bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune microenvironment composition in non‐small cell lung cancer and its association with survival
Authors: Tamminga Menno , Hiltermann Thijo Jeroen N , Schuuring Ed , Timens Wim , Fehrmann Rudolf SN , Groen Harry JM 
Published: June 2020

AbstractObjectivesIn non‐small cell lung cancer (NSCLC), the immune system and possibly its composition affect survival. In this in silico study, the immune infiltrate composition in NSCLC patients was evaluated.MethodsGene expression data of tumors from early NSCLC patients were obtained from Gene Expression Omnibus (GEO). With CIBERSORT, 22 immune cell fractions were estimated.ResultsThe immune infiltrate of 1430 pretreatment NSCLC patients contained mostly plasma cells, macrophages and CD8 T cells. Higher fractions of resting mast and CD4 T‐helper cells were associated with longer overall survival (OS) (HR = 0.95, P < 0.01; HR = 0.98, = 0.04, respectively) and higher fractions of M2 macrophages and active dendritic cells with shorter survival (HR = 1.02, P = 0.03; HR = 1.03, P = 0.05, respectively). Adenocarcinoma patients with survival data (n = 587) showed higher fractions of resting mast and resting CD4 T cells, and lower M0 macrophages than squamous cell carcinoma (n = 254), which were associated with OS (HR = 0.95, P = 0.04; HR = 0.97, P = 0.01; HR = 1.03, P = 0.01, respectively). Fractions of memory B cells, naïve CD4 T cells and neutrophils had different associations with survival depending on the subtype. Smokers had had higher fractions of regulatory T cell, follicular helper T cell, neutrophil and M2 macrophage, which were associated with shorter survival (HR = 1.3, P < 0.01; HR = 1.13, P = 0.02; HR = 1.09, P = 0.03; HR = 1.04, P = 0.02, respectively).ConclusionPretreatment differences in immune cell composition in NSCLC are associated with survival and depend on smoking status and histological subtype. Smokers' immune composition is associated with lower survival.
Multiparameter Flow Cytometry Assay for Analysis of Nitrosative Stress Status in Human Spermatozoa
Authors: Uribe Pamela , Meriño Juan , Manquemilla Emilio , Villagrán Camila , Vega Etelinda , Zambrano Fabiola , Schulz Mabel , Pezo Felipe , Villegas Juana V. , Boguen Rodrigo , Sánchez Raúl 
Published: June 2020

AbstractMale infertility is an increasing health problem, and oxidative/nitrosative stress plays an important role in the etiology of this condition. Nitrosative stress due to excessive levels of reactive nitrogen species (RNS) is associated with impaired male fertility. Flow cytometry may be a useful tool for semen evaluation, but the availability of multiparameter assays for analysis of sperm quality is limited. The present study standardized a multiparameter flow cytometry analysis for nitrosative stress status in human spermatozoa in a single assay. A suitable multicolor fluorochrome panel was designed and consisted of fluorescein‐boronate to detect peroxynitrite, a highly RNS, propidium iodide to analyze viability, tetramethylrhodamine methyl ester perchlorate to detect mitochondrial membrane potential (MMP) and monobromobimane to analyze thiol oxidation. Proper positive and negative controls for each fluorochrome were used to establish the technique, and sperm cells of different qualities and spermatozoa subjected to cryopreservation were analyzed. The results showed that the controls clearly discriminated between the high and low fluorescence intensities for each fluorochrome. The analysis of sperm cells of different quality demonstrated that the assay properly detected differences in all parameters analyzed according to sperm quality. The results may be reported as the mean fluorescence intensity of each fluorochrome and the percentage of cells exhibiting different characteristics. In conclusion, a protocol was standardized to analyze nitrosative stress status, including peroxynitrite production, viability, MMP, and thiol oxidation, in a single analysis using flow cytometry. This protocol may be applied to research approaches and clinical andrology to improve the evaluation of sperm quality and provide a promising tool to increase the use of clinical flow cytometry. © 2020 International Society for Advancement of Cytometry
A multi‐parametric approach to remove the influence of plasma volume on the athlete biological passport during a Union Cycliste Internationale cycling stage race
Authors: Garvican‐Lewis Laura A. , Lobigs Louisa M. , Equey Tristan , Goebel Catrin , Agon Vanessa , McCowan Andrew , Speers Naomi , Schumacher Yorck O. 
Published: June 2020

AbstractFluctuations in plasma volume (PV) present potential confounders within the concentration‐based markers of the haematological athlete biological passport (ABP). Here, a multi‐parametric approach involving a simple blood test is applied to the current ABP adaptive model in an attempt to remove the influence of PV expansion, induced by a cycling stage race. Blood samples were obtained from 29 professional cyclists (14 male, 15 female) before, during and after 4–5 consecutive days of racing. Whole blood was analysed in accordance with the World Anti‐Doping Agency ABP guidelines for haemoglobin ([Hb]) concentration and platelets. Serum and plasma were analysed for transferrin, albumin, calcium, creatinine, total protein and low‐density lipoprotein. PV variation (Z‐scores) was estimated using a multi‐parametric model (consisting of the biomarkers mentioned earlier) and compared against calculated variations in PV (measured via CO‐rebreathing). Significant reductions in [Hb] and the OFF‐score were observed in female cyclists after 3 and 4 days of racing, with accompanying increases in PV, which returned to baseline values 4 days post competition. Similarly, a significant increase in PV was observed in male cyclists after 3 and 5 days of racing. When individual estimations of PV variance were applied to the adaptive model, the upper and lower reference predictions for [Hb] and the OFF‐score were refined such that all outliers consistent with racing‐induced PV changes were removed. The PV model appears capable of reducing the influence of PV on concentration‐dependent markers during competition. This is an important step towards the inclusion of the PV correction in the ABP haematological module.
Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?
Authors: Carey Chelsea J. , Glassman Sydney I. , Bruns Thomas D. , Aronson Emma L. , Hart Stephen C. 
Published: June 2020

AbstractGiant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next‐generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0–5 cm) beneath giant sequoia and co‐occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree‐associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove‐dependent.
Model‐based clustering reveals patterns in central place use of a marine top predator
Authors: Brost Brian M. , Hooten Mevin B. , Small Robert J. 
Published: June 2020

AbstractSatellite telemetry data are commonly used to quantify habitat selection, examine animal movements, and delineate home ranges. These data also contain valuable information concerning dens, nests, roosts, and other central places that are often associated with important life history events and may exhibit unique characteristics; however, using satellite telemetry data to study central places is complicated by common nuances like locational error and animal movement. We coupled a novel modeling framework that accounts for these nuances with an Argos satellite telemetry dataset to examine the spatiotemporal behavior associated with harbor seal haul‐out sites on Kodiak Island, Alaska, USA. The methodology incorporates an observation model that accommodates multiple sources of uncertainty in telemetry data and a flexible Bayesian nonparametric model to uncover latent clustering in the telemetry locations. We also contribute extensions to examine the effect of covariates on site selection and to obtain population‐level inference concerning central place use. Harbor seal haul‐out sites generally occurred in inlets and bays, areas that are isolated from the open water of the Gulf of Alaska. Most individuals selected haul‐out sites that were protected from wave exposure. The effects of bathymetry and shoreline complexity on haul‐out site selection were variable among individual seals, as were the effects of time of day, time since low tide, and day of year on temporal patterns of haul‐out use. As repositories of satellite telemetry data on a wide variety of species accumulate, so do opportunities for using this information to learn about the locations of central places, as well as the temporal patterns in their use. The model‐based approach we describe offers a practical and rigorous means for gaining insight concerning these sensitive locations, knowledge of which is important for the effective management and conservation of many species.
First interactions with the hydrologic cycle determine pyrogenic carbon's fate in the Earth system
Authors: Masiello Caroline Ann , Berhe Asmeret Asefaw 
Published: June 2020

AbstractFires produce an aromatic particulate residue commonly referred to as pyrogenic carbon (PyC). Particulate PyC is low density, high porosity, and is predominantly deposited on the soil surface in post‐fire landscapes. These characteristics create a material that is prone to mobility, both vertically down the soil profile and laterally across the landscape even in low‐relief landforms. Because of its tendency for lateral mobilization, we argue here that PyC's first interaction with water determines its environmental fate and persistence, not its interactions with soil minerals or microbes. PyC's first interactions with water determine: the amount of PyC that will enter the soil profile and experience microbial and geochemical alterations, whether it will be buried in depositional environments and stored on the landscape, or if it will be transported to streams and eventually to the ocean. Here we posit that this crucial first interaction with the hydrologic cycle occurs on the timescale of days to weeks, and therefore supersedes microbial decomposition as the primary control on PyC's environmental persistence. © 2020 John Wiley & Sons, Ltd.
Overexpression of H3K36 methyltransferase NSD in glial cells affects brain development in Drosophila
Authors: Kim Taejoon , Shin Hyewon , Song Bokyeong , Won Chihyun , Yoshida Hideki , Yamaguchi Masamitsu , Cho Kyoung Sang , Lee Im‐Soon 
Published: June 2020

AbstractNSD1 is a histone methyltransferase that methylates the lysine 36 at histone H3. NSD duplication is associated with short stature, microcephaly, intellectual disability, and behavioral defects in humans. Ectopic overexpression of NSD, an NSD1 homolog in Drosophila, was shown to induce developmental abnormalities via apoptosis. In this study, to investigate the effects of NSD overexpression on Drosophila brain development, we first examined the typical NSD expression pattern in larval brains and found that endogenous NSD promoter activity was detected only in subsets of glial cells. Pan‐glial, but not pan‐neuronal, NSD overexpression induced apoptosis in larval brain cells. However, pan‐glial NSD overexpression also induced caspase‐3 cleavage in neuronal cells. Among the various glial cell types, NSD overexpression in only astrocytic glia induced apoptosis and abnormal learning defects in the larval stage. Furthermore, NSD overexpression downregulated the expression of various astrocyte‐specific genes, including draper (drpr), possibly owing to an indirect effect of NSD overexpression‐induced astrocytic apoptosis. Since drpr plays a role in axon pruning during mushroom body (MB) formation in Drosophila astrocytes, we examined the effect of astrocytic NSD overexpression on this process and found that it disrupted the clearance of γ‐neurons in the MB, subsequently inducing arrhythmic locomotor activity of the fly. Thus, these results suggest that aberrant NSD overexpression may cause neurodevelopmental disorders by interfering with crucial functions of astrocytes in the brain, underlining the importance of the tightly controlled astrocytic NSD expression for proper neurodevelopment.
Development and evaluation of a water flow and solute transport model for furrow fertigation with surge flow
Authors: Ojaghlou Hassan , Sohrabi Teymour , Abbasi Fariborz , Javani Hamidreza 
Published: June 2020

AbstractOne of the important factors in fertilizer application efficiency in surface fertigation is the shape of inflow hydrographs. In this research, a fertigation model is developed to analyse the effect of surge flow on furrow fertigation. Saint‐Venant equations and the advection–dispersion equation were used to estimate water flow and solute transport characteristics, respectively. The field experiments, including different fertigation treatments with surge flow, were conducted to calibrate and evaluate the developed model. Most of the water and nitrate losses occurred through runoff; water losses through runoff ranged from 13.8 to 33.4%, while fertilizer losses varied between 5.1 and 47%. Water and nitrate losses in the second fertigation experiments were higher than those in the first due to the reduction of the surge effect. A comparison between simulated and observed data shows appropriate accuracy of the developed model; the root mean squared error (RMSE) index for nitrate and water runoff losses was 8.4 and 12.1%, respectively. Fertigation during all advance surges was recognized as the desirable option in furrow irrigation with a surge flow. © 2020 John Wiley & Sons, Ltd.
Predicting credit card fraud with Sarbanes‐Oxley assessments and Fama‐French risk factors
Authors: Westland James Christopher 
Published: June 2020

SummaryThis research developed and tested machine learning models to predict significant credit card fraud in corporate systems using Sarbanes‐Oxley (SOX) reports, news reports of breaches and Fama‐French risk factors (FF). Exploratory analysis found that SOX information predicted several types of security breaches, with the strongest performance in predicting credit card fraud. A systematic tuning of hyperparamters for a suite of machine learning models, starting with a random forest, an extremely‐randomized forest, a random grid of gradient boosting machines (GBMs), a random grid of deep neural nets, a fixed grid of general linear models where assembled into two trained stacked ensemble models optimized for F1 performance; an ensemble that contained all the models, and an ensemble containing just the best performing model from each algorithm class. Tuned GBMs performed best under all conditions. Without FF, models yielded an AUC of 99.3% and closeness of the training and validation matrices confirm that the model is robust. The most important predictors were firm specific, as would be expected, since control weaknesses vary at the firm level. Audit firm fees were the most important non‐firm‐specific predictors. Adding FF to the model rendered perfect prediction (100%) in the trained confusion matrix and AUC of 99.8%. The most important predictors of credit card fraud were the FF coefficient for the High book‐to‐market ratio Minus Low factor. The second most influential variable was the year of reporting, and third most important was the Fama‐French 3‐factor model R2 – together these described most of the variance in credit card fraud occurrence. In all cases the four major SOX specific opinions rendered by auditors and the signed SOX report had little predictive influence.
Evaluation of Applicants to Predoctoral Dental Education Programs: Review of the Literature
Authors: Ranney Richard R. , Wilson Margaret B. , Bennett Robert B. 
Published: June 2020

AbstractThis review finds that college GPA and DAT scores provide dental schools in the United States and Canada with defensible methods for selecting students. College GPA seems the best predictor of academic performance in dental school. The academic average (AA) of the DAT is a better predictor than is the perceptual ability test (PAT), but dental educators who believe that evidence of manual dexterity or perceptual ability must be a part of the admissions decision can find enough supporting evidence to justify doing so. When added to college GPA and the AA, information from the PAT may in fact enhance predictability. There is also evidence, however, that manual skills can be learned during routine dental curricular experiences. Overall, conventional admissions criteria at best account for about 40 percent of the variance in dental school performance, and most of this variance occurs during the early years of the curriculum. Studies are lacking for evaluating criteria that may predict success in admitting students for preferentially addressing current challenges, including achieving diversity of the workforce, ensuring access to care for all, interprofessional health care, ethics and professionalism, filling faculty positions, and conducting needed research. Schools should periodically validate all of their admissions criteria against expected performances and make corresponding adjustments.
Personality as a Predictor of Professional Behavior in Dental School: Comparisons with Dental Practitioners
Authors: Chamberlain T.C. , Catano V.M. , Cunningham D.P. 
Published: June 2020

AbstractThe purpose of this study was to examine the use of personality measures to predict the success of dental students (N=87) in clinical and academic courses and to compare their personality profiles to those of dental practitioners (N=130). A second purpose of the study was to develop a new criterion measure, the Student Professionalism Scale, based on competencies previously identified as necessary for professional success. The Canadian Dental Aptitude Test (DAT) predicted first‐year, preclinical academic success; the DAT Reading Comprehension component predicted third‐year clinical performance; and Perceptual Ability, the ability to deal with two‐ and three‐dimensional objects, predicted student professionalism. Results from the personality measure indicated that Conscientiousness and Neuroticism, and to a lesser extent Agreeableness, were significant predictors of both first‐year academic performance and professional behavior. In comparing the personality profiles of dental students to dental practitioners, students who were more similar to the dentists did better in their first year of coursework. Implications of the findings are discussed in the context of the dental admissions process.
Dentistry, Nursing, and Medicine: A Comparison of Core Competencies
Authors: Spielman Andrew I. , Fulmer Terry , Eisenberg Elise S. , Alfano Michael C. 
Published: June 2020

AbstractHealth care, including oral health care and oral health education, is under great stress in the United States. The cost of and access to care, the cost of dental education, and a shortage of educators have led leaders in dental education, organized dentistry, and the public sector to underscore the problem. One of the proposed solutions is to find synergies and new health care and education models by building bridges among the health professions. One potential solution is being implemented at the NYU College of Dentistry (NYUCD). Dentistry and nursing are seemingly unrelated professions, and they are rarely if ever modeled together. That is about to change with the joining together of NYUCD and the Division of Nursing of the NYU Steinhardt School of Education in creating a College of Nursing within the College of Dentistry. This process has not been without controversy. Following the Division of Nursing's request to join NYUCD, and the subsequent announcement of the proposed combination by NYU in December 2004, some members of the dental profession responded by questioning the appropriateness of the merger and the similarity of the two programs. Nevertheless, substantial parallels exist in the education and practice of dentists and nurse practitioners (NP) including basic, social, and some clinical science education, practice models, research synergies, and community service. However, similarities in the core competencies of these professions have not been analyzed formally and in detail. Accordingly, the purpose of this study was to compare the core competencies of nurse practitioner and dental education programs. The results show a surprising overlap of the core competencies of the dental and nursing professions (38 percent partial or total overlap). A similar overlap with medicine also exists, albeit lower (25.4 percent). These results are notable because they demonstrate that the three health professions, independently of one another, developed very similar basic competencies and learning objectives. These data should encourage other health professions programs to seek new collaborative models for education, beyond the current silos of training, and new health care delivery systems as has been strongly recommended by the Institute of Medicine. Such collaborative education redirects health care toward providing truly interdisciplinary comprehensive primary care for patients.
Compliance with Infection Control Programs in Private Dental Clinics in Jordan
Authors: Al‐Omari Mohammad Ahmad , Al‐Dwairi Ziad Nawaf 
Published: June 2020

AbstractThe aim of this study was to assess the compliance of general dental practitioners (GDPs) in the private sector in North Jordan with infection control measures. A pilot‐tested questionnaire about infection control measures was distributed in March 2004 to 120 private practices. The response rate was 91.66 percent. About 77 percent of dentists usually ask their patients about medical history, 36 percent were vaccinated against hepatitis B, 81.8 percent wear and change gloves during treatment and between patients, and 54.5 percent wear and change masks during treatment and between patients. Most dental practitioners (95.4 percent) reported that they changed extraction instruments and burs between patients. All dental practitioners reported that they changed saliva ejectors between patients, but only 41.8 percent changed handpieces between patients. Approximately 63 percent (69/110) used autoclaves for sterilization, 47.3 percent (52/110) used plastic bags to wrap sterilized instruments, and only 18 percent (20/110) disinfected impressions before sending them to dental labs. Fourteen percent used rubber dams in their clinics, and only 31.8 percent had special containers for sharps disposal. Based on these responses, approximately 14 percent of general dentists in this sample were considered to be compliant with an inventory of recommended infection control measures. In Jordan, there is a great need to provide formal and obligatory infection control courses and guidelines for private dentists by the Ministry of Health and the dental association in addition to distribution of standard infection control manuals that incorporate current infection control recommendations.