bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferior Oblique Belly Transposition for Small Angle Hypertropia With Inferior Oblique Overaction: A Pilot Study
Authors: Yang Shiqiang , Guo Xin , Tien David Robbins 
Published: October 2017

Purpose:
To evaluate the efficacy of transposition of the belly of the inferior oblique muscle in treating inferior oblique overaction with small angle hypertropia.

Methods:
The medical records of 10 patients who underwent inferior oblique belly transposition from March 2014 to July 2016 were reviewed. Transposition of the inferior oblique muscle belly consisted of suturing the entire body of the muscle to the sclera 5 mm posterior to the temporal insertion of the inferior rectus muscle. All patients had small hypertropias (< 5 prism diopters) in the primary gaze position with associated inferior oblique overaction. Deviations in both primary and lateral gazes, compensatory face turns or head tilts, and the degree of inferior oblique overaction were evaluated preoperatively and postoperatively.

Results:
Nine of the 10 patients had a complete resolution of inferior oblique overaction. In the remaining patient, the inferior oblique overaction improved from +3 to +1. None of the patients had any residual vertical deviation. There was elimination of compensatory head tilting in 5 patients and correction of compensatory face turns in 4 patients. One patient with mild up drifting of the involved eye also improved after the procedure. All patients expressed subjective satisfaction with the surgical outcome.

Conclusions:
Transposition of the inferior oblique muscle belly effectively weakened mild to moderate inferior oblique overaction and corrected small primary position hypertropias. This procedure may be a useful addition to surgical treatment options in patients with small hypertropias associated with inferior oblique overaction.

[
J Pediatr Ophthalmol Strabismus
. 2018;55(1):43–46.]
Customized Corneal Cross-linking Using Different UVA Beam Profiles
Authors: Shetty Rohit , Pahuja Natasha , Roshan Thimmarayappa , Deshmukh Rashmi , Francis Mathew , Ghosh Arkasubhra , Sinha Roy Abhijit 
Published: October 2017

PURPOSE:
To evaluate the performance of different customized corneal cross-linking (CXL) methods.

METHODS:

This was a single-center interventional, prospective, longitudinal case series. Four different customized CXL methods were evaluated in keratoconic eyes: (1) uniform (uniform intensity ultraviolet-A [UVA] beam [9 mW/cm
2
] for 10 minutes) (n = 12 eyes); (2) sector axial map (sector-based UVA irradiation) (n = 12 eyes); (3) ring axial map (concentric rings of UVA beam intensity centered at the steepest curvature of the anterior axial map) (n = 12 eyes); and ring tangential map (same as the ring axial map but centered at the steepest curvature of the anterior tangential map) (n = 14 eyes). Peak UVA energy density in the sector and ring axial map (and ring tangential map) protocols did not exceed 15.0 and 10.8 J/cm
2
, respectively. A 0.1% riboflavin solution was applied after epithelium removal. Corneal tomography and visual acuity were assessed before and 6 months after CXL.

RESULTS:

Average and peak energy density was lowest in the ring tangential protocol and highest in the sector axial map group (
P
< .001). Treated area was lowest in the ring tangential map group and highest in the uniform group (
P
< .001). Decrease in curvature was similar among the uniform, sector axial map, and ring axial map groups (
P
< .05). The ring tangential map group had the greatest decrease in curvature per unit energy dose to the cornea (
P
< .05). Improvement in uncorrected (0.081 ± 0.056 logMAR) and corrected (0.041 ± 0.026 logMAR) distance visual acuity per unit energy density was greatest in the ring tangential map group (
P
> .05).

CONCLUSIONS:
When normalized to the average energy density, the ring tangential map protocol appeared to provide maximum flattening and improvement in visual acuity. Further studies with larger sample sizes are needed to validate the findings of this pilot study.

[
J Refract Surg.
2017;33(10):676–682.]
Accuracy of a New Swept-Source Optical Coherence Tomography Biometer for IOL Power Calculation and Comparison to IOLMaster
Authors: Savini Giacomo , Hoffer Kenneth J. , Shammas H. John , Aramberri Jaime , Huang Jinhai , Barboni Piero 
Published: October 2017

PURPOSE:
To investigate the accuracy of the measurements provided by a new optical biometer (OA-2000, Tomey Corporation, Nagoya, Japan) for calculating the intraocular lens (IOL) power and to compare the refractive outcomes to those obtained with the IOLMaster 500 (Carl Zeiss Meditec, Jena, Germany).

METHODS:
In this interventional multicenter study, consecutive patients having cataract surgery were enrolled. Only the IOL model used in the largest sample of patients was selected and the eyes implanted with that IOL were subsequently analyzed. The OA-2000, an optical biometer based on swept-source optical coherence tomography (SS-OCT), was used to measure axial length and corneal power in all eyes. IOL power was calculated with the Hoffer Q, Holladay 1, and SRK/T formulas. In a subsample of eyes, the IOL power was also calculated with measurements obtained by partial coherence interferometry (IOLMaster 500). The median absolute error and percentage of eyes with a prediction error of ±0.50 diopters (D) or less were calculated.

RESULTS:

Two hundred forty-nine eyes were analyzed. Using SS-OCT, the median absolute error ranged between 0.33 (Holladay 1) and 0.35 (SRK/T) D. The rate of eyes with a prediction error of ±0.50 D or less ranged between 71.5% (Hoffer Q) and 67.1% (SRK/T). In the subsample of 87 eyes with measurements by both devices, the median absolute error was lower with the OA-2000 (Hoffer Q:
P
= .0377; Holladay 1:
P
= .0191; SRK/T:
P
= .0087).

CONCLUSIONS:
The SS-OCT–based optical biometer investigated in the current study provides accurate measurements for IOL power calculation and seems to offer more predictable refractive results compared to the partial coherence interferometry IOLMaster.

[
J Refract Surg.
2017;33(10):690–695.]
Visualizing Patterns and Trends of 25 Years of Published Health Literacy Research
Authors: Massey Philip M. , Kim Meen Chul , Dalrymple Prudence W. , Rogers Michelle L. , Hawthorne Kisha H. , Manganello Jennifer A. 
Published: October 2017

Background:
With an increase in the number of disciplines contributing to health literacy scholarship, we sought to explore the nature of interdisciplinary research in the field.

Objective:
This study sought to describe disciplines that contribute to health literacy research and to quantify how disciplines draw from and contribute to an interdisciplinary evidence base, as measured by citation networks.

Methods:
We conducted a literature search for health literacy articles published between 1991 and 2015 in four bibliographic databases, producing 6,229 unique bibliographic records. We employed a scientometric tool (CiteSpace [Version 4.4.R1]) to quantify patterns in published health literacy research, including a visual path from cited discipline domains to citing discipline domains.

Key Results:

The number of health literacy publications increased each year between 1991 and 2015. Two spikes, in 2008 and 2013, correspond to the introduction of additional subject categories, including information science and communication. Two journals have been cited more than 2,000 times—the
Journal of General Internal Medicine
(
n
= 2,432) and
Patient Education and Counseling
(
n
= 2,252). The most recently cited journal added to the top 10 list of cited journals is the
Journal of Health Communication
(
n
= 989). Three main citation paths exist in the health literacy data set. Articles from the domain “medicine, medical, clinical” heavily cite from one domain (health, nursing, medicine), whereas articles from the domain “psychology, education, health” cite from two separate domains (health, nursing, medicine and psychology, education, social).

Conclusions:

Recent spikes in the number of published health literacy articles have been spurred by a greater diversity of disciplines contributing to the evidence base. However, despite the diversity of disciplines, citation paths indicate the presence of a few, self-contained disciplines contributing to most of the literature, suggesting a lack of interdisciplinary research. To address complex and evolving challenges in the health literacy field, interdisciplinary team science, that is, integrating science from across multiple disciplines, should continue to grow.

[
Health Literacy Research and Practice
. 2017;1(4):e182–e191.]

Plain Language Summary:
The addition of diverse disciplines conducting health literacy scholarship has spurred recent spikes in the number of publications. However, citation paths suggest that interdisciplinary research can be strengthened. Findings directly align with the increasing emphasis on team science, and support opportunities and resources that incentivize interdisciplinary health literacy research.
Association between a Prognostic Gene Signature and Functional Gene Sets
Authors: Hummel Manuela , Metzeler Klaus H. , Buske Christian , Bohlander Stefan K. , Mansmann Ulrich 
Published: October 2017

Background The development of expression-based gene signatures for predicting prognosis or class membership is a popular and challenging task. Besides their stringent validation, signatures need a functional interpretation and must be placed in a biological context. Popular tools such as Gene Set Enrichment have drawbacks because they are restricted to annotated genes and are unable to capture the information hidden in the signature's non-annotated genes. Methodology We propose concepts to relate a signature with functional gene sets like pathways or Gene Ontology categories. The connection between single signature genes and a specific pathway is explored by hierarchical variable selection and gene association networks. The risk score derived from an individual patient's signature is related to expression patterns of pathways and Gene Ontology categories. Global tests are useful for these tasks, and they adjust for other factors. GlobalAncova is used to explore the effect on gene expression in specific functional groups from the interaction of the score and selected mutations in the patient's genome. Results We apply the proposed methods to an expression data set and a corresponding gene signature for predicting survival in Acute Myeloid Leukemia (AML). The example demonstrates strong relations between the signature and cancer-related pathways. The signature-based risk score was found to be associated with development-related biological processes. Conclusions Many authors interpret the functional aspects of a gene signature by linking signature genes to pathways or relevant functional gene groups. The method of gene set enrichment is preferred to annotating signature genes to specific Gene Ontology categories. The strategies proposed in this paper go beyond the restriction of annotation and deepen the insights into the biological mechanisms reflected in the information given by a signature.
The Use of Artificial Neural Networks in Prediction of Congenital CMV Outcome from Sequence Data
Authors: Arav-Boger Ravit , Boger Yuval S. , Foster Charles B. , Boger Zvi 
Published: October 2017

A large number of CMV strains has been reported to circulate in the human population, and the biological significance of these strains is currently an active area of research. The analysis of complex genetic information may be limited using conventional phylogenetic techniques. We constructed artificial neural networks to determine their feasibility in predicting the outcome of congenital CMV disease (defined as presence of CMV symptoms at birth) based on two data sets: 54 sequences of CMV gene UL144 obtained from 54 amniotic fluids of women who contracted acute CMV infection during their pregnancy, and 80 sequences of 4 genes (US28, UL144, UL146 and UL147) obtained from urine, saliva or blood of 20 congenitally infected infants that displayed different outcomes at birth. When data from all four genes was used in the 20-infants’ set, the artificial neural network model accurately identified outcome in 90% of cases. While US28 and UL147 had low yield in predicting outcome, UL144 and UL146 predicted outcome in 80% and 85% respectively when used separately. The model identified specific nucleotide positions that were highly relevant to prediction of outcome. The artificial neural network classified genotypes in agreement with classic phylogenetic analysis. We suggest that artificial neural networks can accurately and efficiently analyze sequences obtained from larger cohorts to determine specific outcomes. The ANN training and analysis code is commercially available from Optimal Neural Informatics (Pikesville, MD).
Effect of Quantitative Nuclear Image Features on Recurrence of Ductal Carcinoma In Situ (DCIS) of the Breast
Authors: Axelrod David E. , Miller Naomi A. , Lickley H. Lavina , Qian Jin , Christens-Barry William A. , Yuan Yan , Fu Yuejiao , Chapman Judith-Anne W. 
Published: October 2017

Background Nuclear grade has been associated with breast DCIS recurrence and progression to invasive carcinoma; however, our previous study of a cohort of patients with breast DCIS did not find such an association with outcome. Fifty percent of patients had heterogeneous DCIS with more than one nuclear grade. The aim of the current study was to investigate the effect of quantitative nuclear features assessed with digital image analysis on ipsilateral DCIS recurrence. Methods Hematoxylin and eosin stained slides for a cohort of 80 patients with primary breast DCIS were reviewed and two fields with representative grade (or grades) were identified by a Pathologist and simultaneously used for acquisition of digital images for each field. Van Nuys worst nuclear grade was assigned, as was predominant grade, and heterogeneous grading when present. Patients were grouped by heterogeneity of their nuclear grade: Group A: nuclear grade 1 only, nuclear grades 1 and 2, or nuclear grade 2 only (32 patients), Group B: nuclear grades 1, 2 and 3, or nuclear grades 2 and 3 (31 patients), Group 3: nuclear grade 3 only (17 patients). Nuclear fine structure was assessed by software which captured thirty-nine nuclear feature values describing nuclear morphometry, densitometry, and texture. Step-wise forward Cox regressions were performed with previous clinical and pathologic factors, and the new image analysis features. Results Duplicate measurements were similar for 89.7% to 97.4% of assessed image features. The rate of correct classification of nuclear grading with digital image analysis features was similar in the two fields, and pooled assessment across both fields. In the pooled assessment, a discriminant function with one nuclear morphometric and one texture feature was significantly (p = 0.001) associated with nuclear grading, and provided correct jackknifed classification of a patient's nuclear grade for Group A (78.1%), Group B (48.4%), and Group C (70.6%). The factors significantly associated with DCIS recurrence were those previously found, type of initial presentation (p = 0.03) and amount of parenchymal involvement (p = 0.05), along with the morphometry image feature of ellipticity (p = 0.04). Conclusion Analysis of nuclear features measured by image cytometry may contribute to the classification and prognosis of breast DCIS patients with more than one nuclear grade.
Comparison of Three Information Sources for Smoking Information in Electronic Health Records
Authors: Wang Liwei , Ruan Xiaoyang , Yang Ping , Liu Hongfang 
Published: October 2017

Objective The primary aim was to compare independent and joint performance of retrieving smoking status through different sources, including narrative text processed by natural language processing (NLP), patient-provided information (PPI), and diagnosis codes (ie, International Classification of Diseases, Ninth Revision [ICD-9]). We also compared the performance of retrieving smoking strength information (ie, heavy/light smoker) from narrative text and PPL Materials and Methods Our study leveraged an existing lung cancer cohort for smoking status, amount, and strength information, which was manually chart-reviewed. On the NLP side, smoking-related electronic medical record (EMR) data were retrieved first. A pattern-based smoking information extraction module was then implemented to extract smoking-related information. After that, heuristic rules were used to obtain smoking status-related information. Smoking information was also obtained from structured data sources based on diagnosis codes and PPI. Sensitivity, specificity, and accuracy were measured using patients with coverage (ie, the proportion of patients whose smoking status/strength can be effectively determined). Results NLP alone has the best overall performance for smoking status extraction (patient coverage: 0.88; sensitivity: 0.97; specificity: 0.70; accuracy: 0.88); combining PPI with NLP further improved patient coverage to 0.96. ICD-9 does not provide additional improvement to NLP and its combination with PPI. For smoking strength, combining NLP with PPI has slight improvement over NLP alone. Conclusion These findings suggest that narrative text could serve as a more reliable and comprehensive source for obtaining smoking-related information than structured data sources. PPI, the readily available structured data, could be used as a complementary source for more comprehensive patient coverage.
Algorithmic Discovery of Methylation “Hot Spots” in DNA from Lymphoma Patients
Authors: Papageorgio Chris , Harrison Robert , Rahmatpanah Farahnaz B. , Taylor Kristen , Davis Wade , Caldwell Charles W. 
Published: October 2017

Summary The computational aspects of the problem in this paper involve, firstly, selective mapping of methylated DNA clones according to methylation level and, secondly, extracting motif information from all the mapped elements in the absence of prior probability distribution. Our novel implementation of algorithms to map and maximize expectation in this setting has generated data that appear to be distinct for each lymphoma subtype examined. A “clone” represents a polymerase chain reaction (PCR) product (on average ~500 bp) which belongs to a microarray of 8544 such sequences preserving CpG-rich islands (CGIs) [ 1 ]. Accumulating evidence indicates that cancers including lymphomas demonstrate hypermethylation of CGIs “silencing” an increasing number of tumor suppressor (TS) genes which can lead to tumorigenesis. Availability Algorithms are available on request from the authors Contact papageorgioc@health.missouri.edu Supplementary Information available on page 453.
Percepción de los científicos y periodistas sobre la divulgación de la ciencia y la tecnología en Chile
Authors: Tabja Salgado Jorge , Broitman Rojas Claudio , Camiñas Hernández Anastasio 
Published: October 2017

El presente artículo muestra la percepción de los científicos y periodistas chilenos sobre la divulgación de las ciencias y las tecnologías en los medios de comunicación. Metodología: Se hizo una consulta dirigida a científicos (n=139), la cual fue triangulada con tres investigaciones periodísticas como validación. Resultados y conclusiones: Los resultados muestran que la divulgación científica en Chile es de mala a regular calidad y las razones para no estar presente en los medios se fundan en la ausencia efectiva de una política pública, falta de interés de los medios y carecer de redes profesionales que incrementen la visibilidad de noticas especializadas. Sin embargo, el 84,2% de los investigadores ha otorgado una entrevista alguna vez. Un hallazgo controversial - de ambos grupos - es considerar el uso insuficiente que los periodistas hacen del lenguaje científico. Es fundamental desarrollar políticas públicas con indicadores de divulgación de las ciencias y profundizar la reflexión de los periodistas científicos.
PALM-USM v1.0: A new urban surface model integrated into the PALM large-eddy simulation model
Authors: Resler Jaroslav , Krč Pavel , Belda Michal , Juruš Pavel , Benešová Nina , Lopata Jan , Vlček Ondřej , Damašková Daša , Eben Kryštof , Derbek Přemysl , Maronga Björn , Kanani-Sühring Farah 
Published: October 2017

Abstract. Urban areas are an important part of the climate system and many aspects of urban climate have direct effects on human health and living conditions. This implies that reliable tools for local urban climate studies supporting sustainable urban planning are needed. However, a realistic implementation of urban canopy processes still poses a serious challenge for weather and climate modelling for the current generation of numerical models. To address this demand, a new urban surface model (USM), describing the surface energy processes for urban environments, was developed and integrated as a module into the PALM large-eddy simulation model. The development of the presented first version of the USM originated from modelling the urban heat island during summer heat wave episodes and thus implements primarily processes important in such conditions. The USM contains a multi-reflection radiation model for shortwave and longwave radiation with an integrated model of absorption of radiation by resolved plant canopy (i.e. trees, shrubs). Furthermore, it consists of an energy balance solver for horizontal and vertical impervious surfaces, and thermal diffusion in ground, wall, and roof materials, and it includes a simple model for the consideration of anthropogenic heat sources. The USM was parallelized using the standard Message Passing Interface and performance testing demonstrates that the computational costs of the USM are reasonable on typical clusters for the tested configurations. The module was fully integrated into PALM and is available via its online repository under the GNU General Public License (GPL). The USM was tested on a summer heat-wave episode for a selected Prague crossroads. The general representation of the urban boundary layer and patterns of surface temperatures of various surface types (walls, pavement) are in good agreement with in situ observations made in Prague. Additional simulations were performed in order to assess the sensitivity of the results to uncertainties in the material parameters, the domain size, and the general effect of the USM itself. The first version of the USM is limited to the processes most relevant to the study of summer heat waves and serves as a basis for ongoing development which will address additional processes of the urban environment and lead to improvements to extend the utilization of the USM to other environments and conditions.