bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global analysis of T-cell groups reveals immunological features and common antigen targets of digestive tract tumors
Authors: Li Xiaoxue , Zhang Yuchao , Guo Shiwei , Wu Zhenchuan , Wang Hailong , Huang Yi , Wang Yue , Qiu Mengni , Lang Jingyu , Xiao Yichuan , Zhu Yufei , Jin Gang , Hu Landian , Kong Xiangyin 
Published: March 2024

Abstract
Background
T cells are key players in the tumor immune microenvironment (TIME), as they can recognize and eliminate cancer cells that express neoantigens derived from somatic mutations. However, the diversity and specificity of T-cell receptors (TCRs) that recognize neoantigens are largely unknown, due to the high variability of TCR sequences among individuals.

Methods
To address this challenge, we applied GLIPH2, a novel algorithm that groups TCRs based on their predicted antigen specificity and HLA restriction, to cluster the TCR repertoire of 1,702 patients with digestive tract cancer. The patients were divided into five groups based on whether they carried tumor-infiltrating or clonal-expanded TCRs and calculated their TCR diversity. The prognosis, tumor subtype, gene mutation, gene expression, and immune microenvironment of these groups were compared. Viral specificity inference and immunotherapy relevance analysis performed for the TCR groups.

Results
This approach reduced the complexity of TCR sequences to 249 clonally expanded and 150 tumor-infiltrating TCR groups, which revealed distinct patterns of TRBV usage, HLA association, and TCR diversity. In gastric adenocarcinoma (STAD), patients with tumor-infiltrating TCRs (Patients-TI) had significantly worse prognosis than other patients (Patients-nonTI). Patients-TI had richer CD8+ T cells in the immune microenvironment, and their gene expression features were positively correlated with immunotherapy response. We also found that tumor-infiltrating TCR groups were associated with four distinct tumor subtypes, 26 common gene mutations, and 39 gene expression signatures. We discovered that tumor-infiltrating TCRs had cross-reactivity with viral antigens, indicating a possible link between viral infections and tumor immunity.

Conclusion
By applying GLIPH2 to TCR sequences from digestive tract tumors, we uncovered novel insights into the tumor immune landscape and identified potential candidates for shared TCRs and neoantigens.
A methodological framework for optimizing the energy consumption of deep neural networks: a case study of a cyber threat detector
Authors: Karamchandani Amit , Mozo Alberto , Gómez-Canaval Sandra , Pastor Antonio 
Published: March 2024

AbstractThe growing prevalence of deep neural networks (DNNs) across various fields raises concerns about their increasing energy consumption, especially in large data center applications. Identifying the best combination of optimization techniques to achieve maximum energy efficiency while maintaining system performance is challenging due to the vast number of techniques available, their complex interplay, and the rigorous evaluation required to assess their impact on the model. To address this gap, we propose an open-source methodological framework for the systematic study of the influence of various optimization techniques on diverse tasks and datasets. The goal is to automate experimentation, addressing common pitfalls and inefficiencies of trial and error, saving time, and allowing fair and reliable comparisons. The methodology includes model training, automatic application of optimizations, export of the model to a production-ready format, and pre- and post-optimization energy consumption and performance evaluation at inference time using various batch sizes. As a novelty, the framework provides pre-configured "optimization strategies" for combining state-of-the-art optimization techniques that can be systematically evaluated to determine the most effective strategy based on real-time energy consumption and performance feedback throughout the model life cycle. As an additional novelty, "optimization profiles" allow the selection of the optimal strategy for a specific application, considering user preferences regarding the trade-off between energy efficiency and performance. Validated through an empirical study on a DNN-based cyber threat detector, the framework demonstrates up to 82% reduction in energy consumption during inference with minimal accuracy loss.
Mineralogy and geochemistry of multi-coloured sapphires at the Portezuelo de Pajas Blancas' deposits, northern Chile: revealing crystal growth processes
Authors: Miranda-Díaz Gustavo , Menzies Andrew , Riveros-Jensen Karl , Heide Gerhard , Bußmann Lena , Härtel Birk , Tagle Roald , Medina Eduardo , Griem Wolfgang 
Published: March 2024

Abstract
Portezuelo de Pajas Blancas' primary metasomatic deposits host sapphires that differ in size, colour, and colour distribution through different lithological units. The discovery of sapphire-bearing secondary aeolian placer deposits enabled a detailed analysis of sapphire types to determine the causes of this heterogeneity. Representative single sapphires from the primary and secondary deposits were analysed using various techniques, including SEM-CL, OM-CL, Micro-XRF, Raman spectroscopy, and polarised transmitted light multi-focus optical microscopy. Based on the results, seven sapphire types were identified according to their colours and colour distribution. Fe and Ti concentrations mainly contribute to the colour and micro-textures occurrence. The primary growth textures include cores, progressive, oscillatory, and diffusion zoning, whereas the secondary alteration features correspond to micro-brecciation, re-arrangement, and overgrowth. Inclusions such as euhedral andalusite, anhedral anhydrite, and anhedral rutile were identified in the sapphires. The formation of Portezuelo de Pajas Blancas sapphires can be divided into five genetic stages: (i) core growth development; (ii) chemical imbalance due to open system behaviour that produces progressive and oscillatory zoning; (iii) low-temperature deformations that produce micro-brecciation; (iv) re-arrangement of pre-formed sapphire fragments and subsequent sapphire overgrowth; (v) diffusion zoning that produce Fe- and Ti-enriched outer rims. In conclusion, the Portezuelo de Pajas Blancas' sapphires were formed through at least five stages of oxidised contact metasomatism at varying temperatures and low pressures, where a heterogeneous forming condition predominates during sapphire formation.

Graphical Abstract
Patient satisfaction and patient-reported outcomes do not vary by BMI class in total hip arthroplasty
Authors: Huffman Nickelas , Pasqualini Ignacio , Redfern Roberta E. , Murray Trevor G. , Deren Matthew E. , Israelite Craig L. , Nelson Charles L. , Van Andel Dave , Cholewa Jason M. , Anderson Mike B. , Klika Alison K. , McLaughlin John P. , Piuzzi Nicolas S. 
Published: March 2024

Abstract
Purpose
Obesity has been identified as a risk factor for postoperative complications in patients undergoing total hip arthroplasty (THA). This study aimed to investigate patient-reported outcomes, pain, and satisfaction as a function of body mass index (BMI) class in patients undergoing THA.

Methods
1736 patients within a prospective observational study were categorized into BMI classes. Pre- and postoperative Hip disability and Osteoarthritis Outcome Score for Joint Replacement (HOOS JR), satisfaction, and pain scores were compared by BMI class using one-way ANOVA.

Results
Healthy weight patients reported the highest preoperative HOOS JR (56.66 ± 13.35) compared to 45.51 ± 14.45 in Class III subjects. Healthy weight and Class III patients reported the lowest (5.65 ± 2.01) and highest (7.06 ± 1.98, p < 0.0001) preoperative pain, respectively. Changes in HOOS JR scores from baseline suggest larger improvements with increasing BMI class, where Class III patients reported an increase of 33.7 ± 15.6 points at 90 days compared to 26.1 ± 17.1 in healthy weight individuals (p = 0.002). Fewer healthy weight patients achieved the minimal clinically important difference (87.4%) for HOOS JR compared to Class II (96.5%) and III (94.7%) obesity groups at 90 days postoperatively. Changes in satisfaction and pain scores were largest in the Class III patients. Overall, no functional outcomes varied by BMI class postoperatively.

Conclusion
Patients of higher BMI class reported greater improvements following THA. While risk/benefit shared decision-making remains a personalized requirement of THA, this study highlights that utilization of BMI cutoff may not be warranted based on pain and functional improvement.
Multiple surgical resections for progressive IDH wildtype glioblastoma—is it beneficial?
Authors: Honeyman Susan Isabel , Owen William J. , Mier Juan , Marks Katya , Dassanyake Sohani N. , Wood Matthew J. , Fairhead Rory , Martinez-Soler Pablo , Jasem Hussain , Yarlagadda Ananya , Roach Joy R. , Boukas Alexandros , Stacey Richard , Apostolopoulos Vasileios , Plaha Puneet 
Published: March 2024

Abstract

Purpose
The role of repeat resection for recurrent glioblastoma (rGB) remains equivocal. This study aims to assess the overall survival and complications rates of single or repeat resection for rGB.

Methods
A single-centre retrospective review of all patients with IDH-wildtype glioblastoma managed surgically, between January 2014 and January 2022, was carried out. Patient survival and factors influencing prognosis were analysed, using Kaplan–Meier and Cox regression methods.

Results
Four hundred thirty-two patients were included, of whom 329 underwent single resection, 83 had two resections and 20 patients underwent three resections. Median OS (mOS) in the cohort who underwent a single operation was 13.7 months (95% CI: 12.7–14.7 months). The mOS was observed to be extended in patients who underwent second or third-time resection, at 22.9 months and 44.7 months respectively (p < 0.001). On second operation achieving > 95% resection or residual tumour volume of < 2.25 cc was significantly associated with prolonged survival. There was no significant difference in overall complication rates between primary versus second (p = 0.973) or third-time resections (p = 0.312). The use of diffusion tensor imaging (DTI) guided resection was associated with reduced post-operative neurological deficit (RR 0.37, p = 0.002), as was use of intraoperative ultrasound (iUSS) (RR 0.45, p = 0.04).

Conclusions
This study demonstrates potential prolongation of survival for rGB patients undergoing repeat resection, without significant increase in complication rates with repeat resections. Achieving a more complete repeat resection improved survival. Moreover, the use of intraoperative imaging adjuncts can maximise tumour resection, whilst minimising the risk of neurological deficit.
Analysis of the treatment of RT2 recessions with a xenogeneic collagen matrix vs. connective tissue graft combined with a coronally advanced flap. A double-blinded randomized clinical trial
Authors: Elena Ruiz-de-Gopegui-Palacios , Miren Vilor-Fernández , Ana-María García-De-La-Fuente , Xabier Marichalar-Mendía , Luis-Antonio Aguirre-Zorzano 
Published: March 2024

Abstract
Objectives
To compare the clinical efficacy in terms of mean root coverage in RT2 recession treated with a coronally advanced flap combined with a xenogeneic collagen matrix versus a connective tissue graft.

Materials and methods
A total of 20 patients were randomized to receive one of two treatments: coronally advanced flap + xenogeneic collagen matrix (test group) and coronally advanced flap + connective tissue graft (control group). Patient-related outcomes measures and professional aesthetic assessment by root esthetic score were performed. A descriptive and analytical statistical analysis of the variables was performed.

Results
At 12 months, the mean root coverage was 56.48% in the test group and 69.72% in the control group (p = 0.048), with a 35% and 40% complete root coverage in the xenogeneic collagen matrix and connective tissue graft, respectively. Test group presented less pain (3.65 vs. 5.2 VAS units) (p = 0.015) and less surgical time (45 vs. 49.15 min) (p = 0.004) than control group.

Conclusion
The use of xenogeneic collagen matrix in RT2 recessions was effective for recession reduction to those obtained using autologous grafts; with the advantage that the duration of surgery and patient morbidity decreased. Therefore, xenogeneic collagen matrix in RT2 recessions could be an alternative to autologous grafts.

Clinical relevance
The use of xenogeneic collagen matrix decreases the surgery time and patient morbidity but connective tissue graft results in significantly better mean root coverage and complete root coverage. Xenogeneic collagen matrix can be used in the treatment of RT2 gingival recessions.

Study registration
NCT 03344315.
Generative AI for pentesting: the good, the bad, the ugly
Authors: Hilario Eric , Azam Sami , Sundaram Jawahar , Imran Mohammed Khwaja , Shanmugam Bharanidharan 
Published: March 2024

AbstractThis paper examines the role of Generative AI (GenAI) and Large Language Models (LLMs) in penetration testing exploring the benefits, challenges, and risks associated with cyber security applications. Through the use of generative artificial intelligence, penetration testing becomes more creative, test environments are customised, and continuous learning and adaptation is achieved. We examined how GenAI (ChatGPT 3.5) helps penetration testers with options and suggestions during the five stages of penetration testing. The effectiveness of the GenAI tool was tested using a publicly available vulnerable machine from VulnHub. It was amazing how quickly they responded at each stage and provided better pentesting report. In this article, we discuss potential risks, unintended consequences, and uncontrolled AI development associated with pentesting.
$$\chi$$-linguistic sets and its application for the linguistic multi-attribute group decision making
Authors: Xian Sidong , Liu Mengnan , Xian Zhiyu , Chai Jiahui , Lu Sicong , Qing Ke 
Published: March 2024

AbstractThe information in the real world often contains many properties such as fuzziness, randomness, and approximation. Although existing linguistic collections attempt to solve these problems, with the emergence of more and more constraints and challenges, this information cannot fully express the problem, leading to an increasing demand for methods that can contain multiple uncertain information. In this paper, we comprehensively consider the various characteristics of information including membership degree, credibility and approximation based on rough sets, and propose the concept of $$\chi$$
χ
-linguistic sets ($$\chi$$
χ
LSs), which depend on original data rather than prior knowledge and effectively solve the problem of incomplete information representation. At the same time, the corresponding theories such as the comparison method and operational rules have also been proposed. Subsequently, we construct a new $$\chi$$
χ
-linguistic VIKOR ($$\chi$$
χ
LVIKOR) method for multi-attribute group decision making (MAGDM) problem with $$\chi$$
χ
LSs, and apply it to the risk assessment of COVID-19. Through comparative analysis, we discuss the effectiveness and superiority of $$\chi$$
χ
LSs.
Time to get your hands dirty: Bricolage or pro-organizational unethical response to entrepreneurial adversity
Authors: Jeong Inseong , Gong Yaping 
Published: March 2024

AbstractAs the business landscape escalates the level of uncertainty and thus profoundly disrupts entrepreneurship, it is crucial to understand risk-taking as a coping strategy for entrepreneurs with limited resources. Past studies have been fragmented: Some researchers have focused on creative risk-taking, whereas others have looked at unethical risk-taking. Little is known about how and when entrepreneurs respond to adversity in either a creative or an expedient manner. We posit that entrepreneurs respond to adversity by using either entrepreneurial bricolage behavior (EBB) or unethical pro-organizational behavior (UPB). Drawing from the emotivational account, we develop each theoretical model of bricolage and UPB to better understand how entrepreneurs’ emotional states play a critical role in their reactions to adversity. We theorize that, and test whether, entrepreneurial adversity is positively related to EBB and increase in EBB over time through increased interest when trait resilience is high. Also, we conceptualize and examine whether entrepreneurial adversity is positively related to UPB and increase in UPB over time through increased anger when trait resilience is low. We conducted a five-month longitudinal study of 100 entrepreneurs (482 observations). Our findings largely corroborated the hypotheses. Our study advances our understanding of entrepreneurs’ risk-taking by showing when and how they respond creatively or unethically.
Graphene Oxide Treated by Temperature with Enhancement of Adsorption for Organic Pollutants and Catalytic Degradation with Hydrogen Peroxide
Authors: Lu Kui , Zhu Mengxiang , Ding Tao , Chen Junjie , Yue Dongting , Liu Xing , Fang Xiaoqin , Xia Junfang , Qin Zhiyuan , Wu Minghong , Shi Guosheng 
Published: March 2024

AbstractGraphene oxide (GO) has been used in the range of organic pollutants adsorption and degradation. It’s important to improve the performance of GO in the treatment of organic pollutants. Here, we found that the organic pollutants were more efficiently removed in the catalytic degradation of hydrogen peroxide (H2O2) after being pre-adsorbed with GO. The performance of GO in degrading organic pollutants firstly enhanced and then weakened as the treated temperature increases in the air. The adsorption ability of GO for organic pollutants and catalytic activity of H2O2 were highest at 500 ℃, which can be ascribed to the highest oxygen-containing functional groups and the lowest defects on GO after 500 ℃ treatment in the air. This finding will improve the understanding and application of GO in organic pollutants treatment.
Graphical Abstract
An aligned corpus of Spanish bibles
Authors: Sierra Gerardo , Bel-Enguix Gemma , Díaz-Velasco Ameyali , Guerrero-Cerón Natalia , Bel Núria 
Published: March 2024

AbstractWe present a comprehensive and valuable resource in the form of an aligned parallel corpus comprising translations of the Bible in Spanish. Our collection encompasses a total of eleven Bibles, originating from diverse centuries (XVI, XIX, XX), various religious denominations (Protestant, Catholic), and geographical regions (Spain, Latin America). The process of aligning the verses across these translations has been meticulously carried out, ensuring that the content is organized in a coherent manner. As a result, this corpus serves as a useful convenient resource for various linguistic analyses, including paraphrase detection, semantic clustering, and the exploration of biases present within the texts. To illustrate the utility of this resource, we provide several examples that demonstrate how it can be effectively employed in these applications.
Climate change impacts on rainfall intensity–duration–frequency curves in local scale catchments
Authors: Xu Muyuan , Bravo de Guenni Lelys , Córdova José Rafael 
Published: March 2024

AbstractThe increasing intensity and frequency of rainfall events, a critical aspect of climate change, pose significant challenges in the construction of intensity–duration–frequency (IDF) curves for climate projection. These curves are crucial for infrastructure development, but the non-stationarity of extreme rainfall raises concerns about their adequacy under future climate conditions. This research addresses these challenges by investigating the reasons behind the IPCC climate report’s evidence about the validity that rainfall follows the Clausius-Clapeyron (CC) relationship, which suggests a 7% increase in precipitation per 1 °C increase in temperature. Our study provides guidelines for adjusting IDF curves in the future, considering both current and future climates. We calculate extreme precipitation changes and scaling factors for small urban catchments in Barranquilla, Colombia, a tropical region, using the bootstrapping method. This reveals the occurrence of a sub-CC relationship, suggesting that the generalized 7% figure may not be universally applicable. In contrast, our comparative analysis with Illinois, USA, an inland city in the north temperate zone, shows adherence to the CC relationship. This emphasizes the need for local parameter calculations rather than relying solely on the generalized 7% figure.
Strategic behaviour and decision making in competitive hospital markets: an experimental investigation
Authors: Han Johann , Kairies-Schwarz Nadja , Vomhof Markus 
Published: March 2024

AbstractWe investigate quality provision and the occurrence of strategic behaviour in competitive hospital markets where providers are assumed to be semi-altruistic towards patients. For this, we employ a laboratory experiment with a hospital market framing. Subjects decide on the quality levels for one of three competing hospitals respectively. We vary the organizational aspect of whether quality decisions within hospitals are made by individuals or teams. Realized monetary patient benefits go to real patients outside the lab. In both settings, we find that degrees of cooperation quickly converge towards negative values, implying absence of collusion and patient centred or competitive quality choices. Moreover, hospitals treat quality as a strategic complement and adjust their quality choice in the same direction as their competitors. The response magnitude for team markets is weaker; this is driven by non-cooperative or altruistic teams, which tend to set levels of quality that are strategically independent.
Strong Convergent Inertial Two-subgradient Extragradient Method for Finding Minimum-norm Solutions of Variational Inequality Problems
Authors: Opeyemi Alakoya Timilehin , Temitope Mewomo Oluwatosin 
Published: March 2024

AbstractIn 2012, Censor et al. (Extensions of Korpelevich’s extragradient method for the variational inequality problem in Euclidean space. Optimization 61(9):1119–1132, 2012b) proposed the two-subgradient extragradient method (TSEGM). This method does not require computing projection onto the feasible (closed and convex) set, but rather the two projections are made onto some half-space. However, the convergence of the TSEGM was puzzling and hence posted as open question. Very recently, some authors were able to provide a partial answer to the open question by establishing weak convergence result for the TSEGM though under some stringent conditions. In this paper, we propose and study an inertial two-subgradient extragradient method (ITSEGM) for solving monotone variational inequality problems (VIPs). Under more relaxed conditions than the existing results in the literature, we prove that proposed method converges strongly to a minimum-norm solution of monotone VIPs in Hilbert spaces. Unlike several of the existing methods in the literature for solving VIPs, our method does not require any linesearch technique, which could be time-consuming to implement. Rather, we employ a simple but very efficient self-adaptive step size method that generates a non-monotonic sequence of step sizes. Moreover, we present several numerical experiments to demonstrate the efficiency of our proposed method in comparison with related results in the literature. Finally, we apply our result to image restoration problem. Our result in this paper improves and generalizes several of the existing results in the literature in this direction.