bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timely Cancer Genetic Counseling and Testing for Young Women With Breast Cancer: Impact on Surgical Decision-making for Contralateral Risk-reducing Mastectomy
Authors: Dettwyler Shenin , Thull Darcy , McAuliffe Priscilla , Steiman Jennifer , Johnson Ronald , Diego Emilia , Mai Phuong 
Published: January 2022

Abstract
PURPOSE: Genetic testing (GT) can identify individuals with pathogenic variants (PV) in breast cancer (BC) predisposition genes, who may consider contralateral risk-reducing mastectomy (CRRM). We report on CRRM rates in young women newly diagnosed with BC who received GT through a multidisciplinary clinic. METHODS: Clinical data was reviewed for patients seen between November 2014 and June 2019. Patients with non-metastatic, unilateral BC diagnosed at age ≤45 and completed GT prior to surgery were included. Associations between surgical intervention and age, BC stage, family history, and GT results were evaluated. RESULTS: Of the 194 patients, 30 (15.5%) had a PV in a BC predisposition gene (ATM , BRCA1, BRCA2, CHEK2, NBN, NF1), with 66.7% in BRCA1 or BRCA2. Of 164 (84.5%) uninformative results, 132 (68%) were negative and 32 (16.5%) were variants of uncertain significance (VUS). Overall, 67 (34.5%) had CRRM, including 25/30 (83.3%) PV carriers and 42/164 (25.6%) non-carriers. Only a positive test result was associated with CRRM (p < 0.01). For the 164 with uninformative results, CRRM was not associated with age (p = 0.23), a VUS, (p = 0.08), family history (p = 0.19), or BC stage (p = 0.10). CONCLUSION: In this cohort of young women with BC, the identification of a PV in a BC predisposition gene was the only factor associated with the decision to pursue CRRM. Thus, incorporation of genetic services in the initial evaluation of young patients with a new BC could contribute to the surgical decision-making process.
Maximizing Coverage, Reducing Time: A Usability Evaluation Method for Web-Based Library Systems
Authors: Iqbal Shumaila , Ikram Naveed , Imtiaz salma , Imtiaz Saima 
Published: January 2022

Abstract
Usability of a Web Based Library Systems (WBLS) is a major quality attribute. Checklists have become common and easy method to evaluate the usability of these WBLS; however the available checklists support evaluation of general usability aspects of WBLS only. The domain specific usability aspects are required to maximize the usability for such systems. This research proposes and validates a checklist based usability evaluation method that supports the evaluation of general as well as specific usability aspects of WBLS. The usability evaluation checklist is proposed based on analysis of literature and data of a controlled experiment. The checklist is validated in comparison to the “Academic Library Website Evaluation Checklist” via another controlled experiment. The proposed checklist is applied to the WBLS of universities in Pakistan. The manual and statistical result shows that, the proposed usability evaluation checklist identifies more general and specific usability aspects. It is found that both the checklists are equally efficient while identifying the usability errors. The proposed checklist is beneficial for the academia as well as industry to evaluate the usability of WBLS to an optimal level.
Improved Wood Species Identification Based On Multi-View Imagery of The Three Anatomical Planes
Authors: Silva Núbia Rosa Da , Deklerck Victor , Baetens Jan , Bulcke Jan Van den , De Ridder Maaike , Rousseau Mélissa , Bruno Odemir Martinez , Beeckman Hans , Acker Joris Van , De Baets Bernard , Verwaeren Jan 
Published: January 2022

Abstract
Background: The identification of tropical African wood species based on microscopic imagery is a challenging problem due to the heterogeneous nature of the composition of wood combined with the vast number of candidate species. Image classification methods that rely on machine learning can facilitate this identification, provided that sufficient training material is available. Despite the fact that the three main anatomical sections contain information that is relevant for species identification, current methods only rely on the transversal section. Additionally, commonly used procedures for evaluating the performance of these methods neglect the fact that multiple images often originate from the same tree, leading to an overly optimistic estimate of the performance. Results: We introduce a new image dataset containing microscopic images of the three main anatomical sections of 77 Congolese wood species. A dedicated multiview image classification method is developed and obtains an accuracy (computed using the naive but common approach) of 95%, outperforming the singleview methods by a large margin. An in-depth analysis shows that naive accuracy estimates can lead to a dramatic over-prediction, of up to 60%, of the accuracy. Conclusions: Additional images from the non-transversal sections can boost the performance of machine-learning-based wood species identification methods. Additionally, care should be taken when evaluating the performance of machine-learningbased wood species identification methods to avoid an overestimation of the performance.
Integrated Clinical and Genomic Models to Predict Optimal Cytoreduction in High Grade Serous Ovarian Cancer
Authors: Cardillo Nicholas , Devor Eric , Nobre Silvana Pedra , Newtson Andreea , Leslie Kimberly , Bender David , Smith Brian , Goodheart Michael , Gonzalez-Bosquet Jesus 
Published: January 2022

Abstract
Background: Advanced high grade serous (HGSC) ovarian cancer is treated with either primary surgery followed by chemotherapy or neoadjuvant chemotherapy followed by interval surgery. The decision to proceed with surgery either primarily or after chemotherapy is based on a surgeon’s clinical assessment and prediction of an optimal outcome. Optimal surgery is correlated with improved overall survival. This clinical assessment results in an optimal surgery approximately 70% of the time. We hypothesize that this prediction can be improved by using biological tumor data to predict optimal cytoreduction.Methods: With access to a large biobank of ovarian cancer tumors, we obtained genomic data on 83 patients encompassing gene expression, exon expression, long non-coding RNA, micro RNA, single nucleotide variants, copy number variation, DNA methylation, and fusion transcripts. We then used machine learning to incorporate this data with pre-operative clinical information to create predictive models which successfully predicted whether or not a patient’s cytoreductive surgery would have an optimal outcome. These models were then validated within The Cancer Genome Atlas (TCGA) HGSC database. Results: Of the 124 models created and validated, 21 performed at least equal if not better than our historical clinical rate of optimal debulking in advanced-stage HGSC as a control, 78%. Conclusions: This is the first time tumor genomic data has been used to predict surgical outcome in ovarian cancer. Prospective validation of these models could result in improving our ability to objectively predict which patients will undergo optimal cytoreduction and, therefore, improve our ovarian cancer outcomes.
How Does Climate Change Affect Rice Production in Thailand? Assessing the Role of Financial Development
Authors: Chandio Abbas Ali , Twumasi Martinson Ankrah , Ahmad Fayyaz , Sargani Ghulam Raza , Jiang Yuansheng 
Published: January 2022

Abstract
The study aims to examine the impacts of climate change (CC) and financial development (FD) on rice production (RP) in Thailand from the period 1969 to 2016 by using the ARDL and VECM framework. The empirical results revealed that in the long- run (LR) and short-run (SR) there is a reduction in rice production as temperature increase. The carbon dioxide (CO2) positively affects rice production in the (LR), while this connection is negative in the SR. The empirical results further confirmed that in the LR and SR domestic credit provided by the financial sector positively and significantly improved rice production, while domestic credit to private sector by banks negatively affect rice production. The important input factors including cultivated area, fertilizers use and labor force positively and significantly contributed to rice production in both LR and SR. The LR causal link of all variables with rice production is validated. The SR causal association is unidirectional among temperature, CO2 emissions, financial development, labor force and rice production. Additionally, the IRF and VDM outcomes also confirm that both climate change and socioeconomic development are crucial for rice production in Thailand. The study offers important policy implications to improve rice production with the help of improved financial system and climate controls.
Assessing Spatiotemporal Built-up Dynamics in Chiang Mai City, Thailand using Entropy approach
Authors: Gyeltshen Sangay , Tran Thuong V. , Khunta Wanwilai , Kannaujiya Suresh 
Published: January 2022

Abstract
The rates of urban dynamics affecting by industrialization, urban agglomeration, and large-scale migration turn its behaviour from monocentric to polycentric metropolitan resulting in unprecedented urban growth. Therefore, the present study incorporated an entropy-based approach to measure the degree of compactness and dispersiveness of urban development in Chiang Mai City. The Object-based machine learning was deployed for the image classifications with an overall accuracy above the minimum requirements (i.e., 90%) and kappa statistic of agreement above 0.85. The study reveals that Chiang Mai city has undergone urban development outskirts from the urban centre (CBD) and north and south-west direction from the CBD. A considerable increase in urban demographic and physical urban patches was observed in last 1998 to 2018. The research emphasized the significant role of Shannon Entropy to analyze the built-up growth supplemented by Remote Sensing and Geographic Information System (GIS) in respective zones and geographical directions.
Investigations of The Hybrid Effects of The Operational Parameters In The Radial Forging Process Based On The Validation of The Hardness Test
Authors: Darki Saeed , Raskatov Evgeniy Yurevich 
Published: January 2022

Abstract

In this study, considering all the parameters in radial forging and a three-dimensional model has been simulated using the finite element method. By implementing an elastoplastic state for the specimen tube, parameters such as friction type, residual stress distribution, effective strain distribution, material flow velocity and its effect on the neutral plate and the distribution of force in the die have been studied and analyzed. The effects of angle on the quality and characteristics of the specimen and the longevity of the die have also been obtained. Experimental results have been used to confirm the accuracy of the simulation. The results of the hardness test after forging were compared with the simulation results. Good agreement between the results indicates the accuracy of the simulation in terms of hardness. Therefore, this validation allows confirming the other obtained results for the analysis and prediction of various components in the forging process. After the validation and confirmation of the results through the hardness test, the hardness distribution was obtained by considering temperature changes and the effective strain on the specimen.
Construction of an Immune-related Gene Model for Predicting Prognosis and Immune Infiltration in Clear Cell Renal Cell Carcinoma
Authors: Ji Fengping , Liu Xin , Zhang Yanping , Liu Erpeng , Wen Jianguo 
Published: January 2022

Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is a common pathological type of kidney cancer with high immune infiltration that has been proven to be treatable with immune checkpoint inhibitor (ICI) therapy. However, the role of immunity in ccRCC remains poorly understood. Therefore, this paper aimed to develop and validate a novel immune-related prognostic marker to predict both the overall survival rate (OS) of ccRCC patients and the response to ICI therapy.Methods: Based on the transcriptome and clinicopathological data of ccRCC from The Cancer Genome Atlas (TCGA) dataset and immune-related genes (IRGs) from immune datasets, IRGs related to prognosis were screened to construct an IRG prognostic index (IRGPI) via coexpression analysis and Cox regression. After verifying that IRGPI was a prognostic indicator independent of clinical parameters, a nomogram was established. In addition, functional enrichment analysis, the CIBERSORT algorithm and single-sample gene set enrichment analysis (ssGSEA) were performed to compare the molecular and immune characteristics of IRGPI-defined subgroups. Finally, the expression of immunosuppressive genes, tumor mutational burden (TMB) and the TIDE algorithm were used to predict the response of ICI therapy in different IRGPI subgroups. Results: A total of 11 IRGs (IFNG, XCL1, APOBEC3G, CD86, CXCR3, IL10RA, IL2RG, CD244, SH2D1A, CD3D and FCER1G) were included in the IRGPI module. IRGPIhigh patients had a worse OS and had poorer clinical pathological status than IRGPIlow patients. A nomogram containing clinical features and IRGPI scores may guide the clinical practice of ccRCC. Chemokine signaling pathways were mainly involved in functional enrichment analysis. Furthermore, the IRGPI could effectively reflect the immune characteristics and immune checkpoint gene expression of ccRCC and the response to ICI therapy.Conclusions: The IRGPI is a promising biomarker for determining prognosis and has the potential to be used to predict immunotherapy response in ccRCC.
In Vitro Efficacy of Cyclosporine A and Various Antiseptics and Antiviral Drugs on Adenovirus Genotype 8, a Common Cause of Epidemic Keratoconjunctivitis
Authors: Aydamirov Aynura Sariyeva , Harbiyeli Ibrahim Inan , Ozturk Gokhan , Yarkin Fugen , Erdem Elif , Yagmur Meltem 
Published: January 2022

Abstract
Purpose: To evaluate the in vitro efficacy of cidofovir, ganciclovir, povidone iodine, chlorhexidine, and cyclosporine A on adenovirus genotype 8 Methods: Conjunctival samples were collected from patients with adenoviral conjunctivitis and cultured in A549 cells. Adenovirus diagnosis was confirmed by RT-PCR. For each drug, the 50% cytotoxic concentration (CC₅₀) was determined. Subsequently, the antiviral activity was tested at concentrations below CC₅₀, and the 50% inhibitor concentration (IC₅₀) of drugs was determined.Results: While the IC₅₀ of cidofovir against adenovirus genotype 8 was 3.07 ± 0.8 µM, ganciclovir, povidone iodine, chlorhexidine, and cyclosporine A were not found to be effective against adenovirus genotype 8 at concentrations below the CC₅₀ value.Conclusions: Cidofovir was found effective and the IC₅₀ value was within the ranges in the literature. Ganciclovir and cyclosporine A were found to be ineffective at doses below the cytotoxic dose, povidone iodine and chlorhexidine were found to be highly cytotoxic.
New Prognostic Frontiers for Lung Neuroendocrine Tumors
Authors: Salvia Anna La , Persano Irene , Siciliani Alessandra , Verrico Monica , Bassi Massimiliano , Modica Roberta , Audisio Alessandro , Zanata Isabella , Marinucci Beatrice Trabalza , Trevisi Elena , Puliani Giulia , Rinzivillo Maria , Parlagreco Elena , Baldelli Roberto , Feola Tiziana , Sesti Franz , Razzore Paola , Mazzilli Rossella , Mancini Massimiliano , Panzuto Francesco , Volante Marco , Giannetta Elisa , Romero Carmen , Appetecchia Marialuisa , Isidori Andrea , Venuta Federico , Ambrosio Maria Rosaria , Zatelli Maria Chiara , Ibrahim Mohsen , Colao Annamaria , Brizzi Maria Pia , Carbonero Rocio Garcia , Faggiano Antongiulio 
Published: January 2022

Abstract
Purpose Well-differentiated lung neuroendocrine tumors (Lu-NET) are classified as typical (TC) and atypical (AC) carcinoids, based on mitotic counts and necrosis. However, prognostic factors, other than tumor node metastasis (TNM) stage and the histopathological diagnosis, are still lacking. The current study is aimed to identify potential prognostic factors to better stratify lung NET, thus, improving patients’ treatment strategy and follow-up. Methods A multicentric retrospective study, including 300 Lung NET, all surgically removed, from Italian and Spanish Institutions. Results Median age 61 years (13-86), 37.7% were males, 25.0% were AC, 42.0% were located in the lung left parenchyma, 80.3% presented a TNM stage I-II. Mitotic count was ≥2 per 10 high power field (HPF) in 24.7%, necrosis in 13.0%. Median overall survival (OS) was 46.1 months (0.6-323), median progression free survival (PFS) was 36.0 months (0.3-323). Female sex correlated with a more indolent disease (T1; N0; lower Ki67; lower mitotic count and the absence of necrosis). Left-sided primary tumors were associated with higher mitotic count and necrosis. At Cox multivariate regression model, age, left-sided tumors and nodal (N) positive status resulted independent negative prognostic factors for OS and PFS. Conclusions This study confirms the prognostic relevance of TNM stage and diagnosis to stratify LuNET. However, the current analysis suggests a wider spectrum of clinical and pathological prognostic factors, including age and primary tumor’s location. These parameters could help clinicians to personalize the management of Lu-NET.
TP53 Germline Mutations are Associated with HR+/HER2+ in BRCA1/2-Negative Early-Onset Breast Cancer in China
Authors: Chen Lili , Huang Meng , Chen Minyan , Lin Yuxiang , Li Jing , Guo Wenhui , Wang Chuan , Fu Fangmeng 
Published: January 2022

Abstract
Background: Except for BRCA1/2, there is no data on the relationship between genetic counseling for the range of mutations and early-onset breast cancer populations. We looked for a link between inherited genes and the molecular subtype of early-onset breast cancer.﻿Methods: We genotyped 1214 individuals with early-onset sporadic breast cancer (age≤40 years) who were BRCA1/2-negative in 3 genes: TP53, PALB2, and RECQL. We focus on the immunohistochemistry characteristics that are unique to each patient. Results: The mutation rates of TP53, PALB2, and RECQL in 1214 BRCA-negative young individuals were 4/1214(0.33%), 8/1214(0.66%), 2/1214(0.16%), respectively. The fact that the TP53 mutation rate was 3.49% among estrogen receptor-and/or progesterone receptor-positive, human epidermal growth factor receptor 2 (HER-2) amplification patients under the age of 35 (P<0.001) was particularly noteworthy. Conclusion: According to the findings, TP53 genetic testing should focus on women under 35 with HR-positive and HER2-positve IDC patients.
Solitons, Rogues and Interaction Behaviors of Third-Order Nonlinear Schrodinger Equation
Authors: Bo Ren , Kai-Zhong Shi , Shen Shou-Feng , Guo-Fang Wang , Jun-Da Peng , Wan-Li Wang 
Published: January 2022

Abstract
In this paper, we investigate the third-order nonlinear Schr\"{o}dinger equation which is used to describe the propagation of ultrashort pulses in the subpicosecond or femtosecond regime. Based on the independent transformation, the bilinear form of the third-order NLSE is constructed. The multiple soliton solutions are constructed by solving the bilinear form. The multi-order rogue waves and interaction between one-soliton and first-order rogue wave are obtained by the long wave limit in multi-solitons. The dynamics of the first-order rogue wave, second-order rogue wave and interaction between one-soliton and first-order rogue wave are presented by selecting the appropriate parameters. In particular parameters, the positions and the maximum of amplitude of rogue wave can be confirmed by the detail calculations.PACS numbers: 02.30.Ik, 05.45.Yv.
PRTN3/FCER1A Transcriptomic Ratio Predicts Hospitalization in Primary Care Attenders With Respiratory Infection
Authors: Herrero-Rodríguez Carmen , Almansa Raquel , Fuente Amanda de la , Martínez-Huélamo Misericordia , Vicente-Andres Maria Pilar , Nieto-Barbero Jose Angel , Martín-Ballesteros Miryam , Rodilla-Carvajal Maria Mar , Ortega Alicia , Doncel Cristina , García-Ortiz Luis , Bermejo-Martin Jesús F , group PREVISE study 
Published: January 2022

Abstract
Early detection of patients with respiratory infection at risk of deteriorating could help to improve their outcome by facilitating immediate transfer to the hospital to receive the adequate level of care. In this regard, gene expression profiling is emerging as a promising tool to identify patients with infection at risk of suffering a complicated outcome. In a cohort of patients with respiratory infection attending to an Emergency Room at a community health centre, we quantified expression levels in blood of five genes involved in the granulocyte biology that have been previously described to be linked to infection severity: MMP8 (matrix metallopeptidase 8), LCN2 (lipocalin-2), LTF (lactotransferrin) and PRTN3 (proteinase 3) and FCER1A (receptor for Fc fragment of IgE, high affinity I). Expression levels of these genes were evaluated to predict hospitalization. Multivariate analysis adjusted by the National Early Warning Score (NEWS), neurovascular disease, hypertension and age revealed that all these genes independently predicted hospitalization. Nonetheless, the ratio between PRTN3/FCER1A outperformed individual genes to predict necessity of hospitalization (OR [CI95%], p: 8.36 [2.02-34.52],0.003). In conclusion, quantification of PRTN3/FCER1A gene expression ratio could represent a useful test to early identify those patients with respiratory infection at risk of deterioration in extra-hospital settings.
Ureaplasma and Prevotella Colonization with Lactobacillus Abundance During Pregnancy Facilitates Term Birth
Authors: Park Sunwha , You Young-Ah , Kim Young-Han , Kwon Eunjin , Ansari AbuZar , Kim Soo Min , Lee Gain , Hur Young Min , Jung Yun Ji , Kim Kwangmin , Kim Young Ju 
Published: January 2022

Abstract
Ureaplasma and Prevotella infections are well-known bacteria associated with preterm birth. However, with the development of metagenome sequencing techniques, it has been found that not all Ureaplasma and Prevotella colonizations cause preterm birth. The purpose of this study was to determine the association between Ureaplasma and Prevotella colonization with the induction of preterm birth even in the presence of Lactobacillus. In this matched case-control study, a total of 203 pregnant Korean women were selected and their cervicovaginal fluid samples were collected during mid-pregnancy. The microbiome profiles of the cervicovaginal fluid were analyzed using 16S rRNA gene amplification. Sequencing data were processed using QIIME1.9.1. Statistical analyses were performed using R software, and microbiome analysis was performed using the MicrobiomeAnalyst and Calypso software. A positive correlation between Ureaplasma and other genera was highly related to preterm birth, but interestingly, there was a negative correlation with Lactobacillus and term birth, with the same pattern observed with Prevotella. Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth, although Ureaplasma and Prevotella are associated with preterm birth. Balanced colonization between Lactobacillus and Ureaplasma and Prevotella is important to prevent preterm birth.