bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Determinants of Response to HER Kinase Inhibition inHER2-Mutant Metastatic Breast Cancer
Authors: Smyth Lillian M. , Piha-Paul Sarina A. , Won Helen H. , Schram Alison M. , Saura Cristina , Loi Sherene , Lu Janice , Shapiro Geoffrey I. , Juric Dejan , Mayer Ingrid A. , Arteaga Carlos L. , de la Fuente Macarena I. , Brufksy Adam M. , Spanggaard Iben , Mau-Sørensen Morten , Arnedos Monica , Moreno Victor , Boni Valentina , Sohn Joohyuk , Schwartzberg Lee S. , Gonzàlez-Farré Xavier , Cervantes Andrés , Bidard François-Clement , Gorelick Alexander N. , Lanman Richard B. , Nagy Rebecca J. , Ulaner Gary A. , Chandarlapaty Sarat , Jhaveri Komal , Gavrila Elena I. , Zimel Catherine , Selcuklu S. Duygu , Melcer Myra , Samoila Aliaksandra , Cai Yanyan , Scaltriti Maurizio , Mann Grace , Xu Feng , Eli Lisa D. , Dujka Melanie , Lalani Alshad S. , Bryce Richard , Baselga José , Taylor Barry S. , Solit David B. , Meric-Bernstam Funda , Hyman David M. 
Published: December 2019

AbstractHER2 mutations define a subset of metastatic breast cancers with a unique mechanism of oncogenic addiction to HER2 signaling. We explored activity of the irreversible pan-HER kinase inhibitor neratinib, alone or with fulvestrant, in 81 patients with HER2-mutant metastatic breast cancer. Overall response rate was similar with or without estrogen receptor (ER) blockade. By comparison, progression-free survival and duration of response appeared longer in ER+ patients receiving combination therapy, although the study was not designed for direct comparison. Preexistent concurrent activating HER2 or HER3 alterations were associated with poor treatment outcome. Similarly, acquisition of multiple HER2-activating events, as well as gatekeeper alterations, were observed at disease progression in a high proportion of patients deriving clinical benefit from neratinib. Collectively, these data define HER2 mutations as a therapeutic target in breast cancer and suggest that coexistence of additional HER signaling alterations may promote both de novo and acquired resistance to neratinib.Significance:HER2 mutations define a targetable breast cancer subset, although sensitivity to irreversible HER kinase inhibition appears to be modified by the presence of concurrent activating genomic events in the pathway. These findings have implications for potential future combinatorial approaches and broader therapeutic development for this genomically defined subset of breast cancer.This article is highlighted in the In This Issue feature, p. 161
ВИКОРИСТАННЯ МОБІЛЬНИХ ДОДАТКІВ ПРИ ВИКЛАДАННІ МЕДИЧНОЇ ІНФОРМАТИКИ ІНТЕРНАМ-СТОМАТОЛОГАМ
Authors: Bogdanova T. I. , Pasko M. I. , Avdusenko M. V. 
Published: December 2019

У статті розглянуто можливість використання мобільних додатків для удосконалення викладання медичної інформатики для інтернів-стоматологів. Показано, що традиційна програма для навчання інтернів реалізує два головних напрями: вивчення функціональних особливостей роботи офісних програм та ознайомлення з можливостями програм для статистичної обробки медичних даних. Зазвичай акцент робиться на вивченні статистичних програм, що є цікавим лише інтернам, які планують свою майбутню діяльність пов’язати з наукою. Водночас існує безліч мобільних додатків, які можуть бути корисними лікарю в його практичній діяльності. В даній роботі мобільні додатки пропонується поділити на дві групи: загально-змістовні та спеціальні. Серед найбільш корисних загально-змістовних додатків виділені такі: «3D внутрішні органи анатомія 1.9.8», «Medical Terminologies», «Epocrates», «МБК-10», «Read by QxMD» та «MedAssist». Водночас підкреслюється, що при викладанні медичної інформатики в інтернатурі слід враховувати спеціалізацію майбутніх лікарів, тому для лікарів-стоматологів найбільш корисними можуть бути, наприклад, такі, як: «Dental Patient Education», «Cone Beam CT», «Smile Designer Pro», «Dentist +» або «SimplyCeph». Надається аналіз можливостей кожного додатка. Перспективою подальших досліджень є виявлення педагогічної ефективності використання смарт-технологій для формування професійних компетентностей лікарів-стоматологів.
FORMING THE PROFESSIONAL COMPETENCE OF FUTURE DOCTORS AS A PEDAGOGICAL PROBLEM WHEN STUDYING FOREIGN LANGUAGES
Authors: Nakhaieva Ya. M. , Humenna I. R. 
Published: December 2019

The mаin objectives of higher medicаl educаtion аre professionаl improvement of physiciаns to meet the needs dictаted by the modern world both аt undergrаduаte аnd postgrаduate levels. Educаtion of the future tаkes on the feаtures of innovаtive educаtion integrаted with reseаrch аctivity, charаcterized by а continuous, fundаmental, prаctical orientation. The article deals with the problem of the formation of the professional competence of future doctors in the study of foreign languages in medical institutions of higher education. It is noted, that modern education programmes, introduced as a result of the reform of medical education, are built not only on the principle of knowledge and skills obtaining, but also the acquisition of competencies. Modern trends in planning, organizing, evaluating the quality of education аctually helped to ensure the implementation of competence-based аpproach in the training of doctors. The theoretical aspects of this problem are also considered.
The research has identified the need to develop methodological materials for focusing on and developing the future doctors during studying of foreign languages.
Amplification and overexpression of E2 ubiquitin conjugase UBE2T promotes homologous recombination in multiple myeloma
Authors: Alagpulinsa David A. , Kumar Subodh , Talluri Srikanth , Nanjappa Purushothama , Buon Leutz , Chakraborty Chandraditya , Samur Mehmet K. , Szalat Raphael , Shammas Masood A. , Munshi Nikhil C. 
Published: December 2019

Key Points
UBE2T is frequently amplified and/or overexpressed and is required for homologous recombination activity in multiple myeloma cells. UBE2T is a potential therapeutic target to increase chemosensitivity in multiple myeloma cells.
A Numerical Method for Extrication Characteristics of TBM Cutter-Head with the HVC
Authors: Gong Huasheng , Xie Haibo , Yang Huayong 
Published: December 2019

AbstractAchieving highly efficient extrication of the tunnel boring machine (TBM) cutter-head driving system from the collapsed surrounding rock has become a key problem globally, and significant effort has been directed to improve TBM cutter-head extricating ability. In this study, the characteristics of a hydro-viscous device have been investigated to improve extricating performance of the TBM cutter-head. A numerical method based on an explicit pressure-linked equation is presented for computing the film parameters of the HVC, which is then applied to investigate extrication characteristics of a TBM cutter-head with a hydro-viscous clutch (HVC). The explicit pressure-linked equation is derived from the Navier–Stokes equations and the conservation equation, where boundary conditions are involved. The model of a cutter-head driving system with an HVC is established, and the extrication characteristics of the cutter-head driving system are analyzed and compared with three extrication strategies. The variation in extrication torque shows that the linear strategy or positive parabolic strategy are preferred for their relatively high extrication efficiency and low rigid impact, and the effects of throughflow rate on torque transmission are also investigated. The test rig of the TBM cutter-head driving system was set up to validate the numerical method and the model of a cutter-head driving system, and the feasibility of the proposed numerical method for researching the extrication of the TBM cutter-head is verified.
Hemoptysis from complex pulmonary aspergilloma treated by cavernostomy and thoracoplasty
Authors: Giang Nguyen Truong , Dung Le Tien , Hien Nguyen Thanh , Thiet Truong Thanh , Hiep Phan Sy , Vu Nguyen The , Pho Dinh Cong , Van Nam Nguyen , Hung Pham Ngoc 
Published: December 2019

Abstract
Background
In high-risk patients with complex pulmonary aspergilloma but unable for lung resection, cavernostomy and thoracoplasty could be performed. This study aimed to evaluate this surgery compared two compressing materials.

Methods
A total of 63 in high-risk patients who suffered from hemoptysis due to complex pulmonary aspergilloma and underwent cavernostomy and thoracoplasty surgery from November 2011 to September 2018 at Pham Ngoc Thach hospital were evaluated prospectively studied. Patients were allocated to two groups: the table tennis ball group and tissue expander group. We evaluated at the time of before operation, 6 months and 24 months after operation.

Results
Tuberculosis was the most common comorbidity diseases in both groups. Upper lobe occupied almost in location. Hemoptysis symptoms plunged from time to time. Statistically significant Karnofsky score was observed in both groups. Postoperative pulmonary functions (FVC and FEV1) have remained in both groups at all time points. The remarkable results were no deaths related to surgery and low complications both short and long-term. There was no statistical significance between two groups in operative time, blood loss during operation, ICU length-stay time. Four patients died because of co-morbidity in 24 months follow-up.

Conclusion
Cavernostomy and thoracoplasty was safe and effective surgery for the treatment of complex pulmonary aspergilloma with hemoptysis in high-risk patients. No mortality related to surgery and low complications were recorded. The was no inferiority when compared two compressing materials .
Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer’s disease
Authors: Heo Go Eun , Xie Qing , Song Min , Lee Jeong-Hoon 
Published: December 2019

Abstract
Background
Extracting useful information from biomedical literature plays an important role in the development of modern medicine. In natural language processing, there have been rigorous attempts to find meaningful relationships between entities automatically by co-occurrence-based methods. It has been increasingly important to understand whether relationships exist, and if so how strong, between any two entities extracted from a large number of texts. One of the defining methods is to measure semantic similarity and relatedness between two entities.

Methods
We propose a hybrid ranking method that combines a co-occurrence approach considering both direct and indirect entity pair relationship with specialized word embeddings for measuring the relatedness of two entities.

Results
We evaluate the proposed ranking method comparatively with other well-known methods such as co-occurrence, Word2Vec, COALS (Correlated Occurrence Analog to Lexical Semantics), and random indexing by calculating top-ranked entities related to Alzheimer’s disease. In addition, we analyze gene, pathway, and gene–phenotype relationships. Overall, the proposed method tends to find more hidden relationships than the other methods.

Conclusion
Our proposed method is able to select more useful related entities that not only highly co-occur but also have more indirect relations for the target entity. In pathway analysis, our proposed method shows superior performance at identifying (functional) cross clustering and higher-level pathways. Our proposed method, resulting from phenotype analysis, has an advantage in identifying the common genotype relating to phenotypes from biological literature.
A study of deep learning methods for de-identification of clinical notes in cross-institute settings
Authors: Yang Xi , Lyu Tianchen , Li Qian , Lee Chih-Yin , Bian Jiang , Hogan William R. , Wu Yonghui 
Published: December 2019

Abstract
Background
De-identification is a critical technology to facilitate the use of unstructured clinical text while protecting patient privacy and confidentiality. The clinical natural language processing (NLP) community has invested great efforts in developing methods and corpora for de-identification of clinical notes. These annotated corpora are valuable resources for developing automated systems to de-identify clinical text at local hospitals. However, existing studies often utilized training and test data collected from the same institution. There are few studies to explore automated de-identification under cross-institute settings. The goal of this study is to examine deep learning-based de-identification methods at a cross-institute setting, identify the bottlenecks, and provide potential solutions.

Methods
We created a de-identification corpus using a total 500 clinical notes from the University of Florida (UF) Health, developed deep learning-based de-identification models using 2014 i2b2/UTHealth corpus, and evaluated the performance using UF corpus. We compared five different word embeddings trained from the general English text, clinical text, and biomedical literature, explored lexical and linguistic features, and compared two strategies to customize the deep learning models using UF notes and resources.

Results
Pre-trained word embeddings using a general English corpus achieved better performance than embeddings from de-identified clinical text and biomedical literature. The performance of deep learning models trained using only i2b2 corpus significantly dropped (strict and relax F1 scores dropped from 0.9547 and 0.9646 to 0.8568 and 0.8958) when applied to another corpus annotated at UF Health. Linguistic features could further improve the performance of de-identification in cross-institute settings. After customizing the models using UF notes and resource, the best model achieved the strict and relaxed F1 scores of 0.9288 and 0.9584, respectively.

Conclusions
It is necessary to customize de-identification models using local clinical text and other resources when applied in cross-institute settings. Fine-tuning is a potential solution to re-use pre-trained parameters and reduce the training time to customize deep learning-based de-identification models trained using clinical corpus from a different institution.
Age-related sex differences in the expression of important disease-linked mitochondrial proteins in mice
Authors: Moschinger Michael , Hilse Karolina E. , Rupprecht Anne , Zeitz Ute , Erben Reinhold G. , Rülicke Thomas , Pohl Elena E. 
Published: December 2019

AbstractThe prevalence and progression of many illnesses, such as neurodegenerative and cardiovascular diseases, obesity, and cancer, vary between women and men, often in an age-dependent manner. A joint hallmark of these diseases is some type of mitochondrial dysfunction. While several mitochondrial proteins are known to be regulated by sex hormones, the levels of those proteins have not been systematically analyzed with regard to sex and age, and studies that consider sex and/or age differences in the protein expression are very rare. In this study, we compared the expression patterns of physiologically important mitochondrial proteins in female and male C57BL/6N mice of age cohorts frequently used in experiments. We found that sex-related differences in the expression of uncoupling proteins 1 and 3 (UCP1 and UCP3) occur in an age-dependent manner. The sex-specific expression of UCP1 and UCP3 in brown adipose tissue (BAT) was inversely correlated with differences in body weight. Expression of UCP4 in the brain, Complex I in the spleen, and Complex II in the brain and BAT was least affected by the sex of the mouse. We further demonstrated that there are serious limitations in using VDAC1 and actin as markers in western blot analyses, due to their sex- and age-specific fluctuations. Our results confirm that sex and age are important parameters and should be taken into account by researchers who examine the mechanistic aspects of diseases.HighlightsThe levels of UCP1 and UCP3 protein expression differ between females and males in an age-dependent manner.Pre-pubertal expression of almost all proteins tested in this study does not depend on the sex of the mouse.Expression of VDAC1 and actin, which are often used as loading control proteins in western blot analysis, is tissue-specifically influenced by sex and age.
Effect of the luxI/R gene on AHL-signaling molecules and QS regulatory mechanism in Hafnia alvei H4
Authors: Li Xue , Zhang Gongliang , Zhu Yaolei , Bi Jingran , Hao Hongshun , Hou Hongman 
Published: December 2019

AbstractHafnia alvei H4 is a bacterium subject to regulation by a N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing system and is closely related to the corruption of instant sea cucumber. Studying the effect of Hafnia alvei H4 quorum sensing regulatory genes on AHLs is necessary for the quality and preservation of instant sea cucumber. In this study, the draft genome of H. alvei H4, which comprises a single chromosome of 4,687,151 bp, was sequenced and analyzed and the types of AHLs were analyzed employing thin-layer chromatography (TLC) and high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS). Then the wild-type strain of H. alvei H4 and the luxI/R double mutant (ΔluxIR) were compared by transcriptome sequencing (RNA-seq). The results indicate that the incomplete genome sequence revealed the presence of one quorum-sensing (QS) gene set, designated as lasI/expR. Three major AHLs, N-hexanoyl-l-homoserine lactone (C6-HSL), N-butyryl-l-homoserine lactone (C4-HSL), and N-(3-oxo-octanoyl)-l-homoserine lactone (3-oxo-C8-HSL) were found, with C6-HSL being the most abundant. C6-HSL was not detected in the culture of the luxI mutant (ΔluxI) and higher levels of C4-HSL was found in the culture of the luxR mutant (ΔluxR), which suggested that the luxR gene may have a positive effect on C4-HSL production. It was also found that AHL and QS genes are closely related in the absence of luxIR double deletion. The results of this study can further elucidate at the genetic level that luxI and luxR genes are involved in the regulation of AHL.
International workshop on the future of community child healthcare
Authors: Grossman Zachi , Porter Boaz , Meyerovitch Joseph , Rubin Lisa , Kuint Jacob , Wechsler Efrat , Dushnitzky Doron , Ashkenazi Shai 
Published: December 2019

AbstractIncreasing numbers of children with developmental, emotional, and psychosocial issues require adaptation of the services provided by pediatricians in the community. An international workshop that took place in Israel on June 3–4, 2019, addressed this need. Local policy makers and international experts discussed the following topics: (1) the future of training in community pediatrics; (2) enhancing the prestige of the community pediatrician; (3) development of management and research skills; (4) academic advancement within community pediatrics; (5) the future content of community pediatric practice; (6) visit length and community pediatricians’ reimbursement; (7) developing the collaborative model of care in community pediatrics and (8) integrating child healthcare. The meeting provided a venue to understand the challenges and to formulate recommendations to policymakers. A key target highlighted was the increased exposure of all pediatric residents to community pediatrics. This gained the support of the Chief Executive Officers of all four Health Funds in Israel. This document provides a synopsis of the topics addressed and suggested recommendations.
Do wastewater treatment plants increase antibiotic resistant bacteria or genes in the environment? Protocol for a systematic review
Authors: Rodríguez-Molina Daloha , Mang Petra , Schmitt Heike , Chifiriuc Mariana Carmen , Radon Katja , Wengenroth Laura 
Published: December 2019

Abstract
Background
Antibiotic resistance is a global public health threat. Water from human activities is collected at wastewater treatment plants where processes often do not sufficiently neutralize antibiotic resistant bacteria and genes, which are further shed into the local environment. This protocol outlines the steps to conduct a systematic review based on the Population, Exposure, Comparator and Outcome (PECO) framework, aiming at answering the question “Are antimicrobial-resistant enterobacteriaceae and antimicrobial resistance genes present (O) in air and water samples (P) taken either near or downstream or downwind or down-gradient from wastewater treatment plants (E), as compared to air and water samples taken either further away or upstream or upwind or up-gradient from such wastewater treatment plant (C)?” Presence of antimicrobial-resistant bacteria and genes will be quantitatively measured by extracting their prevalence or concentration, depending on the reviewed study.

Methods
We will search PubMed, EMBASE, the Cochrane database and Web of Science for original articles published from 1 Jan 2000 to 3 Sep 2018 with language restriction. Articles will undergo a relevance and a design screening process. Data from eligible articles will be extracted by two independent reviewers. Further, we will perform a risk of bias assessment using a decision matrix. We will synthesize and present results in narrative and tabular form and will perform a meta-analysis if heterogeneity of results allows it.

Discussion
Antibiotic resistance in environmental samples around wastewater treatment plants may pose a risk of exposure to workers and nearby residents. Results from the systematic review outlined in this protocol will allow to estimate the extend of exposure, to inform policy making and help to design future studies.