bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic polymorphisms in innate immunity genes influence predisposition to tick-borne encephalitis
Authors: Fortova Andrea , Barkhash Andrey V. , Pychova Martina , Krbkova Lenka , Palus Martin , Salat Jiri , Ruzek Daniel 
Published: October 2023

AbstractTick-borne encephalitis (TBE) is a neuroviral disease that ranges in severity from a mild febrile illness to a severe and life-threatening meningoencephalitis or encephalomyelitis. There is increasing evidence that susceptibility to tick-borne encephalitis virus (TBEV)-induced disease and its severity are largely influenced by host genetic factors, in addition to other virus- and host-related factors. In this study, we investigated the contribution of selected single nucleotide polymorphisms (SNPs) in innate immunity genes to predisposition to TBE in humans. More specifically, we investigated a possible association between SNPs rs304478 and rs303212 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 1 (IFIT1), rs7070001 and rs4934470 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 2 (IFIT2), and RIG-I (Retinoic acid-inducible gene I) encoding gene DDX58 rs311795343, rs10813831, rs17217280 and rs3739674 SNPs with predisposition to TBE in population of the Czech Republic, where TBEV is highly endemic. Genotypic and allelic frequencies for these SNPs were analyzed in 247 nonimmunized TBE patients and compared with 204 control subjects. The analysis showed an association of IFIT1 rs304478 SNP and DDX58 rs3739674 and rs17217280 SNPs with predisposition to TBE in the Czech population indicating novel risk factors for clinical TBE but not for disease severity. These results also highlight the role of innate immunity genes in TBE pathogenesis.
A novel Hybrid XGBoost Methodology in Predicting Penetration Rate of Rotary Based on Rock-Mass and Material Properties
Authors: Kazemi Mohammad Mirzehi Kalate , Nabavi Zohre , Armaghani Danial Jahed 
Published: October 2023

AbstractPredicting the drill penetration rate is a fundamental requirement in mining operations, profoundly impacting both the cost-effectiveness of mining activities and strategic mine planning. Given the intricate web of factors influencing rotary drilling performance, the necessity for advanced modeling techniques becomes evident. To this end, the hybrid extreme gradient boosting (XGBoost) was utilized to gauge the penetration rate of rotary drilling machines, utilizing random search, grid search, Harris Hawk optimization (HHO), and the dragonfly algorithm (DA) as metaheuristic algorithms. Our research draws from extensive data collected in copper mine case studies, encompassing both field and investigational data. This dataset incorporates critical material properties, such as tensile strength (TS), uniaxial compressive strength (UCS), as well as vital rock-mass characteristics including joint direction (JD), joint spacing (JS), and bit diameter (D). Our investigation evaluates the reliability of these prediction methods using various performance indicators, including mean absolute error (MAE), root mean square error (RMSE), average absolute relative error (AARE), and coefficient of determination (R2). The multivariate analysis reveals that the HHO-XGB model stands out, demonstrating superior prediction accuracy (MAE: 0.457; RMSE: 2.19; AARE: 2.29; R2: 0.993) compared to alternative models. Furthermore, our sensitivity analysis emphasizes the substantial impact of uniaxial compressive strength and tensile strength on the drill penetration rate. This underlines the importance of considering these material properties in mining operations. In conclusion, our research offers robust models for forecasting the penetration rate of similar rock formations, providing invaluable insights that can significantly enhance mining operations and planning processes.
Adoption of ISO/TS 12913-2:2018 Protocols for Data Collection From Individuals in Soundscape Studies: an Overview of the Literature
Authors: Aletta Francesco , Torresin Simone 
Published: October 2023

Abstract
Purpose of Review
The article reviews the literature on soundscape studies to analyse (i) which of the methods included in the Technical Specification (TS) 12913-2:2018 by the International Organization for Standardization (ISO) for collecting soundscape data from individuals are predominantly used in scientific research and (ii) what is the level of compliance with ISO recommendations of the methods employed in scientific research.

Recent Findings
The ISO/TS 12913-2:2018 provide three possible protocols for individuals’ soundscape data collection (Methods A, B, and C). Despite standardization efforts, a reference method has yet to be identified to improve comparability amongst studies and the formation of scientific evidence.

Summary
The analysis of 50 peer-reviewed papers published from 2018 (year of release of ISO/TS 12913-2) showed that Method A is the prevalent one, adopted by 94.4% of the identified studies. Full compliance with ISO technical specification recommendations is in any case quite limited, and almost no study is strictly adhering to them. Attributes are not always suitable to cover all the acoustic contexts (e.g. indoor environments). This is an indicator that the field is still developing, but it also signals that technical specification recommendations leave room for ambiguity or are not always implementable. This study is ultimately intended to offer recommendations on future development of the protocols in the standardization process.

Graphical Abstract
Science religion encounters, epistemic trespass, neighbourliness and overlapping domains: theorisation and quantitative evidence of extent
Authors: Bowie Robert A. , Aantjes Rosanne , Woolley Mary , Hulbert Sabina , Thomas Caroline , Revell Lynn , Riordan John-Paul 
Published: October 2023

AbstractThis study advances a concept of science religion encounter (SRE), with preliminary theorisation and shares findings on the extent and nature of such encounters reported by secondary religious education and science teachers. SREs are interdisciplinary engagements in classrooms involving subject knowledge from more than one subject. The researchers hypothesised they may arise unexpectedly, when a pupil asks a question, or be teacher-planned and intended. This article further elaborates the concept of SRE with reference to the concepts of ‘epistemic trespassing’ (ET), epistemic neighbourliness, and overlapping domains, introducing these to the field of education. The study is contextualised in the school classroom with quantitative data gathered among beginning and experienced teachers measuring whether this ET in SRE topics enter the classroom via ‘spontaneity’ or via a ‘deliberateness’. This clarifies the different roles a teacher may play and offers considerations for teacher development when navigating an SRE in ways that potentially reduce lost learning.
After religious education: lessons from continental pedagogy
Authors: Lewin David 
Published: October 2023

AbstractThis paper takes up the theme of divergent political and educational paths in Religious Education (RE) by drawing out some educational theories from the German tradition of what is sometimes called ‘continental pedagogy’. As a development of work undertaken within the After Religious Education project, my interest in this paper is what these theories have to say about one aspect of education, namely the educational logic governing curricular presentation and representation. Within the German tradition, there is an established focus on ‘didactics’ (the theory and practice of teaching) which informs the approach taken here. Rather than seeing RE as a particular corner of the curriculum with its own unique challenges, my main argument is that RE theory is part of wider educational landscape and therefore it could usefully engage more actively with the tradition of general didactics. The argument will present and contextualize the work of Wagenschein and Klafki, educational theorists who are not well known among Anglophone theorists of RE, but who offer insightful considerations of the holistic formation of the person to which RE can make a vital contribution.
A Deep Convolutional Neural Network for Time Series Classification with Intermediate Targets
Authors: Taherkhani Aboozar , Cosma Georgina , McGinnity T. M. 
Published: October 2023

AbstractDeep Convolutional Neural Networks (CNNs) have been successfully used in different applications, including image recognition. Time series data, which are generated in many applications, such as tasks using sensor data, have different characteristics compared to image data, and accordingly, there is a need for specific CNN structures to address their processing. This paper proposes a new CNN for classifying time series data. It is proposed to have new intermediate outputs extracted from different hidden layers instead of having a single output to control weight adjustment in the hidden layers during training. Intermediate targets are used to act as labels for the intermediate outputs to improve the performance of the method. The intermediate targets are different from the main target. Additionally, the proposed method artificially increases the number of training instances using the original training samples and the intermediate targets. The proposed approach converts a classification task with original training samples to a new (but equivalent) classification task that contains two classes with a high number of training instances. The proposed CNN for Time Series classification, called CNN-TS, extracts features depending the distance of two time series. CNN-TS was evaluated on various benchmark time series datasets. The proposed CNN-TS achieved 5.1% higher overall accuracy compared to the CNN base method (without an intermediate layer). Additionally, CNN-TS achieved 21.1% higher average accuracy compared to classical machine-learning methods, i.e., linear SVM, RBF SVM, and RF. Moreover, CNN-TS was on average 8.43 times faster in training time compared to the ResNet method.
Advancing Personalized Federated Learning: Group Privacy, Fairness, and Beyond
Authors: Galli Filippo , Jung Kangsoo , Biswas Sayan , Palamidessi Catuscia , Cucinotta Tommaso 
Published: October 2023

AbstractFederated learning (FL) is a framework for training machine learning models in a distributed and collaborative manner. During training, a set of participating clients process their data stored locally, sharing only updates of the statistical model’s parameters obtained by minimizing a cost function over their local inputs. FL was proposed as a stepping-stone towards privacy-preserving machine learning, but it has been shown to expose clients to issues such as leakage of private information, lack of personalization of the model, and the possibility of having a trained model that is fairer to some groups of clients than to others. In this paper, the focus is on addressing the triadic interaction among personalization, privacy guarantees, and fairness attained by trained models within the FL framework. Differential privacy and its variants have been studied and applied as cutting-edge standards for providing formal privacy guarantees. However, clients in FL often hold very diverse datasets representing heterogeneous communities, making it important to protect their sensitive and personal information while still ensuring that the trained model upholds the aspect of fairness for the users. To attain this objective, a method is put forth that introduces group privacy assurances through the utilization ofd-privacy (aka metric privacy).d-privacy represents a localized form of differential privacy that relies on a metric-oriented obfuscation approach to maintain the original data’s topological distribution. This method, besides enabling personalized model training in a federated approach and providing formal privacy guarantees, possesses significantly better group fairness measured under a variety of standard metrics than a global model trained within a classical FL template. Theoretical justifications for the applicability are provided, as well as experimental validation on real-world datasets to illustrate the working of the proposed method.
Item analysis of general surgery multi-institutional mock oral exam: opportunities for quality improvement
Authors: Andres Jerome , Huang Ivy A. , Tillou Areti , Wagner Justin P. , Lewis Catherine E. , Amersi Farin F. , Donahue Timothy R. , Chen Formosa C. , Wu James X. 
Published: October 2023

Abstract
Purpose
Mock oral examinations (MOE) prepare general surgery residents for the American Board of Surgery Certifying Exam by assessing their medical knowledge and clinical judgement. There is no standard accepted process for quality analysis among MOE content items. Effective questions should correlate with mastery of MOE content, as well as exam passage. Our aim was to identify opportunities for question improvement via item analysis of a standardized MOE.

Methods
Retrospective review of testing data from the 2022 Southern California Virtual MOE, which examined 64 general surgery residents from six training programs. Each resident was assessed with 73 exam questions distributed through 12 standardized cases. Study authors indexed questions by clinical topic (e.g. breast, trauma) and competency category (e.g. professionalism, operative approach). We defined MOE passage as mean percentage correct and mean room score within 1 standard deviation of the mean or higher. Questions were assessed for difficulty, discrimination between PGY level, and correlation with MOE passage.

Results
Passage rate was 77% overall (49/64 residents), with no differences between postgraduate year (PGY) levels. PGY3 residents answered fewer questions correctly vs PGY4 residents (72% vs 78%, p < 0.001) and PGY5 residents (72% vs 82%, p < 0.001). Out of 73 total questions, 17 questions (23.2%) significantly correlated with MOE passage or failure. By competency category, these were predominantly related to patient care (52.9%) and operative approach (23.5%), with fewer related to diagnosis (11.8%), professional behavior (5.9%), and decision to operate (5.9%). By clinical topic these were equally distributed between trauma (17.7%), large intestine (17.7%), endocrine (17.7%), and surgical critical care (17.7%), with fewer in breast (11.8%), stomach (11.8%), and pediatric surgery (5.9%). We identified two types of ineffective questions: 1) questions answered correctly by 100% of test-takers with no discriminatory ability (n = 3); and 2) questions that varied inversely with exam passage (n = 11). In total, 19% (14/73) of exam questions were deemed ineffective.

Conclusions
Item analysis of multi-institutional mock oral exam found that 23% of questions correlated with exam passage or failure, effectively discriminating which examinees had mastery of MOE content. We also recognized 19% of questions as ineffective that can be targeted for improvement.
Unintended consequences of dieting: How restrictive eating habits can harm your health
Authors: Habib Ashna , Ali Tooba , Nazir Zainab , mahfooz Arisha , Inayat Qurat-ul-Ain , Haque Md Ariful 
Published: October 2023

Abstract
The text explores the negative aspects of dieting. Dieting has been more common in recent years as more people strive to adhere to strict food plans in an effort to achieve their desired body weight and form. Unfortunately, this strategy may have unforeseen repercussions that could have a negative impact on one’s health. Insufficient calorie intake, for instance, might deprive the body of vital nutrients, resulting in malnutrition and a weakened immune system. Similar to too-restricted diets, irregular periods and even infertility can result from a disruption in the hormonal balance. Furthermore, dieting can lead to psychological distress, which in turn promotes disordered eating behaviors such as binge eating, purging, and other eating disorders. These disorders have the potential to have a long-term negative impact on physical and mental health, and in some situations, they may even be fatal. It’s important to exercise caution and knowledge when it comes to various diet regimens that are advertised on social media and online.
Experiences of a Graduate Student Guided by Henry Stommel
Authors: Halpern David 
Published: October 2023

AbstractWhile much has been written about Professor Henry M. Stommel as a scientist, little has been said about his role as a supervisor of graduate students. I had been at the Massachusetts Institute of Technology only 5 months, with no knowledge or experience of the ocean, when Stommel suggested I search for internal gravity waves in Massachusetts Bay. This essay describes my experiences under Stommel's tutelage.
Compounding Heatwave‐Extreme Rainfall Events Driven by Fronts, High Moisture, and Atmospheric Instability
Authors: Sauter Christoph , Catto Jennifer L. , Fowler Hayley J. , Westra Seth , White Christopher J. 
Published: October 2023

AbstractHeatwaves have been shown to increase the likelihood and intensity of extreme rainfall occurring immediately afterward, potentially leading to increased flood risk. However, the exact mechanisms connecting heatwaves to extreme rainfall remain poorly understood. In this study, we use weather type data sets for Australia and Europe to identify weather patterns, including fronts, cyclones, and thunderstorm conditions, associated with heatwave terminations and following extreme rainfall events. We further analyze, using reanalysis data, how atmospheric instability and moisture availability change before and after the heatwave termination depending on whether the heatwave is followed by extreme rainfall, as well as the location of the heatwave. We find that most heatwaves terminate during thunderstorm and/or frontal conditions. Additionally, atmospheric instability and moisture availability increase several days before the heatwave termination; but only if heatwaves are followed by extreme rainfall. We also find that atmospheric instability and moisture after a heatwave are significantly higher than expected from climatology for the same time of the year, and that highest values of instability and moisture are associated with highest post‐heatwave rainfall intensities. We conclude that the joint presence of high atmospheric instability, moisture, as well as frontal systems are likely to explain why rainfall is generally more extreme and likely after heatwaves, as well as why this compound hazard is mainly found in the non‐arid mid and high latitudes. An improved understanding of the drivers of these compound events will help assess potential changing impacts in the future.
Prognostic models predicting transition to psychotic disorder using blood-based biomarkers: a systematic review and critical appraisal
Authors: Byrne Jonah F. , Mongan David , Murphy Jennifer , Healy Colm , Fӧcking Melanie , Cannon Mary , Cotter David R. 
Published: October 2023

AbstractAccumulating evidence suggests individuals with psychotic disorder show abnormalities in metabolic and inflammatory processes. Recently, several studies have employed blood-based predictors in models predicting transition to psychotic disorder in risk-enriched populations. A systematic review of the performance and methodology of prognostic models using blood-based biomarkers in the prediction of psychotic disorder from risk-enriched populations is warranted. Databases (PubMed, EMBASE and PsycINFO) were searched for eligible texts from 1998 to 15/05/2023, which detailed model development or validation studies. The checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies (CHARMS) was used to guide data extraction from eligible texts and the Prediction Model Risk of Bias Assessment Tool (PROBAST) was used to assess the risk of bias and applicability of the studies. A narrative synthesis of the included studies was performed. Seventeen eligible studies were identified: 16 eligible model development studies and one eligible model validation study. A wide range of biomarkers were assessed, including nucleic acids, proteins, metabolites, and lipids. The range of C-index (area under the curve) estimates reported for the models was 0.67-1.00. No studies assessed model calibration. According to PROBAST criteria, all studies were at high risk of bias in the analysis domain. While a wide range of potentially predictive biomarkers were identified in the included studies, most studies did not account for overfitting in model performance estimates, no studies assessed calibration, and all models were at high risk of bias according to PROBAST criteria. External validation of the models is needed to provide more accurate estimates of their performance. Future studies which follow the latest available methodological and reporting guidelines and adopt strategies to accommodate required sample sizes for model development or validation will clarify the value of including blood-based biomarkers in models predicting psychosis.
A novel approach to visualize clinical benefit of therapies for chronic graft versus host disease (cGvHD): the probability of being in response (PBR) applied to the REACH3 study
Authors: Hollaender Norbert , Glimm Ekkehard , Gauvin Jennifer , Stefanelli Tommaso , Zeiser Robert 
Published: October 2023

AbstractOverall response rate (ORR) is commonly used as key endpoint to assess treatment efficacy of chronic graft versus host disease (cGvHD), either as ORR at week 24 or as best overall response rate (BOR) at any time point up to week 24 or beyond. Both endpoints as well as duration of response (DOR) were previously reported for the REACH3 study, a phase 3 open-label, randomized study comparing ruxolitinib (RUX) versus best available therapy (BAT). The comparison between RUX and BAT was performed on ORR and BOR using all randomized patients, while DOR was derived for the subgroup of responders only. Here we illustrate the application of the probability of being in response (PBR), a graphical method presenting simultaneously the time to first response and subsequent failure using all randomized patients. In REACH3, PBR showed an earlier time to first response, a higher probability of being in response and a longer duration of response for RUX compared to BAT. PBR is a clinically easily interpretable measurement and can serve as a novel efficacy endpoint to assess treatments for chronic graft versus host disease.
Total neoadjuvant therapy in oesophageal and gastro-oesophageal junctional adenocarcinoma
Authors: Clements Hollie A. , Underwood Tim J. , Petty Russell D. 
Published: October 2023

AbstractAdenocarcinoma of the oesophagus and gastro-oesophageal junction represent a large burden of cancer death in the Western World with an increasing incidence. In the past two decades, the overall survival of patients on a potentially curative treatment pathway has more than doubled due to the addition of perioperative oncological therapies to surgery. However, patients often fail to respond to oncological treatment or struggle to complete their treatment after surgery. In this review, we discuss the current evidence for total neoadjuvant therapy and options for assessment of treatment response.