bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Nicotine and Porphyromonas gingivalis on the Differentiation Properties of Periodontal Ligament Fibroblasts
Authors: Panpradit Naruemon , Nilmoje Thanapoj , Kasetsuwan Julalux , Sangkhamanee Sujiwan Seubbuk , Surarit Rudee 
Published: July 2021

Abstract
Objectives This study aimed to evaluate the effect of Porphyromonas gingivalis and nicotine on the in vitro osteogenic differentiation of periodontal ligament (PDL) fibroblasts.
Materials and Methods PDLs were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum at 37°C under 5% CO2 and 100% humidified atmosphere. Cells were incubated with various concentrations of nicotine and P. gingivalis extracts, and cell viability was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay. To study cell differentiation, PDLs (5 × 104cells) were treated with the osteogenic differentiation medium containing 10 mM β-glycerophosphate, 10 nM dexamethasone, 50 mg/mL ascorbic acid, 1 μM nicotine, and 50 µg/mL P. gingivalis lysate. mRNA samples were collected at 0, 7, and 14 days. Odontogenic-related gene expression, namely, Runt-related transcription factor 2 (Runx2), collagen type I (COL1A1), and alkaline phosphatase (ALP) was determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Calcified nodule formation was determined on day 28 using Alizarin Red S. Analysis of variance and Tukey’s test were used to compare the difference among groups at significant level of p < 0.05.
Results It showed that 50 µg/mL of P. gingivalis lysate and 1 µM of nicotine showed no toxicity to PDLs. Runx2, COL1A1, and ALP expression were found to decrease significantly after 7 days of treatment, while osteocalcin expression was found to decrease after 14 days. The nodule formation in the control group was much greater in both number and size of nodules than in experimental groups, which implied a positive sign of calcium deposition in controls.
Conclusion The results indicated that nicotine and P. gingivalis showed adverse effect on osteogenic differentiation properties of PDLs.
Right Ventricle Embolization of IVC Filter Fragments: An Incidental Finding
Authors: Miyara Santiago J. , Guevara Sara , Shore-Lesserson Linda , Shoaib Muhammad , Kirsch Claudia , Metz Christine N. , Nair Vinay , Lau Lawrence , Choudhary Rishabh C. , McCann-Molmenti Alexia , Baez Anthony M. , Hayashida Kei , Takegawa Ryosuke , Shinozaki Koichiro , Aoki Tomoaki , Nishikimi Mitsuaki , Cho Young Min , Morell Alexis , Zafeiropoulos Stefanos , Zanos Stavros , Watt Stacey , Montorfano Lisandro , Bartoc Cristian D. , Lumermann Claudio M. , Aronsohn Judith , Becker Lance B. , Molmenti Ernesto P. 
Published: July 2021

AbstractThis case report describes a 52-year-old male patient, with the incidental finding of inferior vena cava filter (IVCF) fragments impacted into the right ventricle, secondary to IVCF fragmentation and subsequent embolization. While IVCFs are prescribed to prevent pulmonary embolizations when anticoagulation is either contraindicated, or has failed, IVCF embolizations to the heart represent an extremely rare, but potentially life-threatening complication. Of note, at the time of writing, the utility and effectiveness of IVCF are not fully established. Intracardiac embolizations of IVCF typically present with complications such as hypotension, cardiac tamponade, arrhythmias, ventricle perforation, bleeding, cardiac arrest, and death. To our knowledge, this is the first case report of an asymptomatic kidney transplant recipient found to have right ventricle embolizations of IVCF fragments through routine assessment. Additionally, this is also the first report of an asymptomatic patient who presented IVCF fragments embolized to the right ventricle and left gonadal vein in the same clinical setting.
Secondary Immune Thrombocytopenia (ITP) Associated with ChAdOx1 Covid-19 Vaccination – A Case Report
Authors: Koch Martin , Fuld Sybille , Middeke Jan M. , Fantana Julia , von Bonin Simone , Beyer-Westendorf Jan 
Published: July 2021

AbstractNovel mRNA and vector-based covid-19 vaccinations have shown high efficacy in preventing symptomatic COVID-19 infections. Compared with the number of performed vaccinations, rates of severe side effects seem low. Rare prothrombotic coagulation disorders with suspected association to ChAdOx1 nCoV-19 (AstraZeneca) have been reported. These cases have gathered considerable media attention and caused a temporary pause of usage of the AstraZeneca vaccine in Europe and several other countries and are currently discussed as vaccine-induced immune thrombotic thrombocytopenia (VITT). However, hemorrhagic complications from ChAdOx1 nCoV-19 vaccination have also been reported but, so far, received less public attention despite considerable potential for life-threatening complications. Here we present a case of severe immune thrombocytopenia after ChAdOx1 covid-19 vaccination and its successful primary management.
The Action of Efflux Pump Genes in Conferring Drug Resistance to Klebsiella Species and Their Inhibition
Authors: Ashwath Priyanka , Sannejal Akhila Dharnappa 
Published: July 2021

AbstractNosocomial infections caused by Klebsiella species are characterized by high rates of morbidity and mortality. The emergence of the multidrug-resistant (MDR) and extensive drug-resistant (XDR) Gram-negative bacteria reduces the antibiotic efficacy in the treatment of infections caused by the microorganisms. Management of these infections is often difficult, due to the high frequency of strains resistant to multiple antimicrobial agents. Multidrug efflux pumps play a major role as a mechanism of antimicrobial resistance in Gram-negative pathogens. Efflux systems are significant in conferring intrinsic and acquired resistance to the bacteria. The emergence of increasing drug resistance among Klebsiella pneumoniae nosocomial isolates has limited the therapeutic options for treatment of these infections and hence there is a constant quest for an alternative. In this review, we discuss various resistance mechanisms, focusing on efflux pumps and related genes in conferring resistance to Klebsiella. The role of various efflux pump inhibitors (EPIs) in restoring the antibacterial activity has also been discussed. In specific, antisense oligonucleotides as alternative therapeutics in combatting efflux-mediated resistance in Klebsiella species have focused upon.
A Descriptive Analysis of Capsule Endoscopy Events in the FDA Manufacturer and User Facility Device Experience (MAUDE) Database
Authors: Ji Hangyu , Wang Shaoli , Gong Yang 
Published: July 2021

Abstract
Introduction The malfunction of capsule endoscopy (CE) devices is a significant reason for the failure of CE procedures, which could hinder and prevent diagnosis. Unfortunately, malfunction-related adverse events (AEs) caused by CE devices are rarely reported in publications. Although most malfunction-related AEs could not lead to physical harm, they could reduce the efficiency of medical care and increase medical costs. The manufacturer and user facility device experience (MAUDE) database, a publicly accessible resource for patient safety, contains not only the common complications of CE but also valuable malfunction-related AEs, which have been underutilized. Therefore, the study aims to discover and analyze the possible AEs associated with CE and demonstrate the utility of the MAUDE reports to promote patient safety.
Materials and Methods We acquired MAUDE reports of CE systems from January 01, 2008, to July 31, 2020, through a systematic search strategy. We utilized the manufacturers, brand names, and product codes as search terms from which medical device reports including structured data and narrative texts were extracted, followed by a manual review of the narrative texts, reporter occupation, device involved, event type and the phase of the event; finally, patient outcomes were recorded and analyzed as per CE categories and characteristics.
Results A total of 377 CEs medical device reports were retrieved, and 342 reports were included after reviewing. There were 327 mandatory reports (96%) and 15 voluntary reports (4%). These reports referred to capsule endoscope (n = 213), sensing system (n = 66), patency capsule (n = 38), and capsule delivery device (n = 26). A total of 349 CE-related AEs were identified, including complications (n = 228), malfunction-related AEs (n = 109), and other events (n = 12). The composition of AEs was not the same for the CE devices. Complications were major AEs of capsule endoscope and patency capsule, but malfunction-related AEs were the most common in AEs of sensing systems and capsule delivery devices.
Conclusion MAUDE serves as an invaluable data source for investigating malfunction-related AEs. In addition to common complications, malfunction of CE devices could threaten patient safety in CE procedures. Improving awareness of the malfunction of CE devices and raising adequate training for staff working in gastrointestinal (GI) endoscopic units could be critical and beneficial in preventing malfunction-related AEs.
Detection of Colon Polyps in India—A Large Retrospective Cohort Study (DoCPIr)
Authors: Jagtap Nitin , Singh Aniruddha Pratap , Inavolu Pradev , Tandan Manu , Godbole Shubhankar , Ambardekar Pranav , Sekaran Anuradha , Lakhtakia Sundeep , Ramchandani Mohan , Kalapala Rakesh , Gupta Rajesh , Reddy P. Manohar , Nabi Zaheer , Chavan Radhika , Rao G. Venkat , Reddy D. Nageshwar 
Published: July 2021

Abstract
Objective Colorectal cancer (CRC) is an emerging public health problem in Asia and India. However, there is scarcity of data on CRC and adenoma. We aimed to study prevalence and characteristics of colonic polyps in a large retrospective cohort.
Methods For this retrospective single center study, all patients with age > 18 years undergoing colonoscopy from January 2018 to December 2019 were included. Age, gender, and polyp characteristics were collected from endoscopy and histology database. Patients with incomplete histology reports and anal canal polyps were excluded. Based on histology, polyps were divided into adenocarcinoma, adenoma with advanced pathology (AAP; size > 10 mm, villous morphology or high-grade dysplasia), nonadvanced adenomas (nAAP), and nonadenomas.
Results Overall colon polyp prevalence was 10.18% (3551/34893). The mean age (standard deviation [SD]) was 51.51 (14.84) with 75.4% males, of which 128 (3.6%) were adenocarcinoma. A total of 1514 (42.64%) were adenomas; 344 (9.7%) were AAP and 1170 (32.9%) were nAAP. The remaining 1909 (53.8%) were nonadenomas. Colonic adenoma prevalence after excluding adenocarcinoma was 4.35% (1514/34893). Adenocarcinoma (68.8% vs. 31.2%), AAP (70.6% vs. 29.4%), other adenomas (75.4% vs. 24.6%), and nonadenomas (76.7% vs. 23.3%) were significantly higher in male compared with female (p < 0.05). Adenomas and adenocarcinomas were more common in left colon and rectum than right colon (p < 0.05). The mean age (SD) were significantly lower in nonadenomas than adenocarcinomas, AAP, and other adenomas (p 0.0001; 49.25 [14.84] vs. 55.97 [12.47], 54.78 [16.40], 53.76 [13.71]).
Conclusions The prevalence of colonic adenoma in India is 4.35%. Male gender and increased age were associated with increased risk of colonic adenoma and adenocarcinoma, which is more common in left colon and rectum. Prospective multicenter studies are required for evaluation of other risk factors of CRC and colonic adenomas.
Assessment and Management of Acute Volar Rim Fractures
Authors: Heifner John J. , Orbay Jorge L. 
Published: July 2021

AbstractThe volar rim of the distal radius is the only bony restraint to volar carpal subluxation. Higher loads across the volar rim require stable and rigid fixation to maintain reduction and allow healing while rehabilitation begins. Volar marginal fragments are not amenable to buttressing by fixed angle volar locking plates. Appropriate management of volar marginal fragments comprises two steps—recognition of their presence and rigid anatomical repair. The best opportunity for success in the presence of a volar marginal fragment is its adequate initial treatment. The purpose of this review is to reinforce the importance of a complete preoperative and intraoperative evaluation of distal radius fractures. Volar marginal fragments can easily be overlooked even following initial reduction and fixation. Understanding the relevant anatomy and loading parameters can facilitate intraoperative decisions on approach and fixation, which are integral to achieving optimal clinical outcomes.
Clinico-radio-pathological Features and Biological Behavior of Breast Cancer in Young Indian Women: A Prospective Study
Authors: Sudhir Rashmi , Sannapareddy Kamala , Potlapalli Alekya , Penmetsa Vidhatri 
Published: July 2021

AbstractAims The aim of the study is to evaluate the characteristic imaging features of breast cancer on mammogram, ultrasound, and magnetic resonance imaging (MRI) in women less than 40 years of age and to assess the degree of correlation between clinico-radio-pathological features and biological behavior.Methods and Materials A prospective observational study on consecutive women under 40 years of age evaluated with ultrasound of breast, digital mammogram, or contrast-enhanced breast MRI, diagnosed with breast cancer on histopathology and molecular analysis done at our center between January and December 2019 were included. Patient demographics, clinical presentation, family history, BRCA mutation status, imaging, pathological findings, and molecular status were determined.Results Out of 2,470 women diagnosed with breast cancer, 354 (14.3%) were less than 40 years of age who were included in this study. Mammography showed positive findings in 85%, ultrasonography in 94.3%, and MRI in 96.4% of women. Majority of the women (69.6%) presented in the late stage (Stage III and IV) with high-grade carcinoma in 39.5% and triple-negative breast cancer (TNBC) in 45.7%. Tumors with human epidermal growth factor-2neu expression were associated with the presence of microcalcifications (p-value = 0.006), and TNBC with circumscribed margins or BI-RADS 3/4a category on imaging (p-value = 0.007) and high-grade invasive carcinoma compared with others (p-value <0.0001).Conclusion The incidence of breast cancer in Indian women less than 40 years of age is relatively high as compared with the West. The detection of breast cancer in young women remains challenging due to dense breast tissue, lower incidence rate, and lack of regular breast screening. While ultrasound is the recommended imaging method for evaluation of breast under the age of 40 years, we found a better characterization of lesions and higher cancer detection rates when they were also evaluated with mammography and MRI.
Detecting mechanical breakpoints during treadmill‐based graded exercise test: Relationships to ventilatory thresholds
Authors: Li Siu Nam , Peeling Peter , Hansen Clint , Van Alsenoy Ken , Ryu Joong Hyun , Girard Olivier 
Published: July 2021

ABSTRACTBackground: While changes in cardio‐respiratory variables during graded exercise tests (GXTs) are well described, less is known about running mechanical alterations. Purpose: We determined mechanical breakpoints during GXT and compared their temporal location with thresholds in ventilation. Methods: Thirty‐one recreational male runners completed continuous GXT on an instrumented treadmill, starting at 2.5 m.s−1 with velocity increases of +0.14 m.s−1 every 30 s. Subsequently, the first and second ventilatory thresholds (VT1 and VT2) were determined from expired gases. Spatio‐temporal and antero‐posterior force variables, and spring‐mass model characteristics were averaged for each stage. Mechanical breakpoints were detected using a linear fit process that partitioned the timeseries into two regions and minimised the error sum of squares. All measurements were normalised to % GXT duration for subsequent comparisons. Results: Fifteen out of 16 mechanical variables (all except leg stiffness) displayed breakpoints occurring between 61.9% and 82.3% of GXT duration; these occurred significantly later than VT1 (46.9 ± 6.4% of GXT duration, p < .05). Mechanical breakpoints for eight variables (step frequency, aerial time, step length, peak push‐off force, braking impulse, peak vertical force, maximal downward vertical displacement and leg compression) occurred at a time point not different to VT2 (75.3 ± 6.2% of GXT duration; all p > .05). Relationships between mechanical breakpoints and either VT1 or VT2 were weak (all r < 0.25). Conclusion: During treadmill GXT, breakpoints can be detected for the vast majority of mechanical variables (except leg stiffness), yet these are not related with ventilatory thresholds.
Elucidating mutual mate choice: effects of trial design on preferences of male zebra finches
Authors: Martin John O , Burley Nancy Tyler 
Published: July 2021

AbstractUnderstanding the dynamics of mutual mate choice requires investigation of mate preferences of both sexes using a variety of designs, but fewer studies have focused on male choice in avian models. Here we conducted two experiments on preferences of male zebra finches to study the impact of trial design on results. Experimental design varied in number of trial participants, inclusion of observer (“audience”) males, and housing design for stimulus females. Females were reared on one of two diets to enhance variation in mating quality: those reared on a protein-supplement diet (HI-diet) were predicted to be more attractive to males than (LO-diet) females that did not receive supplements. Results differed among trial types. Notably, males showed the predicted preference for HI-diet females only in the Group Choice experiment, where two male subjects simultaneously chose from a field of four females, and all six birds interacted freely. In the Dyadic Preference (DP) experiment, a single male was allowed to interact with two stimulus females that were physically isolated; in half of these trials, audience males were present. In DP trials without audience males, test males did not express a preference consensus; however, with audience males present, test males preferred LO-diet females. Results are consistent with a small but growing literature indicating that results of mate choice experiments can be highly sensitive to design considerations.
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions
Authors: Li Gen , Panday Shailesh Kumar , Peng Yunhui , Alexov Emil 
Published: July 2021

Abstract

Motivation
Mutations that alter protein–DNA interactions may be pathogenic and cause diseases. Therefore, it is extremely important to quantify the effect of mutations on protein–DNA binding free energy to reveal the molecular origin of diseases and to assist the development of treatments. Although several methods that predict the change of protein–DNA binding affinity upon mutations in the binding protein were developed, the effect of DNA mutations was not considered yet.

Results
Here, we report a new version of SAMPDI, the SAMPDI-3D, which is a gradient boosting decision tree machine learning method to predict the change of the protein–DNA binding free energy caused by mutations in both the binding protein and the bases of the corresponding DNA. The method is shown to achieve Pearson correlation coefficient of 0.76 and 0.80 in a benchmarking test against experimentally determined change of the binding free energy caused by mutations in the binding protein or DNA, respectively. Furthermore, three datasets collected from literature were used to do blind benchmark for SAMPDI-3D and it is shown that it outperforms all existing state-of-the-art methods. The method is very fast allowing for genome-scale investigations.

Availabilityand implementation
It is available as a web server and a stand-code at http://compbio.clemson.edu/SAMPDI-3D/.

Supplementary information
Supplementary data are available at Bioinformatics online.
O2 Mortality following elective and emergency colorectal surgery in patients with cirrhosis: a population-based cohort study
Authors: Adiamah A , Crooks C J , Hammond J S , Jepsen P , West J , Humes D J 
Published: July 2021

Abstract

Introduction
This population based cohort study, aimed to quantify the risk of mortality following colectomy in patients with cirrhosis by urgency of surgery and stage of cirrhosis.

Method
Linked primary and secondary-care electronic healthcare data from England was used to identify all patients undergoing colectomy from January 2001 to December 2017. Patients were classified into three cohorts, non-cirrhotics, compensated cirrhotics and decompensated cirrhosis and followed up for 90-days from the date of surgery. Cox proportional hazards models were used to estimate the hazard ratio (HR) of postoperative mortality.

Result
A total of 36380 eligible patients were included. Of these, 248(0.7%) had liver cirrhosis and 70% had compensated disease. The proportion undergoing a colectomy who had a diagnosis of cirrhosis increased from 0.40% in 2001 to 1.07% in 2017 (χ2(16, N = 36380)=50.53, P &lt; 0.0001).
Following elective colectomy, 90-day case fatality was 4% in non-cirrhotics , 7% in compensated cirrhotics and 10% in decompensated cirrhotics. Following emergency colectomy 90-day case fatality was higher, it was 16% in non-cirrhotics, 35% in compensated cirrhotics and 41% in decompensated cirrhotics. This corresponded to an adjusted 2-fold (HR 2.57(95% CI 1.75–3.76)) and 3-fold (3.43(95% CI 2.02–5.83)) increased mortality rate in compensated and decompensated cirrhotics respectively compared to non-cirrhotics following emergency colectomy.

Conclusion
Over the study period, the proportion of patients undergoing colectomy who had liver cirrhosis increased to 1 in every 100 colectomies. The 90-day case fatality rates were high in all patients with cirrhosis in both emergency and elective settings but the greatest mortality risk was seen in those with decompensation following emergency surgery.

Take-home Message
1 in 100 colectomy procedures are in patients with cirrhosis. These cirrhotic patients have a very high risk of postoperative mortality, especially, emergency colectomy in patients with decompensated cirrhosis.