bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing Targeted Enhanced-Whole-Genome Sequencing in Precision Oncology for the Treatment of Solid Tumors: A Clinical Perspective
Authors: Helali Aya El , Ackershoek Amy , Barcomb Alexis , Oh Brian Baek-Lok , Bao Chunyang , Kim Jung-Ah , Lee Eun Kyoung , Lee Jeong-Hoon , Lee Sangmoon , Connolly-Strong Erin 
Published: March 2024

Abstract
Background
Genomic alterations in tumors provide key insights into the clinical management of patients. Over the past decade, targeted panel sequencing (TPS) has been a key tool in oncology. With recent advances in sequencing technology and cost reduction, whole-genome sequencing (WGS) has now become a viable and comprehensive method for analyzing cancer genomes.
Methods
A retrospective analysis of 24 cases to evaluate the clinical utility of targeted enhanced whole-genome sequencing (TE-WGS). The TE-WGS assay was evaluated by assessing its impact on targeted therapy selection, clinical trial opportunities, exclusion of non-beneficial therapies, and diagnostic clarity.
Results
TE-WGS demonstrated clinical utility in 71% of cases. 50% of cases reveal actionable genomic alterations aligned to on- and off-label targeted therapies. Notably, 50% of patients exhibited genomic profiles that aligned with ongoing clinical trials.
Conclusion
This report underscores the clinical value of TE-WGS in providing a nuanced genomic landscape that can be integrated into clinical practice for precision oncology, thereby enhancing personalized treatment strategies.
Virtually screened inhibitors for Human Papilloma Virus infections
Authors: Vani Vemula , Alagumuthu Manikandan , Prasad Sanjay , Paul Nikita , Nithya G , Pooja N , Pooja V 
Published: March 2024

Abstract
Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. The current treatment methods consist of the use of chemotherapeutic agents or the application of surgical procedures to remove the developed tumors. The alternatives to treat HPV- associated diseases is the discovery of accessible drug-based therapies. In HPV infected cell, E6 protein complexes with E6AP to form p53 degradation complex and induce tumorigenesis. The objective of this study is to discover potential small molecule inhibitors against HPV16 E6 protein using virtual screening approach. Three novel HPV 16 E6 inhibitors viz. compound 5, compound 7 and compound 10 were designed using a fragment-based approach. The structural information of these three novel compounds was used in virtual screening against in- trials subset of ZINC database and a total of 9800 hits were identified. The obtained molecules from the database were further screened by three stages of virtual screening using GLIDE module of Schrodinger software. The results reveal that Five hit molecules (ZINC000034853956, ZINC000001534965, ZINC000095617673, ZINC000005764481 and ZINC000071606215) showed better glide score in comparison with reference molecule, Luteolin. These molecules exhibited crucial interactions with E6 protein of HPV 16. The pharmacokinetic properties of these hit molecules were analyzed using QikProp program. The results indicate that all the five molecules were found to have good pharmacokinetic properties and human oral absorption. All the five hit molecules were predicted to be no toxic and except ZINC000005764481, all other four molecules showed druglike behavior. Therefore, the four hit molecules (ZINC000034853956, ZINC000001534965, ZINC000095617673 and ZINC000071606215) can be used as lead molecules in the development of HPV 16 E6 inhibitors for treatment of HPV related diseases.
Au Coated Photonic Crystal Fiber based Surface Plasmon Resonance Sensor: Design and Investigation
Authors: Afrin Sadia , Sarker Sanchita , Paul Bikash Kumar , Hossain Md Abir , Islam Md Kabirul 
Published: March 2024

Abstract

We propose in this research an idiosyncratic, shallow to erect, and highly perceiving Plasmonic material-coated photonic crystal fiber (PCF) based micro-structured biosensor. Our precedence has a cardinal pattern of circular air holes inside the fiber, which leads to a superior sensing performance. The evaluation of all the sensor characteristics has been expelled by sustaining the finite element method (FEM) of COMSOL Multiphysics. The gold (Au) layer just around the fiber acts as the plasmonic material. Gold is picked out due to its high stable rate and maximum resonance peak value in the sensing environment. After the swelling of all the fiber parameters, we derived a maximum amplitude sensitivity (AS) and wavelength sensitivity (WS) of 114 RIU− 1 and 20000 nm/RIU, respectively, with a maximum sensor resolution of 1.15×10− 9 for wavelength. The overall analyte sensing range is from refractive indices 1.36 to 1.4. With its enhanced performance in terms of sensitivity, we believe that this Plasmonic material-coated PCF biosensor can potentially contribute to the detection of unknown analytes.
Treatment patterns and patient journey in progressive pulmonary fibrosis: a cross-sectional survey
Authors: Chaudhuri Nazia , Spagnolo Paolo , Valenzuela Claudia , Amatto Valeria C. , Carter Oliver-Thomas , Lee Lauren , Small Mark , Kreuter Michael 
Published: March 2024

Abstract

Background
For patients with interstitial lung diseases (ILD) with a progressive pulmonary fibrosis (PPF) phenotype, current knowledge of disease characteristics at diagnosis, patient journey, and treatment is limited. This study aimed to describe demographics and clinical experiences of patients presenting with PPF in a European real-world setting.
Methods
Data were analysed from the Adelphi Real World PPF-ILD Disease Specific Programme™, a cross-sectional survey of pulmonologists and rheumatologists in five European countries (France, Germany, Italy, Spain, United Kingdom) and internal medicine specialists (France) from April to October 2022. Physicians provided data for up to 12 consecutive patients with physician-confirmed ILD with a progressive phenotype other than idiopathic pulmonary fibrosis. Analyses were descriptive.
Results
Overall, 265 physicians reported on 1,335 patients. Mean (standard deviation [SD]) age at survey date was 60.4 (11.6) years, 91.2% were white, 58.1% female, 44.0% non-smokers. The mean age (SD) at first healthcare professional (HCP) visit was 57.6 (12.1) years, with 63.3% patients first consulting a primary care physician. There was a mean delay of 7.8 (22.7) months between first ILD symptom and HCP visit, and another 7.7 (12.8) months to ILD diagnosis. There were 47.7% patients with physician-reported moderate ILD at survey date, 42.3% with mild and 10.0% with severe ILD. Disease progression was reported in the 12 months prior to the survey for 19.5% of patients; of these, progression was based on worsening symptom severity in 27.3% and on lung function decline in 25.8%. For patients experiencing symptoms prior to ILD diagnosis (72.8%), the most common symptoms were dyspnoea on exertion (80.5%) and cough (57.8%). Overall, 17.4% of patients were misdiagnosed prior to ILD diagnosis, with chronic obstructive pulmonary disease suspected in 39.2% of them. The most frequent comorbidities were anxiety (16.9%) and gastroesophageal reflux (15.5%). Although 77.8% of patients were receiving treatment for ILD at survey date, 15.6% of patients had never been prescribed treatment for ILD.
Conclusions
This real-world study expands our understanding of patients, diagnostic delays and treatment gaps experienced by patients diagnosed with PPF in Europe. Given the progressive nature of PPF, diagnostic delay may lead to poor outcomes, including shorter survival.
Trial registration:
n/a
Psychometric validation of the Arabic version of the Irrational Procrastination Scale (IPS)
Authors: Chahine Abdallah , Yakın Ecem , Malaeb Diana , Hallit Rabih , Obeid Sahar , Hallit Souheil , Fekih-Romdhane Feten 
Published: March 2024

Abstract

Background: Procrastination can be defined as voluntarily delaying or postponing a task that is often regarded as important or necessary to do. It often has short term benefits but high future burdens. The Irrational Procrastination Scale (IPS) is a 9-item self-reporting scale that focuses on the implemental aspect of procrastination and are formulated in a simple and direct to the point form, making it easier for participants to express their opinion. No real effort was made to translate and provide procrastination scales to Arabic speaking populations and countries. The objectives of our study were to evaluate the validity of the Arabic version of IPS, assess its internal reliability and explore concurrent validity of the IPS based on patterns of correlations between procrastination and time perspectives.
Methods: This cross-sectional study was conducted from February to March 2023 and involved 341 participants from various regions of Lebanon. The Exploratory-to-Confirmatory (EFA-CFA) strategy was used to confirm the IPS validity.
Results: The results from the EFA revealed a three-factor solution explaining 58.79% of the common variance. However, the CFA of the three-factor model obtained in the EFA indicated modest fit indices. An examination of the modification indices revealed that the item 6 cross loaded on two factors (above .48). Accordingly, a modified CFA model, omitting item 6 was applied; compared to the original one, the modified version indicated a significantly improved model fit. The internal reliability of the scale was good (α = .81 and ω = .83). Model fit for configural, metric and scalar invariance was shown. Higher time perspective dimensions’ scores, namely past negative, past positive, present fatalistic and present hedonistic, were significantly associated with higher irrational procrastination.
Conclusion: The Arabic version of the IPS can be used as a screening tool to assess procrastination in an adult population.
Development and Initial Validation of the Counselor Self-Discrepancy Inventory
Authors: Lee Donghun , Nam Sojeong , Jeong Jeongwoon , Kim Isak , Park Eunji , Higgins Kristin 
Published: March 2024

Abstract

This study provides preliminary evidence for the Counselor Self-Discrepancy Inventory (CSDI), designed to assess the professional and personal selves of counselors and the discrepancies between them. Using a sample of 366 counselors in the United States, initial item development involved a literature review and expert review, and 22 characteristics and qualities that reliably predict the clinical success of counseling were selected for data analyses. An exploratory factor analysis identified a three-factor structure comprising 12 items. This structure included three factors related to ‘Resilient,’ ‘Responsive/Flexible,’ and ‘Client-centered,’ which represent the essential qualities of competent counselors. The concurrent and discriminant validities of this newly developed measure were supported by its correlations with the Counselor Burnout Inventory subscales, excluding the Negative Work Environment subscale. The findings of our study suggest the CSDI’s versatility in identifying counselors’ self-discrepancies and enhancing the supervision process.
Intentions and barriers to help-seeking in children and adolescents differing in depression severity: Cross-sectional results from a school-based mental health project
Authors: Baldofski Sabrina , Scheider Jelena , Kohls Elisabeth , Klemm Sarah-Lena , Koenig Julian , Bauer Stephanie , Moessner Markus , Kaess Michael , Eschenbeck Heike , Lehner Laya , Becker Katja , Krämer Jennifer , Diestelkamp Silke , Thomasius Rainer , Rummel-Kluge Christine 
Published: March 2024

Abstract

Background: Mental health problems, such as depression, have a high prevalence in children and adolescents (C&A). However, the majority of C&A suffering from depression do not seek professional help. In addition to general barriers, the specific psychopathology related to depressive symptoms may decrease their intentions to seek professional help. This study aimed to compare help-seeking behavior, intentions and perceived barriers between C&A with different levels of depressive symptoms.
Methods:This cross-sectional study is part of a large-scale, multi-center project. Participants were
N = 9,509 C&A who were recruited in German schools and completed a baseline screening questionnaire. Based on their depressive symptoms, C&A were allocated to the following three subgroups: a) without depressive symptoms, b) with subclinical symptoms, c) with clinical symptoms (measured by PHQ-A). Quantitative analyses compared previous help-seeking behavior (AHSQ), help-seeking intentions (GHSQ) and perceived barriers (Barriers questionnaire) between those different subgroups. A qualitative content analysis examined text answers on other perceived barriers to help-seeking.
Results:Participants were mostly female (n = 5,575, 58.6%) and 12 to 24 yearsold (M =15.09, SD = 2.37). Participants with different levels of depressive symptoms differed significantly in help-seeking behavior, intentions and perceived barriers. Specifically, participants with clinical depressive symptoms reported more previous help-seeking, but lower intentions to seek help compared to participants without symptoms (all p < .05). Participants with subclinical depressive symptoms reported a similar frequency of previous help-seeking, but higher intentions to seek help compared to participants without symptoms (all p <.05). Perception of barriers was different across subgroups: participants with clinical and subclinical depressive symptoms perceived the majority of barriers such as stigma, difficulties in accessibility, and family-related barriers as more relevant than participants without depressive symptoms. Across all subgroups, participants frequently mentioned intrapersonal reasons, a high need for autonomy, and a lack of mental health literacy as barriers to help-seeking.
Conclusions: C&A with higher levels of depressive symptoms are more reluctant to seek professional help and perceive higher barriers. This underlines the need for effective and low-threshold interventions to tackle barriers, increase help-seeking, and lower depressive symptoms in C&A differing in depression severity.
Trial Registration: DRKS00014685
Nitrogen Accountancy in Space Agriculture
Authors: Yates Kevin , Berliner Aaron J. , Makrygiorgos Georgios , Kaiyom Farrah , McNulty Matthew J. , Khan Imran , Kusuma Paul , Kinlaw Claire , Miron Diogo , Legg Charles , Wilson James , Bugbee Bruce , Mesbah Ali , Arkin Adam P. , Nandi Somen , McDonald Karen A. 
Published: March 2024

Abstract

Food production and pharmaceutical synthesis are posited as essential biotechnologies for facilitating human exploration beyond Earth. These technologies not only offer critical green space and food agency to astronauts but also promise to minimize mass and volume requirements through scalable, modular agriculture within closed-loop systems, offering an advantage over traditional bring-along strategies. Despite these benefits, the prevalent model for evaluating such systems exhibits significant limitations. It lacks comprehensive inventory and mass balance analyses for crop cultivation and life support, and fails to consider the complexities introduced by cultivating multiple crop varieties, which is crucial for enhancing food diversity and nutritional value. Here we expand space agriculture modeling to account for nitrogen dependence across an array of crops and demonstrate our model with experimental fitting of parameters. By adding nitrogen limitations, an extended model can account for potential interruptions in feedstock supply. Furthermore, sensitivity analysis was used to distill key consequential parameters that may be the focus of future experimental efforts.
Comparing Inquiry-Based and Design-Based Approaches in STEM Education: The Case of the Archimedean Screw Activity
Authors: Öndeş Rabia Nur 
Published: March 2024

Abstract
The diversity of instructional approaches, methods, and strategies in STEM education leads to a wide range of implementations. STEM activities, traditionally associated with the engineering design process, can be implemented using various approaches such as problem-based, project-based, design-based, and inquiry-based methods. In line with this, the aim of this study was to apply the Archimedean Screw activity to students with similar backgrounds using both inquiry-based and design-based methods. The observed differences were then analysed to identify the dimensions that highlight these distinctions. In the inquiry-based STEM activity, students utilized an activity sheet with leading questions, fill in the blanks, graphs, and tables related to the screw's variables. They constructed a mathematical model using the screw formula (h = a.n) and designed their own Archimedean Screw, considering scientific information and the mathematical model. They acted as engineers, making improvements based on variables impacting efficiency and solving the initial problem. In the design-based STEM activity, students followed the EDP with teacher guidance to design their own Archimedean Screw. They made improvements based on variables impacting efficiency, successfully solving the initial problem. Additionally, the comparison of the two cases revealed differences across multiple dimensions, including timeframe, knowledge in focus, activity application, learning approach, cognitive engagement, path to a solution, application of mathematics, skills in focus, adaptability and flexibility, motivation and engagement, assessment methods, teacher's role, and student's role. This comparison aids in informed decision-making for teachers, researchers, and stakeholders when designing STEM activities, considering the advantages and disadvantages of both approaches.
Application of EEM fluorescence spectroscopy for characterizing organic DBP precursors in different water sources: a review
Authors: Hu Jinglong , Xiao Rong , Zhang Ruihua , Wu Zhengdi , Jiang Fangyuan , Ye Cheng , Qu Ruixin , Chu Wenhai 
Published: March 2024

Abstract

Disinfection by-products (DBPs), generated from the reaction of disinfectants with DBP precursors, have been found to pose unintentional risks to human health. Considering that the concentration and speciation of DBPs formed during disinfection will be affected by the content and composition of dissolved organic matter (DOM), widespread concern about the characteristics of DBP precursors in water sources have been prompted. Three-dimensional excitation–emission matrix (EEM) can quickly and efficiently determine the properties and composition of DOM in water, and thus is generally used to investigate the origin of DBP precursors in water sources. This study overviews the fluorescent properties of different DBP precursors, summarizes the application of different EEM interpretation methods in DBP precursors and analyses the key factors affecting the correlation between the fluorescent components and DBP precursors (e.g., natural organic matter, algal organic matter, effluent organic matter and organic matter derived from other sources). A series of factors, including composition of fluorophores, bromide concentration, spatio-temporal characteristics and disinfectant types, could impact the correlation between DBP formation potential and fluorescent components. As for future research needs, it is of significance to select suitable fluorescence analysis methods and investigate the combination of EEM with other characterization technologies based on different situations.
Water quality emergency monitoring networks: A method for identifying non-critical variables based on Shannon's entropy
Authors: Cruz Fábio Monteiro , Silva Talita Fernanda das Graças 
Published: March 2024

Abstract

In the occurrence of environmental disasters involving water resources, deploying an emergency monitoring network for assessing water quality is within the first measures to be taken. Emergency networks usually cover a large set of water quality variables and monitoring stations along the watershed. Focusing on variables that represent greater risk to the environment and have less predictable spatial and temporal distribution is a strategy to optimize efforts on monitoring. The goal of this study is to assess the use of Shannon's entropy to identify non-critical water quality variables in an emergency monitoring network implemented in a watershed impacted by the collapse of a mining iron tailing dam, the Doce River watershed (Brazil). Monitoring stations were grouped into water quality subregions through cluster analysis and Shannon's entropy was used to estimate information redundancy of monitored variables. From information redundancy and after checking for compliance with environment normative, non-critical water quality variables were identified. Results indicated that non-critical variables represent 32–50% of the variables monitored. Emergency network managers find in this method a robust tool to improve the network performance. However, special attention should be paid to outliers' presence that can bias analyses based on Shannon's entropy.
Trend analysis of hydro-climatic variables in the Great Lakes Depression region of Mongolia
Authors: Dorjsuren Batsuren , Zemtsov Valery A. , Batsaikhan Nyamdavaa , Demberel Otgonbayar , Yan Denghua , Hongfei Zhou , Yadamjav Otgonbayar , Chonokhuu Sonomdagva , Enkhbold Altanbold , Ganzorig Bolorjargal , Bavuu Erdenebayar , Namsrai Oyunchimeg , Xiang Liu , Yingjie Yan , Siyu Wang 
Published: March 2024

Abstract

Arid and semi-arid regions are the first to be affected by hydro-climatic changes. The Great Lakes Depression Basin in western Mongolia is the most notable example of such a region. Therefore, analyzing hydro-climatic changes in the Great Lakes Depression region is essential for future climate, hydrological, eco-hydrological processes, and ecosystem studies in similar areas and basins. In this study, Mann–Kendall (MK), innovative trend analysis method (ITAM), and Sen's slope estimator test (SSET) were used to determine the interrelationship between climate and river discharge changes and lake water level changes through statistical analysis. During the last 30 years, the air temperature has increased by 1.2 °C (Z = 1.16). Total annual precipitation decreased by 23.44 mm, resulting in 134.16 mm (Z = −0.79). The river discharge of the major rivers, such as Khovd River (Z = −3.51) and Zavkhan River (Z = −6.01), has significantly decreased. In Uvs (Z = 0.30) and Khyargas (Z = 2.03) lakes, the water level has also dropped. This study confirms that the increase in air temperature in the depression area of the Great Lakes reduces the amount of precipitation, and the decrease in precipitation affects the decrease in river discharge, which further affects the water level of the inflowing lakes.
Impact of climate change on the water resources of the Atbara River using novel hydrological models
Authors: El-Mahdy Mohamed El-Sayed , Abdel-Monsef Mohamed , Abo-Elella Salwa , Shahba Mohamed 
Published: March 2024

Abstract

Rivers respond directly to climate change, as well as incorporating the effects of climate-driven changes occurring within their watersheds. In this research, climate change's impact on the Atbara River, one of the main tributaries of the Nile River, was studied. Various statistical methods of analysis were applied to study the basic characteristics of the climatic parameters that affect the discharge of the Atbara River. The three hydrological gauging stations on the Atbara River, namely, the Upper Atbara and Setit reservoirs, Khashm el-Girba reservoir, and Atbara Kilo 3 station, were included in the study. The correlation between the meteorological parameters and the hydrology of the Atbara River and the prediction of the future hydrology of the Atbara River Basin was determined. Many hydrological models were developed and tested to predict the hydrology of the river. Finally, forecasting for river hydrology was built. No significant trend was found in the precipitation in the study area. The developed model simulates the observed data with a high coefficient of determination ranging from 0.7 to 0.91 for the three hydrological gauging stations studied. Results predicted a slight decrease in river discharge in future years.