bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unstructured Data Are Superior to Structured Data for Eliciting Quantitative Smoking History From the Electronic Health Record
Authors: Ruckdeschel John C. , Riley Mark , Parsatharathy Sriram , Chamarthi Rajesh , Rajagopal Chakethraman , Hsu Hui Shuang , Mangold Doug , Driscoll Chiny 
Published: February 2023

PURPOSE Develop a method for extracting smoking status and quantitative smoking history from clinician notes to facilitate cohort identification for low-dose computed tomography (LDCT) scanning for early detection of lung cancer. MATERIALS AND METHODS A sample of 4,615 adult patients were randomly selected from the Multiparameter Intelligent Monitoring in Critical Care (MIMIC-III) database. The structured data were obtained by queries of the diagnosis tables using the International Classification of Diseases codes in use at that time. Unstructured data were drawn from clinician notes via natural language processing (NLP) using named entity recognition and our clinical data processing and extraction algorithms to identify two main clinical criteria for each smoking patient: (1) pack years smoked and (2) time from quit date (if applicable). A subset of 10% of the patient charts were manually reviewed for accuracy and precision. RESULTS The structured data revealed 575 (12.5%) ever smokers (current plus past use). None of these patients had quantification of their smoking history, and 4,040 (87.5%) had no smoking information in the diagnosis tables; consequently, a cohort of patients eligible for LDCT could not be determined. Review of the physician notes by NLP disclosed 1,930 (41.8%) ever smokers of whom 537 were active smokers and 1,299 former smokers, and in 94 cases, it could not be determined if they were active or former smokers. A total of 1365 patients (29.6%) had no smoking data recorded. When the smoking and the age criteria for LDCT were applied to this group, 276 were found to be eligible for LDCT using the USPSTF criteria. As determined by clinician review, our F-score for identifying patients eligible for LDCT was 0.88. CONCLUSION Unstructured data, obtained by NLP, can accurately identify a precise cohort that meets the USPSTF guidelines for LDCT.
High-Grade Serous Carcinoma at Risk-Reducing Salpingo-Oophorectomy in Asymptomatic Carriers of BRCA1/2 Pathogenic Variants: Prevalence and Clinical Factors
Authors: Stroot Iris A.S. , Brouwer Jan , Bart Joost , Hollema Harry , Stommel-Jenner Denise J. , Wagner Marise M. , van Doorn Helena C. , de Hullu Joanne A. , Gaarenstroom Katja N. , Beurden Marc , van Lonkhuijzen Luc R.C.W. , Slangen Brigitte F.M. , Zweemer Ronald P. , Gómez Garcia Encarna B. , Ausems Margreet G.E.M. , Boere Ingrid A. , van Engelen Klaartje , van Asperen Christi J. , Schmidt Marjanka K. , Wevers Marijke R. , de Bock Geertruida H. , Mourits Marian J.E. ,   on behalf of the HEBON Investigators
Published: February 2023

PURPOSE To investigate the prevalence of and clinical factors associated with high-grade serous carcinoma (HGSC) at risk-reducing salpingo-oophorectomy (RRSO) in asymptomatic BRCA1/2-pathogenic variant (PV) carriers. PATIENTS AND METHODS We included BRCA1/2-PV carriers who underwent RRSO between 1995 and 2018 from the Hereditary Breast and Ovarian cancer in the Netherlands study. All pathology reports were screened, and histopathology reviews were performed for RRSO specimens with epithelial abnormalities or where HGSC developed after normal RRSO. We then compared clinical characteristics, including parity and oral contraceptive pill (OCP) use, for women with and without HGSC at RRSO. RESULTS Of the 2,557 included women, 1,624 had BRCA1, 930 had BRCA2, and three had both BRCA1/2-PV. The median age at RRSO was 43.0 years (range: 25.3-73.8) for BRCA1-PV and 46.8 years (27.6-77.9) for BRCA2-PV carriers. Histopathologic review confirmed 28 of 29 HGSCs and two further HGSCs from among 20 apparently normal RRSO specimens. Thus, 24 (1.5%) BRCA1-PV and 6 (0.6%) BRCA2-PV carriers had HGSC at RRSO, with the fallopian tube identified as the primary site in 73%. The prevalence of HGSC in women who underwent RRSO at the recommended age was 0.4%. Among BRCA1/2-PV carriers, older age at RRSO increased the risk of HGSC and long-term OCP use was protective. CONCLUSION We detected HGSC in 1.5% ( BRCA1-PV) and 0.6% ( BRCA2-PV) of RRSO specimens from asymptomatic BRCA1/2-PV carriers. Consistent with the fallopian tube hypothesis, we found most lesions in the fallopian tube. Our results highlight the importance of timely RRSO with total removal and assessment of the fallopian tubes and show the protective effects of long-term OCP.
Aldosterone- and Cortisol Co-secreting Adrenal Cortical Neoplasm With Lipomatous and Myelolipomatous Metaplasia
Authors: Jinna Sruthi , Taftaf Rokana , Petros Firas G , Jun John Y 
Published: February 2023

Abstract
We report a case of a 58-year-old woman with a history of hypertension diagnosed at aged 35 years, on 5 antihypertensive agents and a history of intermittent spontaneous hypokalemia, was found to have a 6-cm left adrenal mass on computed tomography scan of the abdomen. The unenhanced computed tomography attenuation of the adrenal mass was −16 Hounsfield units (HU). The biochemical evaluation showed potassium of 2.8 mEq/L (SI unit, mmol/L) (reference range, 3.5-5.0), plasma aldosterone concentration of 61.3 ng/dL (SI unit, 1701 pmol/L) with plasma renin activity of 0.4 ng/mL/h (SI unit, μg/L/h). An overnight 1-mg dexamethasone suppression test showed nonsuppressible serum cortisol of 10.8 μg/dL (SI unit, 298 nmol/L). Dehydroepiandrosterone sulfate and ACTH were measured at 24.5 μg/dL (age-adjusted, 26-200) (SI unit, 0.66 μmol/L; 0.70-5.43) and &lt;5 pg/mL (SI unit, &lt; 1.1 pmol/L), respectively. Left adrenalectomy was performed and hydrocortisone therapy was initiated. Postoperatively and thereafter, her blood pressure was controlled with no antihypertensive agent. Seven months later, hydrocortisone therapy was stopped once her cortisol level had normalized. Pathology showed adrenal cortical neoplasm of uncertain malignant potential with associated lipomatous and myelolipomatous metaplasia. This is a rare case of aldosterone and cortisol co-secreting adrenal cortical neoplasm of uncertain malignant potential with lipomatous and myelolipomatous metaplasia. Although the majority of cases of myelolipoma are benign and nonfunctioning, this case emphasizes the importance of thorough hormonal and morphologic evaluation of the tumor.
SARS-CoV-2 infection alkalinizes the ERGIC and lysosomes through the viroporin activity of the viral envelope protein
Authors: Wang Wen-An , Carreras-Sureda Amado , Demaurex Nicolas 
Published: February 2023

ABSTRACTThe coronavirus SARS-CoV-2, the agent of the deadly COVID-19 pandemic, is an enveloped virus propagating within the endocytic and secretory organelles of host mammalian cells. Enveloped viruses modify the ionic homeostasis of organelles to render their intra-luminal milieu permissive for viral entry, replication and egress. Here, we show that infection of Vero E6 cells with the delta variant of the SARS-CoV-2 alkalinizes the endoplasmic reticulum (ER)–Golgi intermediate compartment (ERGIC) as well as lysosomes, mimicking the effect of inhibitors of vacuolar proton ATPases. We further show the envelope protein of SARS-CoV-2 accumulates in the ERGIC when expressed in mammalian cells and selectively dissipates the ERGIC pH. This viroporin action is prevented by mutations of Val25 but not Asn15 within the channel pore of the envelope (E) protein. We conclude that the envelope protein acts as a proton channel in the ERGIC to mitigate the acidity of this intermediate compartment. The altered pH homeostasis of the ERGIC likely contributes to the virus fitness and pathogenicity, making the E channel an attractive drug target for the treatment of COVID-19.
Detection of vertical root fractures by cone-beam computed tomography based on deep learning
Authors: Yang Pan , Guo Xiaolong , Mu Chuangchuang , Qi Senrong , Li Gang 
Published: February 2023

Objectives: This study aims to evaluate the performance of ResNet models in the detection of in vitro and in vivo vertical root fractures (VRF) in Cone-beam Computed Tomography (CBCT) images. Methods: A CBCT image dataset consisting of 28 teeth (14 intact and 14 teeth with VRF, 1641 slices) from 14 patients, and another dataset containing 60 teeth (30 intact and 30 teeth with VRF, 3665 slices) from an in vitro model were used for the establishment of VRFconvolutional neural network (CNN) models. The most popular CNN architecture ResNet with different layers was fine-tuned for the detection of VRF. Sensitivity, specificity, accuracy, PPV (positive predictive value), NPV (negative predictive value), and AUC (the area under the receiver operating characteristic curve) of the VRF slices classified by the CNN in the test set were compared. Two oral and maxillofacial radiologists independently reviewed all the CBCT images of the test set, and intraclass correlation coefficients (ICCs) were calculated to assess the interobserver agreement for the oral maxillofacial radiologists. Results: The AUC of the models on the patient data were: 0.827(ResNet-18), 0.929(ResNet-50), and 0.882(ResNet-101). The AUC of the models on the mixed data get improved as:0.927(ResNet-18), 0.936(ResNet-50), and 0.893(ResNet-101). The maximum AUC were: 0.929 (0.908–0.950, 95% CI) and 0.936 (0.924–0.948, 95% CI) for the patient data and mixed data from ResNet-50, which is comparable to the AUC (0.937 and 0.950) for patient data and (0.915 and 0.935) for the mixed data obtained from the two oral and maxillofacial radiologists, respectively. Conclusions: Deep-learning models showed high accuracy in the detection of VRF using CBCT images. The data obtained from the in vitro VRF model increases the data scale, which is beneficial to the training of deep-learning models.
Genomic profiles of Indonesian colorectal cancer patients
Authors: Abdullah Murdani , Meilany Sofy , Trimarsanto Hidayat , Malik Safarina G. , Sukartini Ninik , Idrus Firhat , Nursyirwan Saskia A. , Muzellina Virly N. , Pribadi Rabbinu R. , Utari Amanda P. , Maulahela Hasan , Syam Ari F. 
Published: February 2023

Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.
Determinants of pre-lacteal feeding practice in Ethiopia: Evidence from the 2019 Mini Demographic and Health Survey (MDHS), a community-based cross-sectional study
Authors: Molla Gebeyaw , Getachew Fikreselassie , Tadele Ashenif , Taye Girum , Taddele Tefera , Gonfa Geremew , Getnet Misrak , Shumet Tigist , Defar Atkure , Teklie Habtamu , Achamyeleh Hiwot , Tesfaye Hanim , Getachew Theodros 
Published: February 2023

Background: Every year, 10.9 million people die around the world. More than two-thirds of deaths were associated with inappropriate feeding practices. Within the first three days after birth, nearly two out of every five newborns are given fluids other than breast milk. The aim of this study was to assess the determinants of pre-lacteal feeding practice in Ethiopia among mothers who had a live birth child under the age of 24 months. Methods: Secondary data from Ethiopia's 2019 Mini Demographic and Health Survey (MDHS) were used. A stratified, two-stage cluster sampling method was employed in the MDHS. A total of 8,885 reproductive-age women were interviewed in the survey, but only 2,061 women with a live birth child under the age of two years were included. Our study focused on the details obtained for these 2,061 women. Logistic regression analysis was used to identify factors associated with pre-lacteal feeding practices among them. A Hosmer-Lemeshow goodness of fit test was used to check the model fitness and a multicollinearity test was used to diagnosis collinearity between independent variables. Results: The results revealed that 12.1% (95%CI; 10.30%, 13.9%) of the women practiced pre-lacteal feeding. Mothers who lived in pastoralist regions (AOR:3.2; 95%CI: 1.5-6.84), who hadn’t attended antenatal care (ANC) visits (AOR:3.83; 95%CI: 1.55-6.27), who had attended 1-3 visits (AOR:1.65; 95%CI: 1.15-3.94), who delivered at home (AOR:1.72, 95%CI: 1.20-2.43), those who delivered by Caesarean section (AOR:3.72; 95%CI: 2.32-5.96), mothers who started breastfeeding after one hour (AOR:4.41; 95%CI: 3.23-6.02) were identified as the groups most associated with pre-lacteal feeding. Conclusions: Pre-lacteal feeding was practiced by a significant number of women in this study. Living in a pastoralist region, attending 1-3 ANC visits, home delivery, caesarean section delivery, and late initiation of breastfeeding were the determinant factors of prelacteal feeding among the women.
A Prospective Study on the Transmission dynamics of Corona virus disease (2019) (COVID-19) among Household contacts in Delhi, India.
Authors: Sharma Pragya , Rao Shivani , Saxena Sonal , Manchanda Vikas , Chawla Rohit , Mariam Warisha , Basu Saurav , Rahman Anisur , Singh Meghachandra , Rana Neha , Athotra Aditya , Sharma Himanshi , Ahmad Mohammad 
Published: February 2023

Background: This study was conducted to understand the transmission dynamics of COVID-19 virus among the household contacts of RT-PCR confirmed cases to have an insight on key epidemiological characteristics of the infection. Methods: This was a prospective case-ascertained study conducted among the contacts of laboratory-confirmed COVID-19 cases residing in the same household in the Central and North-East districts of Delhi between 28th December 2020, and 28th June 2021. Data and specimen for reverse transcription polymerase chain reaction (RT-PCR) and serology were collected from the primary case and their contacts on day one of the visit, and follow-up collection of data and specimen was done on day 7, 14 and 28. A daily symptom diary was also maintained for all the primary cases and their contacts till 28 days from enrolment in the study. A total of 109 houses were enrolled in the study. Results: The secondary attack rate (SAR) estimated among the household contacts was 13.86% [95% C.I. 9.71%, 19.39%] and the secondary infection rate was 33.16% [95% C.I. 26.97%, 40.00%]. The serial interval and basic reproduction number (R0) within the household were estimated to be 3.6± 5.73 days and 1.26 [95% C.I. 1.21—1.31], respectively. Significant predictors of the infection were location of household in central district (SAR = 20% [13.75, 28.16]) versus North-East District (SAR = 4.87% [1.83-12.35]) p= 0.002, sharing of utensils (SAR= 42.85% [14.26—77.11], p=0.02), and using the room to sleep where a specific case has been isolated (SAR= 25% [12.97—42.71], p=0.047). Transmission from the symptomatic primary case was observed to be five times higher. Conclusion: Our analysis showed that the secondary infection rate was higher among household contacts. This study suggests a dose-response association between severity of the primary case of SARS CoV-2 and infection among contacts.
Multi-layer modelling of masonry structures strengthened through textile-reinforced mortar
Authors: Boem Ingrid 
Published: February 2023

Background Textile-reinforced mortar (TRM) is an innovative strategy for the reduction of the seismic vulnerability of existing masonry buildings consisting in the application on the masonry surface, of a mortar coating with fiber-based grids or textiles embedded. The paper presents the calibration and application of a simplified modelling approach, based on multi-layered elements, for the simulation of existing masonry elements and structures strengthened through TRM. Methods The strengthened masonry is modelled by using 20-nodes brick elements formed by a stacking sequence of layers representing the different material components (the masonry, the mortar coating and the embedded reinforcement). The nonlinear behavior of the materials is considered and calibrated on the basis of experimental characterization tests on individual components available in the literature. The simplified assumption of perfect bond among layers is considered. Results Non-linear static analyses are performed on samples of increasing complexity: elementary panels, structural elements (piers and spandrels) and a pilot building. The results of some tests on TRM strengthened masonry, available in the literature, are considered to assess the model reliability in terms of capacity curves and collapse mode. The model is capable of detecting the typical failure mechanism of both unstrengthened and TRM strengthened masonry, namely the diagonal cracking, the in-plane bending and the out-of-plane bending and is able to detect the activation also of mixed failure modes, that often occur in actual configurations. Conclusions Given the coarse mesh size and the smear plasticization assumption, the model is not suitable for the rigorous reproduction of individual cracks but represents a good compromise between the goal to grasp the structural performances at the wide scale, including failure modes, and the analysis optimization.
Comparative study of the attributive effects of fresh and canned Naftussya water
Authors: Popovych Andriy , Fil Vitaliy , Ruzhylo Sofiya , Zakalyak Nataliya , Żukow Xawery , Popovych Dariya 
Published: February 2023

Background. There are several patented methods of preservation of medicinal waters of the Naftussya type. The authors of the patents as evidence of the correctness of the methods cite the facts of preservation of the ability of canned water to enhance motility rat’s v. portae in vitro and/or increase diuresis. However, such tests are not attributive. The most characteristic manifestation of the biological activity of Naftussya water is the stimulation of phagocytosis. Another "Method of preservation of hydrogen sulfide mineral waters" was recently patented. Based on the above, we will use attributive tests for its verification. Materials and Methods. The object of clinical-physiological observation were residents of the city of Truskavets’ (21 men aged 24-67 years and 8 women 33-76 years) with chronic pyelonephritis in remission. The subject of the study were the phagocytic function of neutrophils, excretory function of kidneys as well as leukocyturia and bacteriuria levels and components of microbiota of feces. Results. Weekly use of fresh Naftussya water causes an increase in the reduced content of probiotics in the microbiota and a decrease in the increased content of conditionally pathogenic microflora, which is accompanied by an increase in reduced bactericidal capacity of neutrophils against both E. coli and Staph. aureus, normal diuresis, phosphaturia, magnesiumuria, ureauria while reduction of bacteriuria and leveling of leukocyturia as well as decrease in concentration of uric acid in urine and creatinine and cholesterol in plasma. The beneficial effect on the listed parameters of canned Naftussya water is less pronounced, but the differences are statistically insignificant. Conclusion. The obtained results confirm the effectiveness of the Dovzhenko© method for Naftusya water conservation and provide grounds for continuing research into the effects of canned Naftusya water on the body of urological patients.
Implant survival of total elbow arthroplasty: analysis of 514 cases from the Dutch Arthroplasty Registry
Authors: Macken Arno A. , Prkić Ante , van Oost Iris , Spekenbrink-Spooren Anneke , The Bertram , Eygendaal Denise 
Published: February 2023

AimsThe aim of this study is to report the implant survival and factors associated with revision of total elbow arthroplasty (TEA) using data from the Dutch national registry.MethodsAll TEAs recorded in the Dutch national registry between 2014 and 2020 were included. The Kaplan-Meier method was used for survival analysis, and a logistic regression model was used to assess the factors associated with revision.ResultsA total of 514 TEAs were included, of which 35 were revised. The five-year implant survival was 91%. Male sex, a higher BMI, and previous surgery to the same elbow showed a statistically significant association with revision (p < 0.036). Of the 35 revised implants, ten (29%) underwent a second revision.ConclusionThis study reports a five-year implant survival of TEA of 91%. Patient factors associated with revision are defined and can be used to optimize informed consent and shared decision-making. There was a high rate of secondary revisions.Cite this article: Bone Jt Open 2023;4(2):110–119.