bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Tissue Yield Using Frictional Fabric Brush Versus Sharp Curettage For Endocervical Curettage
Authors: Diedrich Justin T. , Rathore Sumra , Bentz Joel S. 
Published: July 2017

Objective
The aim of the study was to evaluate and compare the diagnostic yield of conventional endocervical curettage (ECC) with fabric-based ECC in a consistent physician group.

Materials and Methods
This is a retrospective case-control study of patients who underwent ECC both before and after introduction of a fabric-based ECC device. Histologic examination of curettings was categorized as satisfactory, limited, or inadequate. The Kruskall-Wallis test was used to compare proportions of gross descriptions and final diagnoses between groups.

Results
Between January 2010 and July 2011, 9234 ECCs were performed using conventional ECC technique. From September 2011 to October 2013, 774 ECCs were performed with the fabric-based ECC. Using the conventional ECC technique, 7809 (84.6%) of specimens were satisfactory, 1037 (11.2%) were limited, and 388 (4.2%) were inadequate and repeat biopsy was recommended. With fabric ECC, 705 (91.1%) of specimens were satisfactory, 64 (8.3%) were limited, and 5 (0.6%) were inadequate, and repeat biopsy was recommended. There were significantly fewer inadequate specimens with the fabric-based ECC (4.2% vs 0.6%, p < .001).

Conclusions
Fabric-based ECC may significantly decrease inadequate and limited ECC specimens.
The Marginal Costs of Adverse Drug Events Associated With Exposures to Anticoagulants and Hypoglycemic Agents During Hospitalization
Authors: Spector William D. , Limcangco Rhona , Furukawa Michael F. , Encinosa William E. 
Published: July 2017

Background:
Anticoagulants and hypoglycemic agents are 2 of the most challenging drug classes for medical management in the hospital resulting in many adverse drug events (ADEs).

Objective:
Estimating the marginal cost (MC) of ADEs associated with anticoagulants and hypoglycemic agents for adults in 5 patient groups during their hospital stay and the total annual ADE costs for all patients exposed to these drugs during their stay.

Research Design and Subject:
Data are from 2010 to 2013 Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases and Medicare Patient Safety Monitoring System (MPSMS). Deidentified patients were linked using probabilistic matching in the same hospital and year for 5 patient groups. ADE information was obtained from the MPSMS using retrospective structured record review. Costs were derived using HCUP cost-to-charge ratios. MC estimates were made using Extended Estimating Equations controlling for patient characteristics, comorbidities, hospital procedures, and hospital characteristics. MC estimates were applied to the 2013 HCUP National Inpatient Sample to estimate annual ADE costs.

Results:
Adjusted MC estimates were smaller than unadjusted measures with most groups showing estimates that were at least 50% less. Adjusted anticoagulant ADE costs added >45% and Hypoglycemic ADE costs added >20% to inpatient costs. The 2013 hospital cost estimates for ADEs associated with anticoagulants and hypoglycemic agents were >$2.5 billion for each drug class.

Conclusions:
This study demonstrates the importance of accounting for confounders in the estimation of ADEs, and the importance of separate estimates of ADE costs by drug class.
Prediction of Orthokeratology Lens Decentration with Corneal Elevation
Authors: Chen Zhi , Xue Feng , Zhou Jiaqi , Qu Xiaomei , Zhou Xingtao 
Published: July 2017

SIGNIFICANCE
Lens decentration is common and unavoidable to some extent during ortho-k treatment. By using a simplified method, we are able to predict the magnitude and direction of ortho-k lens decentration, which provides useful insights in screening for ideal ortho-k candidates and to make a quick decision when decentration happens.

PURPOSE
The aim of this study was to investigate the influence of corneal elevation asymmetry on ortho-k lens decentration.

METHODS
Thirty-six eyes of 36 subjects were fitted with four-curve reverse geometry ortho-k contact lenses. Corneal topography was collected before and 1 month after ortho-k lens wear. The difference in corneal elevation at the 8-mm chord of the respective two principal meridians of corneal astigmatism was calculated. Vector analyses were performed on these differences to calculate the magnitude and direction of a vector (corneal asymmetry vector). The relationship between the angle and magnitude of corneal asymmetry vector and lens decentration was analyzed.

RESULTS
Baseline refractive sphere and cylinder for the 36 tested eyes were −2.84 ± 1.04 diopters (D) (range, −4.75 to −1.00 D) and −0.21 ± 0.28 D (range, −1.00 to 0 D), respectively. The mean magnitude of lens decentration was 0.72 ± 0.26 mm (0 to 1.34 mm). For overall displacement, inferotemporal decentration was the most common as observed in 24 eyes (67%). The mean angle of the corneal asymmetry vector (202 ± 39 degrees) was significantly correlated to the mean angle of lens decentration (200 ± 39 degrees) (r = 0.76, P < .001). The magnitude of corneal asymmetry vector significantly contributed to the magnitude of lens decentration (standardized β = 0.448, P = .002) whereas the other tested variables did not affect lens decentration (all P > .05).

CONCLUSIONS
Lens decentration is a common phenomenon in ortho-k that mostly happens toward the inferotemporal quadrant of the cornea. The magnitude and direction of lens decentration are predetermined by paracentral corneal asymmetry.
The Influence of Chloride for the Interpretation of Plasma Bicarbonate During the Treatment of Diabetic Ketoacidosis
Authors: Ferreira Juan Pablo , Hamui Magali , Torrents Milagros , Carrano Romina , Ferraro Mabel , Toledo Ismael 
Published: July 2017

Introduction
Hyperchloremic metabolic acidosis can occur in diabetic ketoacidosis (DKA) and may affect the acid-base interpretation during treatment.

Objectives
This study aims to describe the prevalence of hyperchloremia during the treatment of DKA and its effect on the interpretation of bicarbonate value.

Methods
A cross-sectional study, including all cases of DKA in patients aged 1 to 18 years old admitted from 2010 to 2015, was performed. Laboratory tests were performed on admission (baseline), 2 and 6 hours after admission, and when resolution of DKA was achieved. Adjusted bicarbonate value was calculated using regression equations.

Results
Seventy-nine DKA episodes were included. The average age was 13.3 ± 3.8 years. Baseline levels were as follows: plasma glucose, 479 ± 133 mg/dL; pH 7.1 ± 0.083; bicarbonate, 9.65 ± 2.9; and anion gap, 23.9 ± 7.5. The time to achieve resolution of DKA was 12.2 ± 4.4 hours, and the decrease in capillary glucose was 25.5 (19.7–38.2) mg/dL per hour. After 6 hours of treatment, the proportion of patients presenting hyperchloremia increased from 23% to 77%. By using adjusted bicarbonate, the percentage of patients achieving resolution of DKA after 6 hours of treatment would have been 35.4% (confidence interval 95%, 28–49), in comparison with 24.1% (confidence interval 95%, 18–37) using observed bicarbonate (P = 0.004).

Conclusions
The hyperchloremia developed during the treatment of DKA could modify the value of measured plasma bicarbonate concentration and unnecessarily prolong the initial phase of treatment.
Evaluation of Gadolinium Retention After Serial Administrations of a Macrocyclic Gadolinium-Based Contrast Agent (Gadobutrol)
Authors: Yoo Roh-Eul , Sohn Chul-Ho , Kang Koung Mi , Yun Tae Jin , Choi Seung Hong , Kim Ji-hoon , Park Sun-Won 
Published: July 2017

Objective
There has been controversy as to whether gadobutrol, one of the widely used macrocyclic gadolinium-based contrast agents, can lead to gadolinium retention after serial injections. Our aim was to validate whether serial administrations of gadobutrol can cause signal increase in the dentate nucleus (DN) and globus pallidus (GP) on unenhanced T1-weighted magnetic resonance (MR) images due to gadolinium retention.

Materials and Methods
A total of 189 patients who had undergone at least 2 contrast-enhanced MR scans using only gadobutrol between August 2009 and August 2016 were retrospectively included. The DN–to–pons and GP-to-thalamus signal intensity (SI) ratio differences on unenhanced T1-weighted MR images were calculated by subtracting the SI ratios at the first MR images from those at the last MR images. One-sample t tests were used to evaluate whether the SI ratio differences differed from 0. Linear regression and Pearson correlations were performed to assess correlations between SI ratio differences and various confounding variables, including the number of MR scans, mean time interval between MR scans, age, sex, history of radiation therapy or chemotherapy, and renal and liver functions.

Results
Patients underwent a mean of 5.9 ± 6.3 contrast-enhanced MR scans with a mean interval of 42.8 ± 49.5 weeks between the scans. Sixty-three patients underwent 6 or more MR scans, whereas 126 patients underwent fewer than 6 MR scans. Neither the DN-to-pons SI nor the GP-to-thalamus SI ratio differences differed significantly from 0, with mean values of −0.012 ± 0.115 (P = 0.148) and 0.012 ± 0.111 (P = 0.126), respectively.

Conclusions
Serial administrations of gadobutrol did not result in signal increases in the DN or GP on unenhanced T1-weighted MR images due to gadolinium retention.
Specialist Physicians’ Attitudes and Practice Patterns Regarding Disclosure of Pre-referral Medical Errors
Authors: Dossett Lesly A. , Kauffmann Rondi M. , Lee Jay S. , Singh Harkamal , Lee M. Catherine , Morris Arden M. , Jagsi Reshma , Quinn Gwendolyn P. , Dimick Justin B. 
Published: July 2017

Objective:
Our objective was to determine specialist physicians’ attitudes and practices regarding disclosure of pre-referral errors.

Summary Background Data:
Physicians are encouraged to disclose their own errors to patients. However, no clear professional norms exist regarding disclosure when physicians discover errors in diagnosis or treatment that occurred at other institutions before referral.

Methods:
We conducted semistructured interviews of cancer specialists from 2 National Cancer Institute-designated Cancer Centers. We purposively sampled specialists by discipline, sex, and experience-level who self-described a >50% reliance on external referrals (n = 30). Thematic analysis of verbatim interview transcripts was performed to determine physician attitudes regarding disclosure of pre-referral medical errors; whether and how physicians disclose these errors; and barriers to providing full disclosure.

Results:
Participants described their experiences identifying different types of pre-referral errors including errors of diagnosis, staging and treatment resulting in adverse events ranging from decreased quality of life to premature death. The majority of specialists expressed the belief that disclosure provided no benefit to patients, and might unnecessarily add to their anxiety about their diagnoses or prognoses. Specialists had varying practices of disclosure including none, non-verbal, partial, event-dependent, and full disclosure. They identified a number of barriers to disclosure, including medicolegal implications and damage to referral relationships, the profession's reputation, and to patient–physician relationships.

Conclusions:
Specialist physicians identify pre-referral errors but struggle with whether and how to provide disclosure, even when clinical circumstances force disclosure. Education- or communication-based interventions that overcome barriers to disclosing pre-referral errors warrant development.
Idiopathic Intracranial Hypertension Progressing to Venous Sinus Thrombosis, Subarachnoid Hemorrhage, and Stroke
Authors: Hardin Joshua S. , Ramakrishnaiah Raghu H. , Pemberton John D. , Phillips Paul H. , Chacko Joseph G. 
Published: July 2017

Abstract:
Idiopathic intracranial hypertension (IIH) is a syndrome characterized by increased intracranial pressure (ICP), the absence of structural lesions on neuroimaging, and normal cerebrospinal fluid composition. Cerebral venous sinus thrombosis (CVST) is a common cause of increased ICP and can be differentiated from IIH with magnetic resonance venography. We describe a young woman with typical IIH who underwent lumbar puncture and was treated with a short course of high-dose corticosteroids followed by acetazolamide. She subsequently developed CVST, subarachnoid hemorrhage, and stroke. Risk factors that may have resulted in CVST are discussed.
The CURE for Cultivating Fastidious Microbes
Authors: Bakshi Arundhati , Webber Austen T. , Patrick Lorelei E. , William Wischusen E. , Cameron Thrash J. 
Published: July 2017

ABSTRACTCourse-based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.
beachmat: a Bioconductor C++ API for accessing single-cell genomics data from a variety of R matrix types
Authors: Lun Aaron T. L. , Pagès Hervé , Smith Mike L. 
Published: July 2017

AbstractRecent advances in single-cell RNA sequencing have dramatically increased the number of cells that can be profiled in a single experiment. This provides unparalleled resolution to study cellular heterogeneity within biological processes such as differentiation. However, the explosion of data that are generated from such experiments poses a challenge to the existing computational infrastructure for statistical data analysis. In particular, large matrices holding expression values for each gene in each cell require sparse or file-backed representations for manipulation with the popular R programming language. Here, we describe a C++ interface namedbeachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with simple, sparse and HDF5-backed matrices, amongst others. We perform simulations to examine the performance ofbeachmaton each matrix representation, and we demonstrate howbeachmatcan be incorporated into the code of other packages to drive analyses of a very large single-cell data set.
Mosquito Mapper: a phone application to map urban mosquitoes
Authors: Guilbaud Camille S.E. , Guilbaud Théophile G.D.P.V. 
Published: July 2017

AbstractThis paper presents mosquito mapper: an android phone application created with the goal of giving science-driven citizens the means to monitor mosquito populations in an urban environment. Mosquito mapper allows the recording of mosquito encounters as well as conditions surrounding the encounter. It also features a rudimentary identification tool. The goal of the application is to create a database and construct a map of the encounters free to consult for citizens and scientists. Such database constitutes a necessary first step for the development of useful management strategies addressing potential human health threats induced by mosquitoes. The citizen scientist may voluntarily provide other additional information on the circumstances of the encounter that may contain scientifically useful information. We describe the current features of the application, discuss their strength, limits, potential scientific value and suggest possible future extensions. The original city for which the application was developed is Berlin, Germany, but the application is coded in such a way that it is easily applicable to any urban environment.
Conformational dynamics of Cas9 governing DNA cleavage revealed by single molecule FRET
Authors: Yang Mengyi , Peng Sijia , Sun Ruirui , Lin Jingdi , Wang Nan , Chen Chunlai 
Published: July 2017

SummaryOff-target binding and cleavage by Cas9 pose as major challenges in its applications. How conformational dynamics of Cas9 governs its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms all spontaneously transits between three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We furthermore uncovered a surprising long-range allosteric communication between the HNH domain and RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox.
Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Authors: Laimighofer M. , Lickert R. , Fürst R. , Theis F. J. , Winkler C. , Bonifacio E. , Ziegler A.-G. , Krumsiek J. 
Published: July 2017

AbstractBackgroundBirth by Cesarean section increases the risk of developing type 1 diabetes later in life; however, the underlying molecular mechanisms of this effect remain unclear. We aimed to elucidate common regulatory processes observed after Cesarean section and the development of islet autoimmunity, which precedes type 1 diabetes, by investigating the transcriptome of blood cells in the developing immune system.MethodsWe analyzed gene expression of peripheral blood mononuclear cells taken at several time points from children with increased familial and genetic risk for type 1 diabetes (n = 109). We investigated effects of Cesarean section on gene expression profiles of children in the first year of life using a generalized additive mixed model to account for the longitudinal data structure. To investigate the effect of islet autoimmunity, we compared gene expression differences between children after initiation of islet autoimmunity and age-matched children who did not develop islet autoantibodies. Finally, we compared both results to identify common regulatory patterns of Cesarean section and islet autoimmunity at the gene expression level.ResultsWe identified two differentially expressed pathways in children born by Cesarean section: the pentose phosphate pathway and pyrimidine metabolism, both involved in nucleotide synthesis and cell proliferation. Islet autoantibody analysis revealed multiple differentially expressed pathways generally involved in immune processes, including both of the above-mentioned nucleotide synthesis pathways. Comparison of global gene expression signatures showed that transcriptomic changes were systematically and significantly correlated between Cesarean section and islet autoimmunity. In addition, signatures of both Cesarean section and islet autoimmunity correlated with transcriptional changes observed during activation of isolated CD4+ T lymphocytes.ConclusionsWe identified coherent gene expression signatures for Cesarean section, an early risk factor for type 1 diabetes, and islet autoantibodies positivity, an obligatory stage of autoimmune response prior to the development of type 1 diabetes. Both transcriptional signatures were correlated with changes in gene expression during the activation of CD4+ T lymphocytes, reflecting common molecular changes in immune cell activation.
Characterizing and Managing Missing Structured Data in Electronic Health Records
Authors: Beaulieu-Jones Brett K. , Lavage Daniel R. , Snyder John W. , Moore Jason H. , Pendergrass Sarah A , Bauer Christopher R. 
Published: July 2017

ABSTRACTMissing data is a challenge for all studies; however, this is especially true for electronic health record (EHR) based analyses. Failure to appropriately consider missing data can lead to biased results. Here, we provide detailed procedures for when and how to conduct imputation of EHR data. We demonstrate how the mechanism of missingness can be assessed, evaluate the performance of a variety of imputation methods, and describe some of the most frequent problems that can be encountered. We analyzed clinical lab measures from 602,366 patients in the Geisinger Health System EHR. Using these data, we constructed a representative set of complete cases and assessed the performance of 12 different imputation methods for missing data that was simulated based on 4 mechanisms of missingness. Our results show that several methods including variations of Multivariate Imputation by Chained Equations (MICE) and softImpute consistently imputed missing values with low error; however, only a subset of the MICE methods were suitable for multiple imputation. The analyses described provide an outline of considerations for dealing with missing EHR data, steps that researchers can perform to characterize missingness within their own data, and an evaluation of methods that can be applied to impute clinical data. While the performance of methods may vary between datasets, the process we describe can be generalized to the majority of structured data types that exist in EHRs and all of our methods and code are publicly available.
Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules
Authors: Maher Kelsey A. , Bajic Marko , Kajala Kaisa , Reynoso Mauricio , Pauluzzi Germain , West Donnelly A. , Zumstein Kristina , Woodhouse Margaret , Bubb Kerry , Dorrity Michael W. , Queitsch Christine , Bailey-Serres Julia , Sinha Neelima , Brady Siobhan M. , Deal Roger B. 
Published: July 2017

ABSTRACTThe transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how manycis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana,Medicago truncatula,Solanum lycopersicum, andOryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling ofArabidopsisroot hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.