and TCR interactions. Our approach integrates an encoder that concurrently processes structural and sequential data, utilizing convolutional neural networks (CNNs) to extract peptide features from residue contact matrices, as generated by OpenFold, and a Transformer to encode segment-based coded sequence. We further introduce CATCR-D, a discriminator equipped to assess binding by analyzing structural and sequence features of epitopes and CDR3-β regions. Additionally, the framework comprises CATCR-G, a generative module designed for CDR3-β sequences, which applies the pretrained encoder to deduce epitope characteristics and a Transformer decoder for predicting matching CDR3-β sequences. CATCR-D has shown exemplary feature extraction and generalization, achieving an AUROC of 0.89 on previously unseen epitope-TCR pairs and outperforming four benchmark models by a margin of 17.4%. CATCR-G has demonstrated high precision, recall, and F1 scores, surpassing 95% in BERT-score assessments. Our results indicate that CATCR is an effective tool for the prediction of unseen epitope-TCR interactions, and that incorporating structural insights significantly enhances our understanding of the general rules governing TCR-epitope recognition. The prediction of TCRs for novel epitopes using structural and sequence information is promising, and broadening the repository of experimental TCR-epitope data stands to further improve the precision of epitope-TCR binding predictions.
Nutrient Balance in Small Catchments of the Upland Areas of the Gumara River, Northwestern Ethiopia
Authors: Gezie Melese , Adgo Enyew , Assaye Habtamu , Wassie Alemayehu
Published: January 2024

Nutrient balance analysis provides essential information concerning the current nutrient status of the soils and used to take appropriate nutrient replenishment practices. Nutrient flows were analyzed in Enqulal watershed of Dera district, Northwestern Ethiopia in the cropping season of 2018. Direct measurement and empirical formulas were used to identifying and measuring major inputs and outputs of NPK from different land uses within the catchments. Four nutrient inputs (Mineral fertilizer, Organic fertilizer, Atmospheric deposition and Nitrogen fixation) and five nutrient outputs (Crop yield, Crop residue, Gaseous lose, Leaching and Soil erosion) leaving the catchment were directly measured to calculate the partial and full nutrient balances. The results indicated that with the exception of phosphorus, teff cropland had negative partial N and K balances. The results also showed that the partial nutrient balances in wheat cropland were observed positive only for nitrogen. The full nutrient balances for the major cropland (wheat and teff) were found to be -20.9 kg , -0.7 kg , -37.87 kg ha-1 yr-1 and -61.4 kg ,+11 kg, and -26.7 kg ha-1 yr-1of N, P and K respectively. Generally, negative N and K full balances were found in this study for all land use/land cover. Therefore, the negative nutrient balances observed in cultivated land and other land uses indicated nutrient depletion which leads to land degradation and reduced agricultural productivity. Finally, analysis of the overall finding on nutrient balance implies that there is a need to enhance nutrient management in order to improve productivity and agricultural sustainability.
Core Symptoms of Depression in Chinese Teachers and Comparison between Different Gender and Stage of Teaching: A Network Analysis Approach
Authors: Ma Shumeng , Jia Ning
Published: January 2024

Background Depression, increasingly recognized as a critical factor impacting mental health, notably affects various populations, including teachers. This study aimed to delineate the specific characteristics of depressive symptom networks among Chinese teachers, identify the core symptoms of depression within this demographic, and examine the variations in depressive symptom networks across different genders and teaching stages.Method The study encompassed 1,670 teachers. Depressive symptoms were assessed using the Self-Rating Depression Scale (SDS). Central symptoms were identified through centrality indices. Network stability was examined via a case-dropping procedure.Results “Depressed affect” and “emptiness of life” exhibited the highest centrality values in the network. No significant differences were observed in the network structure and global strength of depression between adolescents of different genders. However, significant differences in the network"s global strength were found between junior and senior high school teachers.Conclusion “Depressed affect” and “emptiness of life” emerged as the most noteworthy depressive symptoms among teachers in China. Paying close attention to these symptoms could potentially alleviate the experiences of depression in this demographic.
Transcriptomic analysis reveals key pathways influenced by HIV-2 Vpx
Authors: Szojka Zsófia Ilona , Kunkli Balázs , Kiarie Irene Wanjiru , Linkner Tamás Richárd , Al-Muffti Aya Shamal , Ahmad Hala , Benkő Szilvia , Tőzsér József , Mahdi Mohamed
Published: January 2024

Background Viral protein X (Vpx) is a unique accessory protein encoded by the genome of the Human immunodeficiency virus type 2 (HIV-2) and lineages of the simian immunodeficiency virus of sooty mangabeys. So far, counteracting the cellular restriction factor SAMHD1 and mediating efficient translocation of viral pre-integration complex have been recognized as key functions of Vpx, however, thorough exploration of its effects on the cellular transcriptome and cytokine milieu have not yet been explored.Methods In this study, we carried out transcriptomic analysis of THP-1 cells and determined differential gene expression induced by HIV-2 Vpx, additionally, we analysed the effect of Vpx expression on secretion of key cytokines in the medium of transfected cells.Results Our findings revealed that wild-type HIV-2 Vpx can significantly alter the expression of genes coding for helicases, zinc finger proteins, chaperons, transcription factors and proteins involved in DNA methylation. Differentially altered genes were involved in negative regulation of viral process; type I interferon signaling pathway; DNA-templated transcription, elongation; positive regulation of interferon-beta production and negative regulation of innate immune response. Moreover, Vpx downregulated genes associated with negative regulation of TGF-β1, resulting in stimulation of its production. Importantly, Vpx was also found to decrease the expression of HIV-1 Tat, possibly through downregulation of a crucial splicing factor required for maturation of Tat.Conclusion Transcriptomic analysis revealed that many cellular pathways were affected by HIV-2 Vpx. Studies on cellular cytokine milieu showed that this accessory protein induced key proinflammatory cytokines. Our study provides important information about the complex role played by HIV-2 Vpx in priming and taming the cellular environment to allow for establishment of the infection.
A Pilot Cross-sectional Study Comparing WHO QOL-BREF and SF-36 Questionnaires in Measuring Health-related Quality After Modified Radical Mastectomy
Authors: Brizawasi Abhijeet , Ghoshal Soumya , Dubhashi Siddharth P.
Published: January 2024

Background
Breast cancer is a significant health issue in India, with a growing number of cases and increasing morbidity associated with treatment. Assessing quality of life (QoL) in breast cancer patients is essential for understanding the impact of the disease and treatment on their well-being.
Objective
This study aimed to assess health-related quality of life (QoL) and the factors influencing it in postmodified radical mastectomy (MRM) patients using the World Health Organization Quality of Life Questionnaire (WHO QOL BREF) and the 36-item short-form survey (SF 36) questionnaires. The feasibility of these tools in the outpatient department (OPD) setting and the time taken to administer them were also compared.
Methods
A cross-sectional survey-based study was conducted in the Department of Surgery, All India Institute of Medical Sciences Nagpur, over two months. A total of 30 patients who underwent MRM for breast carcinoma were included. Sociodemographic information was recorded, and QoL was measured using the WHO QOL BREF and SF-36 questionnaires. The questionnaires were administered in the OPD, and the average time of administration was noted. Statistical analyses were performed to evaluate the correlation between QoL scores and various characteristics of the study population. Results: The overall mean QoL score was greater for the WHO QOL-BREF (65.39) than for the SF-36 (53.41). The social health domain had the highest score in the WHO QOL BREF, while the emotional well-being domain had the highest score in the SF-36. The mean administration time was significantly shorter for the WHO QOL BREF than for the SF-36. No significant correlation was found between QoL scores and patient characteristics, except for a weak association between higher stage and lower SF-36 overall QoL score.
Conclusion
The breast cancer patients in this study reported lower health-related QoL than did the healthy Indian individuals. The WHO QOL BREF and SF-36 questionnaires were feasible for use in the OPD setting, with the WHO QOL BREF requiring less time for administration. However, further research with a larger sample size is needed to explore the factors influencing QoL in this population.
Annotated Hands for Generative Models
Authors: Yang Yue , Gandhi Atith N , Turk Greg
Published: January 2024

Generative models such as GANs and diffusion models have demonstrated impressive image generation capabilities. Despite these successes, these systems are surprisingly poor at creating images with hands. We propose a novel training framework for generative models that substantially improves the ability of such systems to create hand images. Our approach is to augment the training images with three additional channels that provide annotations to any hands in the image. These annotations provide additional structure that coax the generative model to produce higher quality hand images. We demonstrate this approach on two different generative models: a generative adversarial network and a diffusion model. We demonstrate our method both on a new synthetic dataset of hand images and also on real photographs that contain hands. We measure the improved quality of the generated hands through higher confidence in finger joint identification using an off-the-shelf hand detector.
Implications of Blasting-Induced Vibration on the Stability of Hydroelectric Power Tunnel
Authors: Nata Refky Adi , Ren Gaofeng , Tanjung Ardhymanto Am , Muzer Fadhilah , Heriyadi Bambang , Syahmer Verra , Pratama Azri Rizki
Published: January 2024

An adit tunnel is a horizontal opening used for accessing a headrace in a hydroelectric power tunnel. PT. Kerinci Merangin Hidro is actively engaged in the construction of hydropower plants, with a focus on creating two types of tunnels. During blasting activities with a target progress rate of 50 m in a month, high explosives are commonly used between 500 and 600 PCS days. However, this method leads to vibrations that negatively impact tunnel stability, causing the formation of new cracks in walls. Data processing was conducted using Blastware 10.7 instant software, RS2/Phase2 software and the finite element method. The classification of rock masses included the use of the Rock Mass Rating (RMR) and the Q-System. The research results showed that Fair Rock class (III) rocks were identified at the six observation stations based on the classification of rock masses according to RMR 1989. There was a significant decrease in the weight of the rock mass before and after blasting at each station. The safety factor ranged from 1.26 to 6.00. A greater blasting agent weight per delay resulted in increased vibration across the six patterns. The most significant decrease in safety factors occurred only in pattern 6, with the highest tremor recorded at 1.1220 m/s2. Comparing patterns 5 and 6 with the same blasting agent weight per delay of 8.8 kg and equal explosive load of 550 kg showed that the highest decrease in safety factor values occurred in pattern 6. This phenomenon can be attributed to the fact that a shorter delay produces greater vibration than a longer delay time.
Examining apathy prevalence and associated factors among older adults after the Great East Japan Earthquake: A mixed-methods study
Authors: Yamashita Mari , Seino Satoshi , Nofuji Yu , Sugawara Yasuhiro , Okamura Tsuyoshi , Kawakubo Kiyo , Shinkai Shoji , Fujiwara Yoshinori
Published: January 2024

Background
This study aimed to clarify the sense of apathy experienced by older adults residing in areas affected by the Great East Japan Earthquake (GEJE) in 2011 and categorized the factors associated with apathy based on their narratives.
Methods
A triangulation-mixed-method sequential explanatory design was employed. Data were collected using a mail survey among 9754 randomly selected community-dwelling independent adults, aged between 65–84 years, living in Kesennuma City, one of the GEJE-affected areas, in October 2019. Of these, 7845 completed the analysis criteria, and participants who scored ≥ 2 on three apathy items of the Geriatric Depression Scale were considered to have apathy. A thematic analysis was performed on the narrative data obtained to categorize the associated factors.
Results
The mail survey results indicated that apathy had a prevalence of 44.2%. Using data from 30 individuals who demonstrated apathy during the interview, the thematic analysis revealed three types of apathy: (A) Decline, caused by decreased physical and social functioning due to aging or illness; (B) Crisis, caused by major life-changing events, such as bereavement, divorce, unexpected retirement, or disaster; and (C) Carry Over, caused by strained family relationships and stressful social situations during old age.
Conclusions
In addressing apathy, it is important to check for the co-occurrence of depression, life satisfaction, and the availability and utilization of social support.
Long-term Outcomes and Associated factors among Intensive Care Unit Survivors in a Low- income Country: A Multicenter Prospective Cohort study
Authors: Matovu. Ham Wasswa , Sendagire Cornelius , Luggya Tonny Stone , Wabule Agnes , Mukiza Nelson , Prisca Auma , Agaba Peter Kaahwa
Published: January 2024

Background
Post-ICU survivors face higher mortality and often require costly rehabilitation or palliative care, such as occupational therapy, physiotherapy and hospice yet there is a lack of data quantifying the demand for these services, particularly in developing countries like Uganda. Moreover, a critical knowledge gap persists regarding long-term outcomes and predictors among post-ICU survivors. Our study aimed to ascertain the 90-day mortality rate, evaluate functional status, and identify risk factors for mortality among patients discharged from three tertiary hospital ICUs in Uganda.
Methods
We conducted a multicenter prospective cohort study that tracked 121 adult patients discharged from three tertiary hospital intensive care units for three months. Data collection utilized open data kit (ODK) software. Follow-up involved telephone assessments by trained research assistants on days 30, 60, and 90 post-discharge, evaluating vital and physical functional status with the Karnofsky Performance status tool. The study's primary outcomes included mortality at 90 days post-ICU discharge and the physical functional status of ICU survivors. Cox regression analysis using Stata version 15 was used to determine the factors associated with 90-day mortality.
Results
A total of 18/121 died following discharge from the ICU giving a mortality rate of 14.9% (95% CI: 9.5%- 22.5%). Approximately 36.36% achieved a normal physical functional status. Factors associated with 90-day mortality included raised intracranial pressure (HR 1.92, 95% CI 1.763–2.787, p = 0.04), acute kidney injury (HR 4.13, 95% CI 2.163–7.890, p < 0.001) and renal replacement therapy (HR 3.34, 95% CI 2.210–5.060, p < 0.001)
Conclusion
High 90-day mortality is observed in post-ICU patients, particularly those with elevated intracranial pressure, acute kidney injury, and prior renal replacement therapy. The fact that nearly two-thirds of patients fail to attain a normal functional status after 90 days highlights the need for post-ICU rehabilitation services.
Unveiling the digital phenotype: A protocol for a prospective study on physical activity behavior in community-dwelling older adults
Authors: Daniels Kim , Vonck Sharona , Robijns Jolien , Spooren Annemie , Hansen Dominique , Bonnechère Bruno
Published: January 2024

Background.
Physical activity (PA) is a recognized boon for older adults, enhancing their overall well-being and mitigating health risks. Nevertheless, to encourage active lifestyles in this demographic, it is vital to understand the factors influencing PA. Conventional approaches predominantly rely on supervised cross-sectional evaluations, presuming both the stability of PA determinants over time and their isolated components. However, the complex nature of real-life dynamics often involves temporal variability in individual-level determinants. Digital phenotyping (DP), employing data recruited from personal digital devices, enables the continuous, unsupervised and real-time quantification of an individual's behavior within their natural context. This approach offers more ecological and dynamic assessments, revolutionizing our understanding of the intricacies underlying individual PA patterns in their environmental context.
Objective.
This paper aims to design a robust research protocol for the DP of PA behavior among healthy community-dwelling older adults aged 65 and above by employing a novel measurement approach.
Methods.
Observational data will be collected over a two-week period to assess various functions combining both cross-sectional and longitudinal data collection methods. Patterns of PA behavior and factors affecting PA outcomes will be detected in order to identify digital phenotypes related to PA. The measurements are based on the Behavior Change Wheel and include self-reporting and clinical assessments for cross-sectional data collection and ecological momentary assessment as well as time series collection for longitudinal data. The statistical analysis involves machine learning which will handle data complexity. Unsupervised learning will be used to uncover patterns, and supervised learning to identify variables. The analysis will be conducted in RStudio (v3.6.3) with significance set at 0.05.
Discussion.
A novel approach to understanding older adults' PA behavior will be used in this study. Challenges include varying technology adoption, usability, and unproven validity of health tech. Ethical considerations, representativeness, participant engagement, and machine learning expertise are also key aspects of the study's success. This study offers promise in bridging traditional and dynamic assessment methods for older adults' PA behavior to promote active lifestyles.
Trial registration:
Clinical Trials.gov: NCT06094374
Investigation of the Effects of Silymarin and Vitamin C on Kidney Damage and Aquaporin-2 Downregulation in Lithium-Induced Nephrogenic Diabetes Insipidus in Rats
Authors: YAKUT Seda , GENÇER Berrin TARAKÇI , YALÇIN Mehmet Hanifi , AYDIN Süleyman , YÜKSEL Hayati
Published: January 2024

While lithium (LIT) therapy is widely regarded as the primary approach for managing bipolar disorder over the long term, it is also a major contributor to the development of acquired Nephrogenic Diabetes Insipidus (NDI) with prolonged use. This study aimed to examine the protective effects of Silymarin, Vitamin C, and the combined administration of SIL + Vit C against nephrotoxicity induced by NDI resulting from long-term LIT treatment in rats. The groups of rats exposed to LIT were provided with 1 kg of regular commercial chow containing an 80 mmol LiCl supplement for 28 days. Meanwhile, SIL and Vit C were orally administered to rats at a dosage of 200 and 100 mg/kg body weight, respectively, throughout the 28 days. Both the levels of reactive oxygen species (ROS) glutathione (GSH) and malondialdehyde (MDA) were assessed and enzyme activities of superoxide dismutase (SOD) were assessed to determine the protective effect of SIL and Vit C against oxidative stress. Aquaporin-2 (AQP2) levels in kidney tissues were evaluated immunohistochemically and by ELISA method to determine the anti-downregulatory effect. In addition, serum and urine parameters were measured. Lithium-induced nephrotoxicity was characterized by elevated levels of renal toxicity markers and reduced antioxidant enzyme activities. Administration of SIL significantly reduced kidney tissue toxicity markers, increased antioxidant enzyme activities, regulation of physiological parameters in blood and urine, and downregulation of AQP2 in the kidney. However, no significant protective effect against lithium-induced renal toxicity was observed with the administration of Vitamin C. These findings indicate that SIL effectively guards against lithium-induced nephrotoxicity, whereas Vitamin C does not possess this protective effect.
Mechanical influence on the chip formation in wet metal cutting
Authors: Denkena Berend , Bergmann Benjamin , Schenzel Jan
Published: January 2024

Cooling lubricants (CL) are used in various machining processes. In addition to the heat dissipation, influencing the tribological system during metal cutting is a key function. In particular, the thermomechanical load on the cutting wedge is influenced by a change in friction in the secondary shear zone on the rake face. In addition to such tribological effects, the mechanical forces of the fluid jet have a significant effect on chip formation, particularly when a high-pressure supply of CL is used. However, investigating the mechanical effect of CL on chip formation is challenging due to poor accessibility of the chip formation zone. Using a planing test rig and a high-speed camera, it is possible to show that the mechanical force of the CL supply reduces the chip curvature radius and influences deformation of the chip during machining. In particular, it was found that the force of the coolant jet force in the cutting normal direction has a significant effect on reducing the chip curvature radius.
Coherent Mesh Representation for Parallel I/O of Unstructured Polyhedral Meshes
Authors: Weiß R. Gregor , Rusche Henrik , Lesnik Sergey , Galeazzo Flavio C. C. , Ruopp Andreas
Published: January 2024

This paper presents a new mesh data layout for parallel I/O of linear unstructured polyhedral meshes. The new mesh representation infers coherence across entities of different topological dimensions, i.e. grid cells, faces, and points. The coherence due to cell-to-face and face-to-point connectivities of the mesh is formulated as a tree data structure distributed across processors. The mesh distribution across processors creates consecutive and contiguous slices that render an optimized data access pattern for parallel I/O. A file format using the coherent mesh representation, developed and tested with OpenFOAM, enables the usability of the software at unprecedented scales. Further implications of the coherent and sliceable mesh representation arise due to simplifications in partitioning and diminished pre- and post-processing overheads.
Breeding confirmation and habitat utilization of Sooty Shearwater (Ardenna grisea) on Isla de los Estados, Argentina
Authors: Rey Andrea Raya , Balza Ulises , Domato Ignacio , Salom Amira , Pütz Klemens
Published: January 2024

The Sooty Shearwater (Ardenna grisea) is a species facing global decline, nesting on southern hemisphere islands, and migrating to the northern hemisphere during the non-breeding season. This study confirms the species ́ breeding presence on Isla de los Estados in the Fuegian archipelago, Argentina. Additionally, we present a preliminary evaluation of its habitat utilization. Active burrows were found along the northern coast of the island on slopes with dense, stumpy subantarctic forests and beneath or alongside rocky outcrops overlooking the coast. These discoveries provide valuable insights into the population status of the species, offering critical insights that can significantly inform and enhance conservation efforts.
Beamforming-based acoustic mapping characterization
Authors: García-Unzueta Emiliano Ehecatl , Rascon Caleb , Mendez-Monroy Paul Erick
Published: January 2024

This article analyzes the performance of a beamforming-based acoustic mapping model that uses signals captured by a wireless acoustic sensor network (WASN) when environmental and signal capture parameters change. The acoustic mapping process can be described in the stages of: distribution of the WASN in the acoustic environment, acoustic signal capture by the WASN nodes, and acoustic mapping model implementation. The analyzed factors are: processing time, shape of the map, and localization performance in the presence of several acoustic elements. The characterization presented in this work consists on the variation of parameters (such as number of proof points, window length, number of microphones, number of sources, type of sources, presence of noise, acoustic signal frequency composition, etc.) and analyzing its impact on three beamforming techniques that have been recently shown to be able to provide an acoustic map using signals captured by a WASN: Delay-and-Sum (DAS), Minimum Variance Distortionless Response (MVDR), and Phase-Based Binary Masking (PBM). As a result of this analysis, an optimal configuration for the acoustic mapping process can be defined for a selected application: MVDR was shown to be more robust against noise and array geometry, but was slower in processing time than PBM which, in turn, only provided better acoustic maps in specific non-noisy scenarios.
Propagation properties of vortex Hermite cosine-hyperbolic-Gaussian beams in uniaxial crystals orthogonal to the optical axis
Authors: Lazrek M. , Khannous F. , Hricha Z. , Belafhal A.
Published: January 2024

The evolution properties of a vortex Hermite cosine-hyperbolic-Gaussian beam (vHChGB) in uniaxial crystals are investigated. Based on the Huygens–Fresnel diffraction integral, the propagation equation for a vHChGB passing through a uniaxial crystal orthogonal to the optical axis is derived in detail. The propagation features of the intensity of the beam in the uniaxial crystal are analyzed with numerical illustrative examples. It is demonstrated that upon propagation, the anisotropy of the uniaxial crystal influences strongly the beam properties. The output beam is astigmatic, and its intensity distributions are strongly related to the ratio of refractive indices of the crystal and the initial beam structure parameters. This study may provide a convenient way to generate astigmatic vortex hollow beams.
Metabolomics-based Investigation of Primary Biliary Cholangitis: A Cholestatic Liver Disease
Authors: de Oliveira Juliana Magalhães , Lopes Thais de Assis , Castro Alex , Signini Étore De Favari , Catai Aparecida Maria , Ferreira Antonio Gilberto , Cançado Eduardo Luiz Rachid , Oliveira Regina Vincenzi
Published: January 2024

Introduction
Primary Biliary Cholangitis (PBC) is a rare disease that affects the liver. It causes the progressive destruction of the intrahepatic bile ducts, leading to liver fibrosis. Currently, the diagnosis of PBC includes a medical and family history, physical exams, blood tests, imaging tests, and occasionally a liver biopsy. If not promptly treated, PBC progresses to cirrhosis, liver failure, and death.
Objectives
To improve the development of new diagnostic or prognostic methods for PBC, a metabolomic-based study was conducted to evaluate the metabolomic profiles reflected in plasma and urine samples from healthy individuals and PBC patients. This study aimed to gain a better understanding of the underlying pathological mechanisms of PBC.
Methods
Blood plasma and urine samples were collected from 30 female PBC patients and 20 female healthy controls. The study used an untargeted metabolomic approach involving liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). The data was processed using multivariate and univariate statistical methods.
Results
Forty-seven plasma and fifty-six urine metabolites demonstrated statistical differences between PBC patients and healthy controls (p ≤ 0.05). The most significant differences were found in metabolites related to bile acid and lipid metabolism (including phospholipids and fatty acids) and branched-chain amino acids. These findings indicate that metabolomic profiling in plasma and urine can help identify new diagnostic biomarkers for PBC.
Conclusions
The study highlights metabolites linked to fatty acid beta-oxidation, bile acid biosynthesis, and amino acid metabolism as potential candidates for biomarkers in PBC, which can assist further studies for PBC diagnosis and therapeutic monitoring.
Preparation and Application of Novel Power Semiconductor Chips
Authors: Zhiwei Yang , Abas Asim
Published: January 2024

The power semiconductor industry, as the cornerstone of the information industry, has become an important indicator for measuring the technological level and development scale competitiveness of an industry, and is also an indispensable part of the energy industry. In order to promote the development of the semiconductor industry and enhance its innovation capabilities and competitiveness, it is necessary to seize the development opportunities in the semiconductor chip market. Therefore, based on elucidating the development direction of thyristor chip structure design, novel gate-level structures and multilayer semiconductor structures have been designed with the aim of improving the triggering current and dynamic characteristics of thyristor chips.
Do interlocked directors affect the governance of companies?
Authors: Stocco Davide , Barucci Emilio
Published: January 2024

The effect of interlocked directors on the corporate governance of listed companies is not easy to assess: interlocked directors are too busy and may not properly monitor the company but both good and poor practices may propagate through them. Adopting a network approach we show that companies sharing directors have similar governance but no significant effect on the quality of corporate governance is detected. The quality of corporate governance is mostly associated to a large quota of small shareholders, company size, the stake of institutional investors and of the State.
JEL Classification: G34, L14
Phylogenetic relationships of Schistosoma japonicum in evolution
Authors: Nelwan Martin
Published: January 2024

Purpose: In this research, I researched the phylogenetic relationships of Sschistosoma sinensium and Schistosoma japonicum, as well as relationships of East Asia Schistosoma japonicum and Southeast Asia S. japonicum.
Results: The results of nucleotide BLAST showed that Sichuan S. sinensium AF465913.1 shared 72.29% identity with Jiangxi S. japonicum FJ852203.1. E-value is < 0.01. Schistosoma sinesium established S. japonicum in Jiangxi. Jiangxi S. japonicum spread to other parts of China, Japan, Southeast Asia, and Taiwan. It is close to, for example, S. japonicum of Anhui Tongling, Hunan Changde, and Indonesia. In ND1 gene sequences, for example, Jiangxi S. japonicum KP793763.1 shared 100% identity with Hunan Chande S. japonicum KP793756.1, 99.89% identity with Anhui Tonling S. japonicum KP793747.1 and Indonesia S. japonicum KP793779.1. E-values = 0.0. Commonly, Indonesia S. japonicum derived from China, which include Anhui Guichi, Anhui Tongling, Hunan Changde, and Hunan Yueyang. Schistosoma japonicum is close to each other in genetic relationships.
Conclusions: Schistosoma japonicum spread from Jiangxi to other parts of East Asia and to Southeast Asia. The parasite has close genetic relationships.
Operational Sensor Adjustment for Structural Health Monitoring Systems in Wind Turbines using Machine Learning
Authors: Rupfle Johannes , Wondra Bernhard , Nowack Markus
Published: January 2024

The digitalization in structural engineering has significantly amplified the importance of Structural Health Monitoring systems, especially in civil engineering and the renewable energy sector. A monitoring system allows for deep analysis of the structure's health state, can detect anomalies, and also allows for the determination of remaining useful life. Initially, after installation, a monitoring system needs adjustment so that it can be used for various analysis purposes. This paper presents three different methods to fully automatically adjust sensor offsets of tilt, acceleration, and strain data in wind turbine towers. In the first method, we make use of an initiated 360-degree nacelle rotation and its unbalanced rotor weight-induced tower bending. In the second method, uniaxial operational data is collected and binned to form a database for a univariate regression. A third method consists of a biaxial operational data set, allowing for a multivariate regression. The applications of the second and third approaches can be extended to any slender structure under environmental load. The presented workflow also allows for fully automated sensor orientation determination and fault detection due to long-term drift observation of sensor characteristics.
Robustness Evaluation of LSTM-based Deep Learning Models for Bitcoin Price Prediction in the Presence of Random Disturbances
Authors: Kanaparthi Vijaya
Published: January 2024

As Deep Learning (DL) continues to be widely adopted, the growing field of study on the robustness of DL approaches in finance is gaining steam. This paper investigates the robustness of a Recurrent Neural Network (RNN) with Long Short-Term Memory (LSTM) intended for daily closing price predictions of Bitcoin (BTC). The research entails reproducing and adjusting an LSTM design from previous research, with an emphasis on evaluating the robustness of the network. The network is trained using data that has been disturbed by Gaussian noise to assess robustness, and the effect on predictions made outside of the sample is examined. To examine the impact of adding Gaussian noise layers and noisy dense layers on training accuracy and out-of-sample predictions, further robustness tests are conducted. The results show that the LSTM network has remarkable robustness to random disturbances in the data. Nevertheless, the Root Mean Square Error (RMSE) of the prediction increases with the addition of Gaussian noise and noisy dense layers. When random noise is present in the training data, the Autoregressive Integrated Moving Average (ARIMA) model is more vulnerable to it than the LSTM, according to the robustness of the two models. These findings highlight how robustness DL techniques are overall when compared to more conventional linear methods. However, because these models are black-box, the study highlights the significance of comprehensive testing. Although the robustness of the LSTM is impressive, it is important to understand that each network may behave differently depending on the circumstances.
Comprehensive assessment of permafrost carbon emissions indicates need for urgent action to keep Paris Agreement temperature goals within reach
Authors: Treharne Rachael , Gasser Thomas , Rogers Brendan M , Turetsky Merritt R , Schädel Christina , MacDonald Erin , Natali Susan
Published: January 2024

Rapid Arctic warming is thawing carbon-rich permafrost, releasing greenhouse gasses to the atmosphere and accelerating global climate change. Despite the importance of this feedback, permafrost-enabled global-scale models simulate only one mechanism of belowground carbon loss: the gradual, top-down thickening of the seasonally-thawed soil layer. This ignores abrupt permafrost thaw and intensifying fire regimes that result in combustion of soil carbon and fire-induced thaw. Here, we expand a compact Earth system model (OSCAR v3.0) to enable first-order estimates of the impacts of abrupt thaw and wildfire, together with gradual thaw, on remaining carbon budgets consistent with the temperature goals of the Paris Agreement. We find that remaining carbon budgets are reduced by up to 20% for 1.5°C, and up to 22% for 2.0°C. Ensuring that these substantial future emissions are accounted for when developing emissions reductions targets consistent with the Paris agreement presents a timely challenge for scientific and policy communities.
Off-label use of Clomiphene citrate to Treat Anabolic-androgenic Steroid induced Hypogonadism upon cessation among men (CloTASH) - a pilot study protocol
Authors: Havnes Ingrid Amalia , Henriksen Hans Christian Bordado , Johansen Per Wiik , Bjørnebekk Astrid , Neupane Sudan Prasad , Hisdal Jonny , Seljeflot Ingebjørg , Wisløff Christine , Jørstad Marie Lindvik , McVeigh Jim , Jørgensen Anders Palmstrøm
Published: January 2024

Introduction:
Non-prescribed anabolic-androgenic steroid (AAS) use is widespread and may induce hypogonadism, and metabolic, cardiovascular and mental health risks. The study aims to explore feasibility and safety of off-label clomiphene citrate therapy, whether the treatment will reduce the symptoms of androgen deficiency, and to study changes in health risks after cessation.
Methods and analysis:
This is a non-randomized proof of concept pilot study to test the feasibility of an off-label hormone intervention. In this open-labeled intervention study, we shall include males with AAS dependence intending to quit AAS use. Clomiphene citrate will be given for a period of 16 weeks to stimulate the endogenous testosterone production. Measures of physical and mental health will be examined from ongoing AAS use, during the intervention period, and at follow-up 6- and 12-months post-cessation.
Change in self-reported symptoms of hypogonadism (fatigue, depression, anxiety, sexual dysfunction) and other withdrawal symptoms will be compared with data from a group of men who ended AAS use temporarily without any medical intervention.
Discussion:
This pilot study is the first study to test feasibility of off-label use of CC with the intention to restart endogenous testosterone production upon cessation of AAS among men with AAS-induced hypogonadism. The study may provide valuable clinical insights, enabling the exploration of whether adjustments are needed for the intervention. The results may be used to determine the sample size and informing the design of future RCTs or case comparison studies.
Ethics and dissemination:
The study is initiated by investigators, funded by public grants and is approved by the Regional Committee for Medical and Health Research Ethics (REC) in Norway, Norwegian Medicines Agency and the Data Protection Officer for Research at Oslo University Hospital.
Trial registration: EudraCT, EudraCT 2020-005938-15, Registered by Norwegian Medicines Agency 3rd November 2021. https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-005938-15/NO
Navigating Pompe Disease Assessment: A Comprehensive Scoping Review
Authors: Rivera Israel Davila , Campos Letícia Nunes , Alegre Daiana M. Ibañez , González Fabiana N. del Puerto ,   Mónica Garrido San Juan1, Zelcer Federico Fernandez , Borgobello Delfina , Gerk Ayla , Sosa Laura F. , Miretti Marcos M. , Argüelles Carina F. , Stegmann Jorgelina
Published: January 2024

Background
Pompe Disease (PD) is a rare progressive autosomal recessive disorder resulting from deficient acid alpha-glucosidase (GAA) enzyme activity, necessitating timely identification and management. This scoping review aimed to synthesize the evidence regarding assessment methods for screening, diagnosing, and following up PD.
Methods and Results
We searched citations in English and Spanish published from 2017 until February 8, 2022, across 11 databases. We included primary studies, reviews, and guidelines that described at least one assessment method for patients with confirmed clinical, genetic, or biochemical PD. Screening and data extraction adhered to PRISMA-ScR. Data was summarized narratively and with descriptive statistics. After screening 2,139 citations, 96 met the eligibility criteria. Cross-sectional studies were the most prevalent design (28%), while guidelines were the least frequent (1%). Newborn screening availability varied among countries, despite its potential to improve PD prevalence estimations. Overall, 81 articles assessed clinical manifestations, with 47 focusing on late-onset PD. We identified considerable heterogeneity in reporting PD phenotypes. The use of dried blood spots for GAA enzyme deficiency detection was described in 18 articles, but reporting lacked standardization. Next-generation sequencing emerged as the gold standard for identifying mutated alleles. Monitoring strategies for pediatric and adult PD lacked consensus, and only one article assessed quality of life.
Conclusion
This scoping review summarized the evidence to comprehensively evaluate PD patients, emphasizing current practices and existing challenges that must be tackled to optimize screening, diagnosis, and follow-up of PD.
ADİ ORTAKLIĞIN ÜÇÜNCÜ KİŞİLERLE İLİŞKİSİNDE ORTAKLIĞIN TEMSİLİ VE ARABULUCULUĞA BAŞVURU
Authors: Solak Ekrem , Çakır Aytuğ Ceyhun
Published: January 2024

Adi ortaklık, kuruluşunun basit ve hızlı olmasından dolayı uygulaması en fazla olan ortaklık türlerinden biridir. Ancak adi ortaklık, tüzel kişiliği haiz olmadığından, ortaklığın hak ehliyeti bulunmamakta ve borçları ortaklar üzerinde doğmaktadır. Adi ortaklık, ortakların durumu, ortaklığın temsili, hak ve taraf ehliyeti bakımından diğer ortaklık türlerinden ayrılmaktadır. Alternatif uyuşmazlık çözüm yollarından biri olan arabuluculuk, 6325 sayılı Hukuk Uyuşmazlıklarında Arabuluculuk Kanunu ile Türk hukuk sisteminin bir parçası olmuştur. Esasen ihtiyari olan arabuluculuk, zaman içerisinde yapılan birtakım yasal değişiklikler ile bazı uyuşmazlıklar açısından zorunlu hale getirilmiştir. Öte yandan, karakteristik özelliklerinden dolayı adi ortaklığın arabuluculuk sürecinde nasıl temsil edilmesi gerektiği, uygulamada bazı tereddütler doğurmaktadır. Çalışmamızda, adi ortaklığın üçüncü kişilerle ilişkisinde ortaklığın temsili ve arabuluculuğa başvuru konusu ele alınmıştır. Bu kapsamda, Türk hukukunda arabuluculuğun uygulama alanının zamanla genişlemesinden bahsedilmiş ve bu doğrultuda dava şartı olarak düzenlenen zorunlu arabuluculuk hallerine değinilmiştir. Arabuluculuğun temel özelliklerine temas edilerek adi ortaklığın tüzel kişiliğinin bulunmamasının önemi ortaya konmuştur. Bu bağlamda, adi ortaklığın temsili ile ortaklığın üçüncü kişilerle ilişkisinden doğan uyuşmazlıklar dolayısıyla arabuluculuğa başvuru, öğretide yer alan görüşler ve yargı kararlarıyla birlikte değerlendirilmiştir.
How village funds influence economic development in South Papua, Indonesia
Authors: Phoek Inez , Bhaumik Amiya , Isaac Osama , Tjilen Alexander
Published: January 2024

This quantitative study aims to determine the elements that influence the efficiency of village funds in terms of social and economic empowerment. Individualized solutions based on the demographics of the village, including financial support, business partners and markets, human resources, sociocultural ecology, and natural resources, are required for economic development. By collecting data from 179 village heads in South Papua province, Indonesia, this study determines that several elements substantially impact the economic empowerment of communities. However, these factors have not been fully optimized to attain economic independence of villages. With the assistance of regular support from the district government, most village heads are graduates who can effectively plan and implement programs. The distinctive qualities of a community are considered in sociocultural development programs. The development of natural resources and tourism are continuing processes that require market access and infrastructure improvement. Human resources are promising, and sociocultural initiatives align with community requirements. Therefore, addressing the problems associated with market access and resource development is vital. Village funds should promote the use of resources in a sustainable manner; however, there are still obstacles to engaging corporate land users, which calls for further investigation.
IA explicável aplicada para identificar genes influentes na classificação do câncer por meio de dados de expressão gênica de RNA-Seq
Authors: Azevedo Karolayne , Souza Luísa , Dalmolin Matheus , Fernandes Marcelo
Published: January 2024

Este artigo faz uso de três técnicas de aprendizagem de máquina (Machine Learnig – ML) para classificar os cinco tipos de câncer mais recorrentes em mulheres, a partir de dados de expressão gênica de RNA-Seq. Os desafios incluem: alta dimensionalidade do conjunto de dados e a falta de transparência dos modelos de ML. Para mitigar esses problemas, foi utilizado a técnica SHAP (SHapley Additive exPlanations) que e uma técnica de inteligência artificial explicável (Explainable artificial intelligence – XAI) utilizada para compreender como esses modelos tomam decisões podendo ser usada como uma estratégia para a seleção de recursos. Como entrada, foram utilizadas 2.105 amostras, sendo 421 amostras referentes a cada tumor, processadas pelos modelos Arvore de Decisão (Decision Tree- DT), Floresta Aleatoria (Random Forest-RF) e Aumento de Gradiente Extremo (eXtreme Gradient Boosting-XGB) treinadas e validadas por meio da técnica de validação cruzada. Os modelos RF, DT e XGB alcançaram precisões de 99, 40%, 97, 60% e 99, 34%. Posteriormente, a técnica SHAP foi utilizada para obter uma lista de recursos visando compreender quais características influenciaram nas tomadas de decisões dos modelos e consequentemente, nos resultados de predição dos cinco tumores. 122, 90 e 11 genes foram obtidos nos modelos RF, XGB e DT, totalizando 223 resultando em 194 genes únicos.
Segmentação Inteligente de Gorduras em Tomografias Abdominais Visando Recomendações para Combater a Recidiva do Câncer de Mama
Authors: Estellita Neto Carlos , Barros Ana Luiza , Campos Gustavo , Gomes Rafael , Araújo Thelmo , Lima Glaucia , Lima Verde Sara Maria
Published: January 2024

De acordo com o Instituto Nacional do Câncer (INCA), atualmente um dos principais riscos para desenvolvimento de câncer é o excesso de peso corporal. O excesso de gordura ocasiona um estado de inflamação crônica de baixa intensidade, que acarreta um aumento na produção de citocinas inflamatorias de desbalanço de adipocitocinas conduzindo ao estímulo de cascatas carcinogênicas que favorecem o desenvolvimento da doença. A Organização Mundial da Saúde (OMS) destaca também que o excesso de gordura corporal e um importante fator de risco envolvido com a gênese de 13 tipos oncológicos distintos, entre esses o de mama. Ferramentas de processamento de imagens tem sido cada vez mais empregadas no contexto médico, para ajudar na reconstrução de imagens, detecção de anomalias, classificação de doenças, e segmentação de diferentes segmentos anatômicos. Neste contexto, este trabalho apresenta a descrição informal da primeira versão de um programa inteligente para segmentar tecido adiposo subcutâneo e visceral em imagens de tomografia computadorizada de abdomen, a fim de auxiliar profissionais da saúde a desenvolver um plano de recomendações personalizado para aconselhar pessoas a prevenir a recidiva do câncer de mama. O programa integra técnicas de pré-processamento de imagens com uma sequência de várias heurísticas simples, envolvendo as noções de superpixels e de similaridade por vizinhança. Nesta primeira versão, o programa esta produzindo resultados aceitáveis de segmentação de gordura subcutânea, enquanto ainda precisar a ser aprimorados para o caso da segmentação de gordura visceral.