bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey and evaluations of histogram-based statistics in alignment-free sequence comparison
Authors: Luczak Brian B , James Benjamin T , Girgis Hani Z 
Published: November 2017

Abstract

Motivation
Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences.

Results
We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover’s distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover’s distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours.

Availability
The source code of the benchmarking tool is available as Supplementary Materials.
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus
Authors: Bada Michael , Vasilevsky Nicole , Baumgartner William A , Haendel Melissa , Hunter Lawrence E 
Published: November 2017

Abstract
Gold-standard annotated corpora have become important resources for the training and testing of natural-language-processing (NLP) systems designed to support biocuration efforts, and ontologies are increasingly used to facilitate curational consistency and semantic integration across disparate resources. Bringing together the respective power of these, the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of full-length, open-access biomedical journal articles with extensive manually created syntactic, formatting and semantic markup, was previously created and released. This initial public release has already been used in multiple projects to drive development of systems focused on a variety of biocuration, search, visualization, and semantic and syntactic NLP tasks. Building on its demonstrated utility, we have expanded the CRAFT Corpus with a large set of manually created semantic annotations relying on Uberon, an ontology representing anatomical entities and life-cycle stages of multicellular organisms across species as well as types of multicellular organisms defined in terms of life-cycle stage and sexual characteristics. This newly created set of annotations, which has been added for v2.1 of the corpus, is by far the largest publicly available collection of gold-standard anatomical markup and is the first large-scale effort at manual markup of biomedical text relying on the entirety of an anatomical terminology, as opposed to annotation with a small number of high-level anatomical categories, as performed in previous corpora. In addition to presenting and discussing this newly available resource, we apply it to provide a performance baseline for the automatic annotation of anatomical concepts in biomedical text using a prominent concept recognition system. The full corpus, released with a CC BY 3.0 license, may be downloaded from http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
Database URL: http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml
Exposure to Point-of-Sale Marketing of Cigarettes and E-Cigarettes as Predictors of Smoking Cessation Behaviors
Authors: Mantey Dale S , Pasch Keryn E , Loukas Alexandra , Perry Cheryl L 
Published: November 2017

Abstract

Introduction
Cue-reactivity theory suggests that smoking-related visual cues such as point-of-sale (POS) marketing (eg, advertising, product displays) may undermine cessation attempts by causing an increase in nicotine cravings among users. This study examined the relationship between recall of exposure to POS marketing and subsequent cessation behaviors among young adult cigarette smokers.

Methods
Participants included 813, 18–29 year old (m = 21.1, SD = 2.70), current cigarette smokers attending 24 Texas colleges. Multivariable logistic regression models examined the impact of baseline self-reported exposure to cigarette and e-cigarette advertising and product displays, on using e-cigarettes for cessation and successful cigarette cessation at 6-month follow-up. Two-way interactions between product-specific advertising and between product-specific displays were examined to determine if the marketing of one product strengthened the cue reactivity of the other. Baseline covariates included sociodemographic factors, past quit attempts, intentions to quit smoking, and nicotine dependence.

Results
Exposure to e-cigarette displays was associated with lower odds of cigarette smoking cessation, controlling for covariates and conventional cigarette display exposure. E-cigarette advertising was positively associated with the use of e-cigarettes for cigarette cessation among participants exposed to low (ie, at least 1 SD below the mean) levels of cigarette advertising. Cigarette advertising was associated with the use of e-cigarettes for cigarette cessation only among those exposed to low levels of e-cigarette advertising. Exposure to cigarette displays was not associated with either outcome.

Conclusion
Smoking-related cues at POS may undermine successful cigarette cessation. Exposure to product displays decrease odds of cessation. Advertising exposure increased odds for using e-cigarettes for cessation attempts, but may have guided smokers towards an unproven cessation aid.

Implications
By examining the interaction of conventional cigarette and e-cigarette marketing exposure, this study adds a unique insight into the impact of retail tobacco marketing on cigarette smoking cessation behavior among young adults. These findings suggest that policies that balance encouraging cigarette smoking cessation while limiting marketing strategies should be considered, such as POS product displays, that may undermine successful cessation attempts.
Congenital Infantile Fibrosarcoma in the Premature Infant
Authors: Edwards Taryn M. , Duran Melissa S. , Meeker Tamara M. 
Published: November 2017

Background:
Congenital infantile fibrosarcoma (CIF) is rare and represents less than 1% of all childhood cancers. It is a tumor that originates in the connective fibrous tissue found at the ends of long bones and then spreads to other surrounding soft tissues. These lesions are typically large, grow rapidly, and can often be mistaken for teratomas. Diagnosis is confirmed by pathology, where cellular proliferation of fibroblasts occurs. Imaging is an important part of the diagnosis, which includes the use of magnetic resonance imaging and/or computed tomography scan. Although surgical resection is the primary treatment, chemotherapeutic agents may be used as adjuvant therapy.

Purpose:
To describe modalities for accurate diagnosis and treatment of CIF.

Methods/Search Strategy:
PubMed was searched using terms “congenital infantile fibrosarcoma” and “infantile fibrosarcoma.” Eleven relevant, English language articles were identified and utilized in the preparation of this case presentation.

Findings/Results:
Complications addressed in this case presentation are prenatal diagnostic challenges, pharmacologic interventions in the setting of prematurity, immunosuppression, and acute liver and renal failure. Pharmacologic treatments will include chemotherapy agents, antimicrobial agents, as well as granulocyte colony-stimulating factor for immunosuppression. Nursing challenges included positioning and integumentary disturbances.

Implications for Practice:
Utilization of diagnostic imaging and pathology to accurately identify and diagnose CIF is essential.

Implications for Research:
Safety and efficacy of chemotherapeutic agents in premature infants with CIF need to be established.
Relationship Between Initial Vancomycin Trough Levels and Early-Onset Vancomycin-Associated Nephrotoxicity in Critically Ill Patients
Authors: Chuma Masayuki , Makishima Makoto , Imai Toru , Tochikura Naohiro , Suzuki Shinichiro , Kuwana Tsukasa , Sawada Nami , Komatsu Tomohide , Sakaue Takako , Kikuchi Norikazu , Yoshida Yoshikazu , Kinoshita Kosaku 
Published: November 2017

Background:
Appropriate initial dosing of vancomycin (VCM) is important in improving survival and in preventing nephrotoxicity in critically ill patients, but the potential relationship between initial VCM trough levels and early-onset nephrotoxicity remains unclear. We examined the relationship between initial VCM trough levels and early-onset VCM-associated nephrotoxicity.

Methods:
We performed a retrospective study of patients who had therapeutic drug monitoring of VCM with initial trough levels within 4 days after the beginning of VCM administration. We excluded patients who received renal replacement therapy from 2 days before to 7 days after the beginning of VCM administration, were younger than 18 years, or had renal dysfunction before the beginning of VCM administration. Early-onset VCM-associated nephrotoxicity was defined as an increase in serum creatinine level of ≥0.5 mg/dL (44.2 μmol/L) or 50% above baseline for 2 or more consecutive days within 7 days after the beginning of VCM administration.

Results:
Among 109 enrolled patients, 13 patients had early-onset VCM-associated nephrotoxicity. Its incidence rate was 31.3% in patients with initial trough levels of ≥20g/mL, which was significantly higher than 6.3% in patients with initial trough levels of <10 mg/L. Multiple logistic regression analysis demonstrated that early-onset VCM-associated nephrotoxicity was associated with initial trough levels of ≥20 mg/L (odds ratio, 5.0; 95% confidence interval, 1.3–19.1) and with vasopressor use (odds ratio, 5.0; 95% confidence interval, 1.3–19.1). Kaplan–Meier analysis showed that the probability of nonnephrotoxicity for patients with initial VCM trough levels of ≥20 mg/L was lower compared with patients with trough levels of <15 mg/L.

Conclusions:
Initial trough levels of ≥20 mg/L but not ≥15 mg/L were associated with early-onset VCM-associated nephrotoxicity in critically ill patients. Future prospective studies are needed to examine outcomes in critically ill patients achieving initial VCM trough levels of 15–20 mg/L.
Identification of the Infection Source of an Outbreak of Mycobacterium Chelonae Keratitis After Laser in Situ Keratomileusis
Authors: Nascimento Heloisa , Viana-Niero Cristina , Nogueira Christiane Lourenço , Martins Bispo Paulo José , Pinto Fernando , de Paula Pereira Uzam Camila , Matsumoto Cristianne Kayoko , Oliveira Machado Antônia Maria , Leão Sylvia Cardoso , Höfling-Lima Ana Luisa , de Freitas Denise 
Published: November 2017

Purpose:
Nontuberculous mycobacteria keratitis is a rare but challenging complication of laser in situ keratomileusis (LASIK). This study was conducted to determine the source(s) of infection in a cluster of cases of keratitis after LASIK and to describe this outbreak and patients' outcomes.

Methods:
In this retrospective, case series, single-center study, 86 patients were included who underwent LASIK or photorefractive keratectomy between December 2011 and February 2012. Corneal scrapes from the affected eyes, samples of tap and distilled water, water from the reservoir of the distilling equipment, steamer, and autoclave cassette; antiseptic and anesthetic solutions and surgical instrument imprints were cultivated in liquid and on solid media. Gram-negative bacteria and yeasts were identified using automated systems and mycobacteria by polymerase chain reaction–restriction enzyme analysis of the hsp65 gene (PRA-hsp65) and DNA sequencing. Mycobacterial isolates were typed by pulsed-field gel electrophoresis. The cases and outcomes are described. The main outcome measure was identification of the source(s) of the mycobacterial infections.

Results:
Eight (15 eyes) of 86 patients (172 eyes) who underwent LASIK developed infections postoperatively; no patients who underwent photorefractive keratectomy developed infections. Mycobacterium chelonae was isolated from 4 eyes. The distilled water collected in the surgical facility contained the same M. chelonae strain isolated from the patients' eyes. Different gram-negative bacteria and yeasts were isolated from samples collected at the clinic but not from the patients' eyes.

Conclusions:
Tap water distilled locally in surgical facilities may be a source of infection after ocular surgery and its use should be avoided.
Microbial Keratitis After Accelerated Corneal Collagen Cross-Linking in Keratoconus
Authors: Maharana Prafulla K. , Sahay Pranita , Sujeeth M. , Singhal Deepali , Rathi Anubha , Titiyal Jeewan S. , Sharma Namrata 
Published: November 2017

Purpose:
To assess the pattern of microbial keratitis after accelerated corneal collagen cross-linkage (aCXL) in patients with keratoconus.

Method:
The medical records of cases of keratoconus that underwent aCXL from June 2014 to May 2017 were reviewed. Cases that developed microbial keratitis after aCXL were included in the study. The clinical, microbiological profile and the treatment outcomes were evaluated.

Results:
Of 532 eyes that underwent aCXL, 7 cases developed microbial keratitis during the study period. Median age at presentation was 11 years (range 8–17). Association with vernal keratoconjunctivitis was noted in 57.1% of cases (n = 4/7). The median time at the onset of infection was 3 days after aCXL (range 1–4). Microbiological reports revealed mixed infection in 3 cases [coagulase-negative Staphylococcus (CoNS) + Aspergillus fumigatus, Staphylococcus aureus and Mucor spp., Staph. aureus and Acanthamoeba], Staph. aureus in 2 cases, and CoNS and Alternaria spp. in 1 case each. Resistance to fourth-generation fluoroquinolones was noted in 83.3% of cases of bacterial keratitis (n = 5/6). All cases were initially managed with empirical antibiotic treatment that was later tailored based on microbiological reports. One case eventually required therapeutic penetrating keratoplasty for corneal perforation. At 6 months, the corrected distance visual acuity was >6/60 in 3 cases while 4 cases had corrected distance visual acuity <6/60.

Conclusions:
Microbial keratitis after aCXL is rare; however, the infection tends to be severe with high preponderance of mixed infection and resistance to fourth-generation fluoroquinolones.
Development of the Adult Vulvar Lichen Sclerosus Severity Scale—A Delphi Consensus Exercise for Item Generation
Authors: Sheinis Michal , Selk Amanda 
Published: November 2017

Objective
To generate a list of items through international expert consensus consisting of both symptoms and clinical signs for inclusion in an adult vulvar lichen sclerosus severity scale.

Methods
This study was carried out as a three-stage Delphi consensus exercise. After an extensive literature review, any items used to determine disease severity in previous clinical trials were compiled into a survey. The Delphi participants were recruited from the International Society for the Study of Vulvovaginal Disease most of whom were gynecologists and in practice for more than 20 years. Participants were asked to rate the importance of these items. Consensus was defined as 75% agreeing that an item was very important or essential toward determining disease severity. Participants were also asked to indicate preferred method of measurement for these items.

Results
Of approximately 400 members of the International Society for the Study of Vulvovaginal Disease, 66 participated in the study. Of the 14 symptoms presented, 7 reached consensus for inclusion. Of the 23 signs presented, 11 reached consensus for inclusion and 1 reached consensus for exclusion. Of the six architectural changes presented, all six reached consensus for inclusion. No consensus was reached regarding method of measurement for any of the symptoms and signs that reached consensus for inclusion.

Conclusion
International consensus was reached for a variety of items for use in an adult vulvar lichen sclerosus severity scale that will be further developed and tested. Ideally, this scale will be used in clinical practice and in research to allow for high-quality trials.
Prospective Evaluation of Patients Undergoing Translabyrinthine Excision of Vestibular Schwannoma with Concurrent Cochlear Implantation
Authors: Rooth Meredith A. , Dillon Margaret T. , Brown Kevin D. 
Published: November 2017

Objective:
Translabyrinthine (TL) vestibular schwannoma (VS) resection may be accomplished with preservation of the cochlear nerve, permitting successful, concurrent cochlear implantation. In this single institution, Food and Drug Administration-approved feasibility study, we wished to determine the success and outcomes of concurrent cochlear implantation at the time of TL resection of VS.

Study Design:
Prospective cohort.

Setting:
Tertiary referral center.

Patients:
Patients with small VS less than 1.5 cm in size.

Intervention:
Concurrent TL VS resection and cochlear implantation.

Main Outcome Measure:
Sound localization and speech understanding.

Results:
All cochlear nerves were anatomically preserved. Five out of seven patients had auditory precepts at the time of activation. At 1 month following surgery, AzBio scores (0 dB SNR, with sound front, noise to normal ear) were improved by an average of 10% with implant on, persisting to 6 months out from surgery. Localization 1 month after surgery was markedly improved with root mean square 78 degrees ±13 in the “implant off” condition and 41 ± 9 degrees in the “implant on” condition. Average tinnitus severity was reduced in subjects and speech and spatial hearing was improved on speech, spatial and qualities of hearing scale (SSQ).

Conclusions:
These data demonstrate preservation of electrical hearing in TL VS surgery is consistently possible, and although speech outcomes do not achieve the same levels seen with other etiologies of hearing loss, excellent improvement in sound localization, improved speech understanding, and substantial reductions in tinnitus are achieved.
Associations of Insulin Resistance and Glycemia With Liver Enzymes in Hispanic/Latino Youths
Authors: Parrinello Christina M. , Rudolph Bryan J. , Lazo Mariana , Gallo Linda C. , Thyagarajan Bharat , Cotler Scott J. , Qi Qibin , Seeherunvong Tossaporn , Vidot Denise C. , Strickler Howard D. , Kaplan Robert C. , Isasi Carmen R. 
Published: November 2017

Background:
Associations of insulin resistance and hyperglycemia with a panel of liver enzymes have not been well studied in a young, heterogenous Hispanic/Latino population. We aimed to assess the associations of insulin resistance and glycemia with nonalcoholic fatty liver disease (NAFLD), as measured by liver enzymes and the pediatric NAFLD fibrosis index (PNFI), and whether these associations are modified by body mass index and mediated by inflammation or endothelial dysfunction.

Materials and Methods:
We conducted a cross-sectional study of 1317 boys and girls aged 8 to 16 years from the Hispanic Community Children’s Health Study/Study of Latino Youth. We used Poisson regression to assess the associations of fasting glucose, hemoglobin A1c, and homeostasis model assessment of insulin resistance (HOMA-IR) with elevated alanine aminotransferase (ALT) (>25 U/L in boys, >22 U/L in girls), aspartate aminotransferase (AST) (≥37 U/L), gamma-glutamyl transpeptidase (GGT) (≥17 U/L), and PNFI (≥9; a function of age, waist circumference, and triglyceride level).

Results:
HOMA-IR was associated with elevated ALT, AST, GGT, and PNFI [prevalence ratios (95% confidence intervals) for each 1-unit increase in the natural log of HOMA-IR: 1.99 (1.40-2.81), 2.15 (1.12-4.12), 1.70 (1.26-2.30), and 1.98 (1.43-2.74), respectively]. Associations were observed in overweight/obese children, but not in normal weight children (P-interaction=0.04 for AST and P-interaction=0.07 for GGT). After further adjustment for adiponectin, high-sensitivity C-reactive protein, e-selectin, and PAI-1, associations of HOMA-IR with liver enzymes and PNFI were attenuated, but remained statistically significant for AST and PNFI.

Conclusion:
Insulin resistance was associated with NAFLD in overweight/obese Hispanic/Latino youth, and this association may be partially mediated by inflammation and endothelial dysfunction.
Data mining of routine laboratory tests can predict liver disease progression in Egyptian diabetic patients with hepatitis C virus (G4) infection: a cohort study of 71 806 patients
Authors: Saad Yasmin , Awad Abobakr , Alakel Wafaa , Doss Wahid , Awad Tahany , Mabrouk Mahasen 
Published: November 2017

Objectives
Hepatitis C virus (HCV) and diabetes mellitus (DM) are prevalent diseases worldwide, associated with significant morbidity, mortality, and mutual association. The aims of this study were as follows: (i) find the prevalence of DM among 71 806 Egyptian patients with chronic HCV infection and its effect on liver disease progression and (ii) using data mining of routine tests to predict hepatic fibrosis in diabetic patients with HCV infection.

Patients and methods
A retrospective multicentered study included laboratory and histopathological data of 71 806 patients with HCV infection collected by Egyptian National Committee for control of viral hepatitis. Using data mining analysis, we constructed decision tree algorithm to assess predictors of fibrosis progression in diabetic patients with HCV.

Results
Overall, 12 018 (16.8%) patients were diagnosed as having diabetes [6428: fasting blood glucose ≥126 mg/dl (9%) and 5590: fasting blood glucose ≥110–126 mg/dl (7.8%)]. DM was significantly associated with advanced age, high BMI and α-fetoprotein (AFP), and low platelets and serum albumin (P≤0.001). Advanced liver fibrosis (F3–F4) was significantly correlated with DM (P≤0.001) irrespective of age. Of 16 attributes, decision tree model for fibrosis showed AFP was most decisive with cutoff of 5.25 ng/ml as starting point of fibrosis. AFP level greater than cutoff in patients was the first important splitting attribute; age and platelet count were second important splitting attributes.

Conclusion
(i) Chronic HCV is significantly associated with DM (16.8%). (ii) Advanced age, high BMI and AFP, low platelets count and albumin show significant association with DM in HCV. (iii) AFP cutoff of 5.25 is a starting point of fibrosis development and integrated into mathematical model to predict development of liver fibrosis in diabetics with HCV (G4) infection.