bluuebunny/crossref_metadata_2025_split huggingface dataset:
Audiological correlates of cone beam computed tomography (CBCT) in cochlear implant recipients
Authors: Abdel Rahman Tayseer Taha , Abdel Kader Hesham Abd El Aty , Abdel Aziz Tougan Taha 
Published: July 2019

Objectives:
To evaluate the role of Cone beam CT (CBCT) regarding the intracochlear electrode position, the exact localization of the electrode in either the Scala tympani or Scala vestibuli and any accompanying inner ear trauma to the delicate intracochlear structures and furthermore correlate these findings with the hearing thresholds and speech tests in patients with unilateral cochlear implant (CI).

Method:
A total number of 20 subjects were examined in this study, 6 males and 14 females, their ages ranged from 3 to 10 years who underwent cochlear implantation. CBCT was done to the entire study group 3 months after surgery. After one year, audio logical evaluation was done in the form of aided warble tone response, aided speech reception threshold and early speech perception test (ESP) both in quiet and in noise. The study group was subdivided according to the degree of inner ear trauma into four groups: grade 0 trauma (9 subjects), grade I trauma (3 subjects), grade II trauma (3 subjects), grade III trauma (5 subjects).

Results:
There was a significant difference among no trauma patients and trauma patients regarding the insertion angle, aided threshold at 250 Hz, percentage of working electrodes and ESP in noise test. Moreover, significant inverse correlation was present between the grade of trauma and both ESP in noise and the percentage of working electrodes.

Conclusions:
The optimal image quality and the small radiation dose renders CBCT as an optimal and secure imaging tool for the assessment of the CI electrode location and evaluation of inner ear trauma as it affects postoperative programing and hearing perspectives.
Implementation of hyperlinks to medication management policies and guidelines in the electronic health record
Authors: Dwenger Andrew T , Fox Erin R , Macdonald Elyse A , Edvalson Bryan J 
Published: July 2019

Abstract

Purpose
The implementation and maintenance of a process for adding and removing hyperlinks to medication management policies and guidelines approved by a pharmacy and therapeutics (P&T) committee into the electronic health record (EHR) are described.

Summary
Medication management policies and guidelines approved by the P&T committee are published on the University of Utah Health intranet, making it possible to add hyperlinks to this information within the EHR. Adding these hyperlinks allows policy and guideline information to be available to clinicians on the medication ordering, verification, and administration screens without requiring a separate search of the intranet. In a quality-improvement project, all medication management policies and guidelines posted on the intranet were reviewed for relevance to the medication ordering, verification, and administration processes. Hyperlinks to relevant policies and guidelines were implemented into the EHR for specific medications. At the beginning of the review, 100 unique drugs associated with 1 or more hyperlinks were identified. The hyperlinks referenced a total of 33 Web documents: 8 policies and 25 guidelines. There are 74 medication management policies and 78 medication management guidelines approved by the P&T committee at University of Utah Health. After investigator review, 12 of 74 policies (16%) and 41 of 78 guidelines (53%) were deemed relevant during the medication ordering, verification, and administration processes. The review and hyperlink implementation process took a total of 101 hours. A continual review process was developed to enable addition and removal of hyperlinks as appropriate.

Conclusion
Providing direct access to relevant medication management policies and guidelines approved by the P&T committee during the medication ordering, verification, and administration processes via hyperlinks in the EHR makes formulary information readily accessible by appropriate staff. These hyperlinks may also improve adherence to formulary information, reduce medication expenditure, and improve safety and therapeutic outcomes of medication therapy.
Creating an immunization content database for knowledge management across clinical systems
Authors: Wen Hamilton , Mathe Janos L , Weinberg Stuart T , Weitkamp Asli Ozdas , Nelson Scott D 
Published: July 2019

Abstract

Purpose
A initiative at an academic medical center to create a single database of immunization-related content to inform the build and configuration of immunization-related knowledge assets across multiple clinical systems is described.

Methods
Semistructured expert interviews were conducted to ascertain the immunization information needs of the institution’s clinical systems. Based on those needs, an immunization domain model constructed with data available from the Centers for Disease Control and Prevention (CDC) website was developed and used to analyze and compare current immunization-related content from CDC data sources with the content of the institution’s clinical systems.

Results
Five identified clinical systems that used immunization-related content collectively required 22 unique information concepts, 11 of which were obtainable from CDC vaccine code sets. The proportion of vaccines designated by CDC as active products (i.e., currently available administrable vaccines) that were included in the 5 clinical systems ranged from 59% to 95%; in addition, some non–active-status vaccines were listed as active-status products in the various clinical systems. Upon further review, updates to immunization-related content in the 5 clinical systems were implemented.

Conclusion
Creating a single database for immunization-related content based on CDC data facilitated an explicit and tractable knowledge management process and helped ensure that clinical systems had correct and current content. The immunization domain model created has the potential to assist in the automated detection of updates and relaying those updates to the applicable clinical systems.
Does bat response to traffic noise support the misleading cue hypothesis?
Authors: Geipel Inga , Amin Bawan , Page Rachel A , Halfwerk Wouter 
Published: July 2019

AbstractThe world has become a noisier place due to the increase in urbanization. Noise is generally considered an impediment, altering an animal’s behavior through masking or distraction. But noise can also provide useful information about the environment. For animals that rely on natural environmental noise as an indicator of favorable foraging conditions, increasing levels of anthropogenic noise might mislead informed decision-making. Bats use rain noise, a natural environmental cue, to delay their emergence from the roost, presumably to avoid sensory and metabolic costs associated with foraging in heavy rain. Here we tested the “misleading cue hypothesis,” asking whether traffic noise is mistaken for rain noise by bats. Given the acoustic similarity between rain noise and traffic noise, we predicted that bats would confuse the two. We conducted a playback experiment using rain, traffic, and ambient noise at natural roosts of common big-eared bats (Micronycteris microtis, Phyllostomidae) and recorded bat emergence behavior. In contrast to their response to rain noise, the bats did not delay roost emergence in response to traffic noise. Thus, we found that bats were able to discriminate between traffic noise and rain noise and were not misled by similarity in acoustic parameters in the two noise types, when emerging from their roost. Emerging bats did show more exploration flights during traffic noise than during rain noise, but not during ambient noise, suggesting that they perceive traffic noise as a novel acoustic cue. Our data provide new insights into perception of traffic noise by bats.
Discovering protein drug targets using knowledge graph embeddings
Authors: Mohamed Sameh K , Nováček Vít , Nounu Aayah 
Published: July 2019

Abstract

Motivation
Computational approaches for predicting drug–target interactions (DTIs) can provide valuable insights into the drug mechanism of action. DTI predictions can help to quickly identify new promising (on-target) or unintended (off-target) effects of drugs. However, existing models face several challenges. Many can only process a limited number of drugs and/or have poor proteome coverage. The current approaches also often suffer from high false positive prediction rates.

Results
We propose a novel computational approach for predicting drug target proteins. The approach is based on formulating the problem as a link prediction in knowledge graphs (robust, machine-readable representations of networked knowledge). We use biomedical knowledge bases to create a knowledge graph of entities connected to both drugs and their potential targets. We propose a specific knowledge graph embedding model, TriModel, to learn vector representations (i.e. embeddings) for all drugs and targets in the created knowledge graph. These representations are consequently used to infer candidate drug target interactions based on their scores computed by the trained TriModel model. We have experimentally evaluated our method using computer simulations and compared it to five existing models. This has shown that our approach outperforms all previous ones in terms of both area under ROC and precision–recall curves in standard benchmark tests.

Availability and implementation
The data, predictions and models are available at: drugtargets.insight-centre.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using three-dimensional printed models to test for aposematism in a carabid beetle
Authors: Fukuda Shinpei , Konuma Junji 
Published: July 2019

AbstractMany studies have demonstrated that bright colours sometimes evolve as warning coloration on the bodies of distasteful prey. However, few studies have demonstrated that the bright structural colours of beetles function as such aposematic signals for predators in the wild. To determine whether body colour might act as an aposematic signal in the carabid beetle Damaster blaptoides, we generated beetle models and conducted camera-trap and field experiments. Elaborate beetle models produced using a three-dimensional printer were used to determine which animals attack them in the wild. Red and black models were placed in forests to test which of the two types was attacked the least frequently. The camera-trap experiments indicated that mammals and birds were the potential predators of D. blaptoides. The field experiments revealed that predators attacked the red models significantly less frequently than the black models in each of three sites where red Damaster subspecies were distributed. In three sites where black Damaster subspecies were distributed, predators attacked both red and black models at similar rates. These results might imply that the predators learned more easily to avoid distasteful red beetles rather than black ones.
Yes-associated protein 1 is required for proliferation and function of bovine granulosa cells in vitro†
Authors: Plewes Michele R , Hou Xiaoying , Zhang Pan , Liang Aixin , Hua Guohua , Wood Jennifer R , Cupp Andrea S , Lv Xiangmin , Wang Cheng , Davis John S 
Published: July 2019

AbstractYes-associated protein 1 (YAP1) is a major component of the Hippo signaling pathway. Although the exact extracellular signals that control the Hippo pathway are currently unknown, increasing evidence supports a critical role for the Hippo pathway in embryonic development, regulation of organ size, and carcinogenesis. Granulosa cells (GCs) within the ovarian follicle proliferate and produce steroids and growth factors, which facilitate the growth of follicle and maturation of the oocyte. We hypothesize that YAP1 plays a role in proliferation and estrogen secretion of GCs. In the current study, we examined the expression of the Hippo signaling pathway in bovine ovaries and determined whether it was important for GC proliferation and estrogen production. Mammalian STE20-like protein kinase 1 (MST1) and large tumor suppressor kinase 2 (LATS2) were identified as prominent upstream components of the Hippo pathway expressed in granulosa and theca cells of the follicle and large and small cells of the corpus luteum. Immunohistochemistry revealed that YAP1 was localized to the nucleus of growing follicles. In vitro, nuclear localization of the downstream Hippo signaling effector proteins YAP1 and transcriptional co-activator with PDZ-binding motif (TAZ) was inversely correlated with GC density, with greater nuclear localization under conditions of low cell density. Treatment with verteporfin and siRNA targeting YAP1 or TAZ revealed a critical role for these transcriptional co-activators in GC proliferation. Furthermore, knockdown of YAP1 in GCs inhibited follicle-stimulating hormone (FSH)-induced estradiol biosynthesis. The data indicate that Hippo pathway transcription co-activators YAP1/TAZ play an important role in GC proliferation and estradiol synthesis, two processes necessary for maintaining normal follicle development.
Simplified integrated nested Laplace approximation
Authors: Wood Simon N 
Published: July 2019

SummaryIntegrated nested Laplace approximation provides accurate and efficient approximations for marginal distributions in latent Gaussian random field models. Computational feasibility of the original Rue et al. (2009) methods relies on efficient approximation of Laplace approximations for the marginal distributions of the coefficients of the latent field, conditional on the data and hyperparameters. The computational efficiency of these approximations depends on the Gaussian field having a Markov structure. This note provides equivalent efficiency without requiring the Markov property, which allows for straightforward use of latent Gaussian fields without a sparse structure, such as reduced rank multi-dimensional smoothing splines. The method avoids the approximation for conditional modes used in Rue et al. (2009), and uses a log determinant approximation based on a simple quasi-Newton update. The latter has a desirable property not shared by the most commonly used variant of the original method.
Unique miRNA profiling of squamous cell carcinoma arising from ovarian mature teratoma: comprehensive miRNA sequence analysis of its molecular background
Authors: Yoshida Kosuke , Yokoi Akira , Kagawa Takumi , Oda Shingo , Hattori Satomi , Tamauchi Satoshi , Ikeda Yoshiki , Yoshikawa Nobuhisa , Nishino Kimihiro , Utsumi Fumi , Niimi Kaoru , Suzuki Shiro , Shibata Kiyosumi , Kajiyama Hiroaki , Yokoi Tsuyoshi , Kikkawa Fumitaka 
Published: July 2019

Abstract
Owing to its rarity, the carcinogenesis and molecular biological characteristics of squamous cell carcinoma arising from mature teratoma remain unclear. This study aims to elucidate the molecular background of malignant transformation from the aspects of microRNA (miRNA) profiling. We examined 7 patients with squamous cell carcinoma and 20 patients with mature teratoma and extracted their total RNA from formalin-fixed paraffin-embedded tissues. Then we prepared small RNA libraries and performed comprehensive miRNA sequencing. Heatmap and principal component analysis revealed markedly different miRNA profiling in cancer, normal ovarian and mature teratoma tissues. Then we narrowed down cancer-related miRNAs, comparing paired-cancer and normal ovaries. Comparisons of cancer and mature teratoma identified two markedly upregulated miRNAs (miR-151a-3p and miR-378a-3p) and two markedly downregulated miRNAs (miR-26a-5p and miR-99a-5p). In addition, these findings were validated in fresh cancer tissues of patient-derived xenograft (PDX) models. Moreover, several miRNAs, including miR-151a-3p and miR-378a-3p, were elevated in the murine plasma when tumor tissues were enlarged although miR-26a-5p and miR-99a-5p were not elucidated in the murine plasma. Finally, we performed target prediction and functional annotation analysis in silico and indicated that targets genes of these miRNAs markedly correlated with cancer-related pathways, including ‘pathway in cancer’ and ‘cell cycle’. In conclusion, this is the first study on miRNA sequencing for squamous cell carcinoma arising from mature teratoma. The study identified four cancer-related miRNAs that were considered to be related to the feature of malignant transformation. Moreover, miRNAs circulating in the murine plasma of the PDX model could be novel diagnostic biomarkers.
An LC-MS/MS Validated Method for Quantification of Chlorzoxazone in Human Plasma and Its Application to a Bioequivalence Study
Authors: He Jiake , Li Ning , Xu Jiaqiu , Zhu Jing , Yu Yang , Chen Xijing , Lu Yang 
Published: July 2019

Abstract
A simple, sensitive, specific, accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for determination of chlorzoxazone in human plasma was developed and validated to evaluate the pharmacokinetic characteristics of chlorzoxazone test or reference formulation. Sample preparation was achieved by one step protein precipitation and dilution with acetontrile. The chromatographic separation was performed at 40°C with a gradient mobile phase (0.3 mL/min) and a Shimadzu VP-ODS C18 analytical column (column size: 150 × 2.0 mm). TSQ quantum access triple-quadrapole MS/MS detection was operated in a negative mode by multiple reaction monitoring. Ion transitions at m/z 168.0→132.1 for chlorzoxazone and m/z 451.3→379.3 for repaglinide (internal standard) were used for the LC-MS/MS analysis. The calibration was linear (r ≥ 0.995) over the tested concentration range of 0.2–20 μg/mL for chlorzoxazone in plasma. Precision, accuracy, recovery, matrix effect and stability for chlorzoxazone were evaluated and were excellent within the range of tested concentrations. This method was successfully applied to a bioequivalence study in 20 healthy Chinese volunteers. This method could also contribute to the personalized medication and therapeutic drug monitoring of chlorzoxazone.
Short-term riparian restoration success measured by territory density and reproductive success of three songbirds along the Trinity River, California
Authors: Stephens Jaime L , Rockwell Sarah M 
Published: July 2019

AbstractWater crises and endangered salmon are pressing environmental concerns influencing restoration decisions in the western United States. When instream restoration necessitates initial loss of riparian cover to restore floodplain function, a short-term goal to minimize harm to riparian-associated wildlife is a worthwhile benchmark. From 2012 to 2015, we examined short-term restoration success, as measured by territory characteristics and reproductive success in restored and reference sites, for 3 riparian bird species (Song Sparrow [Melospiza melodia], Yellow-breasted Chat [Icteria virens], and Yellow Warbler [Setophaga petechia]) along a 64 km stretch of the Trinity River, California. Territory size had the highest relative variable importance in sets of candidate models explaining territory density for all 3 species, and was inversely related to territory density for each. The effect of site type (i.e. restored vs. reference) in explaining territory density was least for Song Sparrow, greater for Yellow Warbler (for which density was 1.4 times greater on reference sites), and greatest for Yellow-breasted Chat (which were more than twice as dense on reference sites). While territory density and mean territory size were inversely related, we found no relationship between territory density or site type and mean productivity per nest, and nest success did not differ between restored and reference sites for any species. In combination, these results suggest that restoration has achieved short-term success as measured by reproductive success, but has not yet been fully successful in supporting similar territory densities as reference sites. In order to determine whether long-term restoration goals are fully achieved, future research should continue to measure density of the 3 focal species as vegetation on the replanted floodplains matures.
Habitat productivity is a poor predictor of body size in rodents
Authors: Alhajeri Bader H , Porto Lucas M V , Maestri Renan 
Published: July 2019

AbstractThe “resource availability hypothesis” predicts occurrence of larger rodents in more productive habitats. This prediction was tested in a dataset of 1,301 rodent species. We used adult body mass as a measure of body size and normalized difference vegetation index (NDVI) as a measure of habitat productivity. We utilized a cross-species approach to investigate the association between these variables. This was done at both the order level (Rodentia) and at narrower taxonomic scales. We applied phylogenetic generalized least squares (PGLS) to correct for phylogenetic relationships. The relationship between body mas and NDVI was also investigated across rodent assemblages. We controlled for spatial autocorrelation using generalized least squares (GLS) analysis. The cross-species approach found extremely low support for the resource availability hypothesis. This was reflected by a weak positive association between body mass and NDVI at the order level. We find a positive association in only a minority of rodent subtaxa. The best fit GLS model detected no significant association between body mass and NDVI across assemblages. Thus, our results do not support the view that resource availability plays a major role in explaining geographic variation in rodent body size.
Assessment of technical efficiency of public hospitals in Turkey
Authors: Küçük Aziz , Özsoy Volkan Soner , Balkan Dursun 
Published: July 2019

AbstractBackgroundTurkish public hospitals have been subjected to health care reform because of increasing cost pressure, inequities in access to health care, poor quality of care and limited patient responsiveness in the last three decades. This study investigates the impact of recent hospital reforms on the efficiency of public hospitals.MethodsThe study provides a comprehensive evaluation of the efficiency of Turkish hospitals by using Data Envelopment Analysis (DEA). The estimation of efficiency of 669 public hospitals of Turkey is performed by an output-oriented model of DEA under the assumption of variable return-to-scale by using data collected from the Ministry of Health (MoH) over the period 2013–17.ResultsThe average efficiency score is equal to 0.83 for all MoH hospitals. Considering the hospital type, the efficiency scores of training and research hospitals are higher than those of the general and branch hospitals. In addition, considering the hospital size, huge-scale hospitals have the highest efficiency score in all years. Moreover, overcrowded regions such as Marmara and South-eastern Anatolia regions had higher efficiency scores than other geographical regions.ConclusionsThe results indicate that recent health reforms did not significantly enhance hospital efficiency. Thus, policymakers and managers should take the necessary precautions to increase hospital efficiency.
Kinderreicher familien or familles nombreuses? French pronatalism in interwar Alsace
Authors: Andersen Margaret 
Published: July 2019

Abstract
This article explores the introduction of family policy in Alsace following the Great War and the efforts of local pronatalist leaders to create a new moral order in the region. While French goals of promoting population growth have been well documented at the national level, relatively little attention has been accorded to the unique way in which the demographic question developed outside Paris. The interwar period in France was marked by shifting boundaries and population movements across borders, both of which shaped French pronatalism. Because such developments factored into understandings of both French identity and concerns about population growth, French demographic policy cannot be fully understood without considering how these questions developed in regions such as Alsace. As this article shows, the introduction of a pronatalist family policy and moral crusade intersected with concurrent efforts to minimize German influences and make the region more ‘French’.