bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus
Authors: Gao Jian , Li Qiye , Wang Zongji , Zhou Yang , Martelli Paolo , Li Fang , Xiong Zijun , Wang Jian , Yang Huanming , Zhang Guojie 
Published: June 2017

Abstract
The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendix II since 1990. A proposal to uplist it to Appendix I was passed at the Convention on International Trade in Endangered Species of Wild Fauna and Flora Seventeenth meeting of the Conference of the Parties in 2016. To promote the conservation of this species, we sequenced the genome of a male Chinese crocodile lizard using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform. In total, we generated ~291 Gb of raw sequencing data (×149 depth) from 13 libraries with insert sizes ranging from 250 bp to 40 kb. After filtering for polymerase chain reaction–duplicated and low-quality reads, ~137 Gb of clean data (×70 depth) were obtained for genome assembly. We yielded a draft genome assembly with a total length of 2.24 Gb and an N50 scaffold size of 1.47 Mb. The assembled genome was predicted to contain 20 150 protein-coding genes and up to 1114 Mb (49.6%) of repetitive elements. The genomic resource of the Chinese crocodile lizard will contribute to deciphering the biology of this organism and provides an essential tool for conservation efforts. It also provides a valuable resource for future study of squamate evolution.
Equivalency of the quality of sublethal lesions after photons and high-linear energy transfer ion beams
Authors: Furusawa Yoshiya , Nakano-Aoki Mizuho , Matsumoto Yoshitaka , Hirayama Ryoichi , Kobayashi Alisa , Konishi Teruaki 
Published: June 2017

Abstract
The quality of the sublethal damage (SLD) after irradiation with high–linear energy transfer (LET) ion beams was investigated with low-LET photons. Chinese hamster V79 cells and human squamous carcinoma SAS cells were first exposed to a priming dose of different ion beams at different LETs at the Heavy Ion Medical Accelerator in the Chiba facility. The cells were kept at room temperature and then exposed to a secondary test dose of X-rays. Based on the repair kinetics study, the surviving fraction of cells quickly increased with the repair time, and reached a plateau in 2–3 h, even when cells had received priming monoenergetic high-LET beams or spread-out Bragg peak beams as well as X-ray irradiation. The shapes of the cell survival curves from the secondary test X-rays, after repair of the damage caused by the high-LET irradiation, were similar to those obtained from cells exposed to primary X-rays only. Complete SLD repairs were observed, even when the LET of the primary ion beams was very high. These results suggest that the SLD caused by high-LET irradiation was repaired well, and likewise, the damage caused by the X-rays. In cells where the ion beam had made a direct hit in the core region in an ion track, lethal damage to the domain was produced, resulting in cell death. On the other hand, in domains that had received a glancing hit in the low-LET penumbra region, the SLD produced was completely repaired.
Measurement Properties of Short Lower Extremity Functional Exercise Tests in People With Chronic Obstructive Pulmonary Disease: Systematic Review
Authors: Johnston Kylie N. , Potter Adrian J. , Phillips Anna 
Published: June 2017

Abstract

Background
An increasing variety of short functional exercise tests are reported in people with chronic obstructive pulmonary disease (COPD). Systematic review of the psychometric properties of these exercise tests is indicated.

Purpose
The aim of this study was to determine the reliability, validity, and responsiveness of short (duration &lt; 6 min) lower extremity functional exercise tests in people with COPD.

Data Sources
Five databases were searched: MEDLINE, Embase, Scopus, AMED, and CINAHL.

Study Selection
Studies reporting psychometric properties of short functional exercise tests in people with COPD were included.

Data Extraction
Two reviewers independently extracted data and rated the quality of each measurement property using the COnsensus-based Standards for the Selection of Health Measurement INstrument (COSMIN).

Data Synthesis
Twenty-nine studies were identified reporting properties of 11 different tests. Four-meter gait speed [4MGS] and 5 repetition sit-to-stand [5STS] demonstrated high reliability (ICC = .95–.99; .97) with no learning effect (COSMIN study ratings = good–-excellent). Their validity for use as a stratification tool anchored against an established prognostic indicator (area under receiver operator characteristics curve [AUC] = 0.72–0.87; 0.82) and responsiveness to change after pulmonary rehabilitation was greatest in more frail people with COPD. Studies of the Timed “Up and Go” [TUG] test support use of a practice test and show discriminative ability to detect falls history and low six-minute walk distance (AUC = 0.77; 0.82, COSMIN ratings = fair–excellent).

Limitations
Earlier studies were limited by small sample size. Limited data of lower study quality was identified for step tests and the Two-Minute Walk Test.

Conclusions
Selected short functional exercise tests can complement established exercise capacity measures, in stratification and measuring responsiveness to change especially in people with COPD and lower functional ability.
Contraception Insurance Coverage and Receipt of Long-Acting Reversible Contraception or Depot Medroxyprogesterone Acetate on the Day of Abortion
Authors: Krashin Jamie W. , Stuart Gretchen S. , Garrett Joanne , Spector Hannah , Bryant Amy G. , Charm Samantha , Morse Jessica E. 
Published: June 2017

OBJECTIVE:
To evaluate whether contraceptive insurance coverage for women who present for an abortion is associated with obtaining long-acting reversible contraception or depot medroxyprogesterone acetate (DMPA) on the day the abortion is completed.

METHODS:
We conducted a prospective cohort study of women presenting for medical or surgical abortion at a single health center in North Carolina. Eligible women were 18 years or older and fluent in English or Spanish. Data were from participant questionnaires, medical charts, and financial records. Our main exposure was whether the woman had insurance coverage for contraception at clinic intake. Our primary outcome was receiving DMPA, an intrauterine device, or a contraceptive subdermal implant on the same day of their surgical abortion or at the visit that determined their medication abortion was complete. We used univariable, bivariable, and multivariable analysis to report our findings.

RESULTS:
Five hundred seventy-five women enrolled in our cohort between September 2015 and April 2016. One hundred twenty-eight (22%) had insurance coverage and 447 (78%) did not. In the group with insurance coverage for contraception, 38% (49/128) received a long-acting reversible contraception method or DMPA compared with 7% (33/447) in the group without insurance coverage for contraception. After adjusting for confounding, women with contraceptive coverage were more than five times as likely to receive immediate postabortion contraception with one of these methods compared with women without coverage (relative risk 5.6, 95% confidence interval 3.8–8.3).

CONCLUSION:
Women with contraceptive insurance coverage on the day of their abortion were more likely to leave the abortion clinic with an intrauterine device or implant in place or receive DMPA injection compared with women without coverage.
Gestational Diabetes Mellitus and Frequency of Blood Glucose Monitoring
Authors: Mendez-Figueroa Hector , Schuster Meike , Maggio Lindsay , Pedroza Claudia , Chauhan Suneet P. , Paglia Michael J. 
Published: June 2017

OBJECTIVE:
To assess whether testing blood glucose four times daily compared with four times every other day would lead to similar birth weights among patients with gestational diabetes mellitus (GDM).

METHODS:
This noninferiority randomized controlled trial was conducted at five centers. After receiving a diagnosis of GDM, women tested their blood glucose every day for 7 days. After that period, compliant women without hyperglycemia requiring treatment were randomized to either blood glucose testing four times a day or every other day. Noninferiority would be declared if the mean birth weight in the every-other-day group was no higher than 165 g (5% difference assuming an average birth weight of 3,296 g) compared with the four times a day group. A total sample size of 286 women allowed noninferiority to be tested (one-sided .05 level of significance).

RESULTS:
From May 2013 to May 2016, of the 293 women with GDM who were randomized, 149 (51%) were tested four times a day and 144 (49%) were tested every other day. Between the two groups, there were no significant differences with regard to need for medical treatment, induction, gestational age at delivery, mode of delivery, rate of preeclampsia, or shoulder dystocia. Birth weight was similar between both groups and the upper bound of the 90% confidence interval (CI) was less than 165 g, establishing noninferiority with a mean difference of −41 g (90% CI −137 to 54 g). Rate of compliance with blood glucose testing was higher in the every-other-day group (89% compared with 92%, P<.01). The differences in rates of macrosomia and birth weight greater than the 95th percentile were not clinically significant. Neonatal outcomes including neonatal hypoglycemia were similar.

CONCLUSION:
Among patients with well-controlled GDM, testing blood glucose values every other day did not increase birth weight, although it did increase compliance with testing when compared with women who tested every day.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT01818557.
Outpatient Hysterectomy Volume in the United States
Authors: Cohen Sarah L. , Ajao Mobolaji O. , Clark Nisse V. , Vitonis Allison F. , Einarsson Jon I. 
Published: June 2017

OBJECTIVE:
To estimate the number of outpatient hysterectomies being performed annually in the United States in an effort to offer more correct estimates of hysterectomy use in light of reported decreasing inpatient case volume.

METHODS:
This is a cross-sectional analysis of State Ambulatory Surgery and Services Databases from 16 states with complete information for year 2011. Adult women undergoing hysterectomy were included. Procedure volume, route, and associated patient and surgical characteristics were calculated.

RESULTS:
There were 64,612 ambulatory hysterectomies reported; 81.5% of surgeries were performed laparoscopically and 16% vaginally. If these numbers are extrapolated to national estimates, this represents 100,000–200,000 outpatient hysterectomies per year. The strongest driver of the laparoscopic, compared with vaginal, route of hysterectomy in this data set was presence of cancer (odds ratio 4.01 [3.19–5.05], P<.001). In addition to indication for surgery, patient characteristics such as age, race, income, location, and primary payer were associated with mode of hysterectomy. The laparoscopic surgeries were associated with shorter length of stay (mean stay 0.65 days, [99% confidence interval 0.65–0.66] compared with 0.79 days [0.78–0.81], adjusted incidence rate ratio 0.89 [0.86–0.92], P<.001) and higher mean charges ($24,227 [$24,053–24,402] versus $14,068 [$13,811–14,330], P<.001) compared with vaginal surgeries.

CONCLUSION:
The perceived decline that has been reported in national hysterectomy volume may represent lack of reporting of surgeries performed in ambulatory settings. This information has considerable implications for business, public health interventions, and insurance carriers among other key stakeholders in women's health care delivery.
Serial Head and Brain Imaging of 17 Fetuses With Confirmed Zika Virus Infection in Colombia, South America
Authors: Parra-Saavedra Miguel , Reefhuis Jennita , Piraquive Juan Pablo , Gilboa Suzanne M. , Badell Martina L. , Moore Cynthia A. , Mercado Marcela , Valencia Diana , Jamieson Denise J. , Beltran Mauricio , Sanz-Cortes Magda , Rivera-Casas Ana Maria , Yepez Mayel , Parra Guido , Ospina Martinez Martha , Honein Margaret A. 
Published: June 2017

OBJECTIVE:
To evaluate fetal ultrasound and magnetic resonance imaging findings among a series of pregnant women with confirmed Zika virus infection to evaluate the signs of congenital Zika syndrome with respect to timing of infection.

METHODS:
We conducted a retrospective case series of pregnant women referred to two perinatal clinics in Barranquilla and Ibagué, Colombia, who had findings consistent with congenital Zika syndrome and Zika virus infection confirmed in maternal, fetal, or neonatal samples. Serial ultrasound measurements, fetal magnetic resonance imaging results, laboratory results, and perinatal outcomes were evaluated.

RESULTS:
We describe 17 cases of confirmed prenatal maternal Zika virus infection with adverse fetal outcomes. Among the 14 symptomatic women, the median gestational age for maternal Zika virus symptoms was 10 weeks (range 7–14 weeks of gestation). The median time between Zika virus symptom onset and microcephaly (head circumference less than 3 standard deviations below the mean) was 18 weeks (range 15–24 weeks). The earliest fetal head circumference measurement consistent with microcephaly diagnosis was at 24 weeks of gestation. The earliest sign of congenital Zika syndrome was talipes equinovarus, which in two patients was noted first at 19 weeks of gestation. Common findings on fetal magnetic resonance imaging were microcephaly, ventriculomegaly, polymicrogyria, and calcifications.

CONCLUSION:
Our analysis suggests a period of at least 15 weeks between maternal Zika virus infection in pregnancy and development of microcephaly and highlights the importance of serial and detailed neuroimaging.
Delirium and Benzodiazepines Associated With Prolonged ICU Stay in Critically Ill Infants and Young Children*
Authors: Smith Heidi A. B. , Gangopadhyay Maalobeeka , Goben Christina M. , Jacobowski Natalie L. , Chestnut Mary Hamilton , Thompson Jennifer L. , Chandrasekhar Rameela , Williams Stacey R. , Griffith Katherine , Ely E. Wesley , Fuchs D. Catherine , Pandharipande Pratik P. 
Published: June 2017

Objectives:
Delirium is prevalent among critically ill children, yet associated outcomes and modifiable risk factors are not well defined. The objective of this study was to determine associations between pediatric delirium and modifiable risk factors such as benzodiazepine exposure and short-term outcomes.

Design:
Secondary analysis of collected data from the prospective validation study of the Preschool Confusion Assessment Method for the ICU.

Setting:
Tertiary-level PICU.

Patients:
Critically ill patients 6 months to 5 years old.

Interventions:
None.

Measurements and Main Results:
Daily delirium assessments were completed using the Preschool Confusion Assessment Method for the ICU. Associations between baseline and in-hospital risk factors were analyzed for likelihood of ICU discharge using Cox proportional hazards regression and delirium duration using negative binomial regression. Multinomial logistic regression was used to determine associations between daily risk factors and delirium presence the following day. Our 300-patient cohort had a median (interquartile range) age of 20 months (11–37 mo), and 44% had delirium for at least 1 day (1–2 d). Delirium was significantly associated with a decreased likelihood of ICU discharge in preschool-aged children (age-specific hazard ratios at 60, 36, and 12 mo old were 0.17 [95% CI, 0.05–0.61], 0.50 [0.32–0.80], and 0.98 [0.68–1.41], respectively). Greater benzodiazepine exposure (75–25th percentile) was significantly associated with a lower likelihood of ICU discharge (hazard ratio, 0.65 [0.42–1.00]; p = 0.01), longer delirium duration (incidence rate ratio, 2.47 [1.36–4.49]; p = 0.005), and increased risk for delirium the following day (odds ratio, 2.83 [1.27–6.59]; p = 0.02).

Conclusions:
Delirium is associated with a lower likelihood of ICU discharge in preschool-aged children. Benzodiazepine exposure is associated with the development and longer duration of delirium, and lower likelihood of ICU discharge. These findings advocate for future studies targeting modifiable risk factors, such as reduction in benzodiazepine exposure, to mitigate iatrogenic harm in pediatric patients.
Antibiotic Therapy in Comatose Mechanically Ventilated Patients Following Aspiration: Differentiating Pneumonia From Pneumonitis*
Authors: Lascarrou Jean Baptiste , Lissonde Floriane , Le Thuaut Aurélie , Bachoumas Konstantinos , Colin Gwenhael , Henry Lagarrigue Matthieu , Vinatier Isabelle , Fiancette Maud , Lacherade Jean Claude , Yehia Aihem , Joret Aurélie , Lebert Christine , Bourdon Sandra , Martin Lefèvre Laurent , Reignier Jean 
Published: June 2017

Objectives:
To determine the proportion of patients with documented bacterial aspiration pneumonia among comatose ICU patients with symptoms suggesting either bacterial aspiration pneumonia or non-bacterial aspiration pneumonitis.

Design:
Prospective observational study.

Setting:
University-affiliated 30-bed ICU.

Patients:
Prospective cohort of 250 patients admitted to the ICU with coma (Glasgow Coma Scale score ≤ 8) and treated with invasive mechanical ventilation.

Interventions:
None.

Measurements and Main Results:
The primary outcome was the proportion of patients with microbiologically documented bacterial aspiration pneumonia. Patients meeting predefined criteria for aspiration syndrome routinely underwent telescopic plugged catheter sampling during bronchoscopy before starting probabilistic antibiotic treatment. When cultures were negative, the antibiotic treatment was stopped. Of 250 included patients, 98 (39.2%) had aspiration syndrome, including 92 before mechanical ventilation discontinuation. Telescopic plugged catheter in these 92 patients showed bacterial aspiration pneumonia in 43 patients (46.7%). Among the remaining 49 patients, 16 continued to receive antibiotics, usually for infections other than pneumonia; of the 33 patients whose antibiotics were discontinued, only two subsequently showed signs of lung infection. In the six patients with aspiration syndrome after mechanical ventilation, and therefore without telescopic plugged catheter, antibiotic treatment was continued for 7 days. Mechanical ventilation duration, ICU length of stay, and mortality did not differ between the 43 patients with bacterial aspiration pneumonia and the 49 patients with non-bacterial aspiration pneumonitis. The 152 patients without aspiration syndrome did not receive antibiotics.

Conclusions:
Among comatose patients receiving mechanical ventilation, those without clinical, laboratory, or radiologic evidence of bacterial aspiration pneumonia did not require antibiotics. In those with suspected bacterial aspiration pneumonia, stopping empirical antibiotic therapy when routine telescopic plugged catheter sampling recovered no microorganisms was nearly always effective. This strategy may be a valid alternative to routine full-course antibiotic therapy. Only half the patients with suspected bacterial aspiration pneumonia had this diagnosis confirmed by telescopic plugged catheter sampling.
Treatment of Complex Fistula-in-Ano With a Nitinol Proctology Clip
Authors: Nordholm-Carstensen Andreas , Krarup Peter-Martin , Hagen Kikke 
Published: June 2017

BACKGROUND:
The treatment of complex anocutaneous fistulas remains a major therapeutic challenge balancing the risk of incontinence against the chance of permanent closure.

OBJECTIVE:
The purpose of this study was to investigate the efficacy of a nitinol proctology clip for closure of complex anocutaneous fistulas.

DESIGN:
This is a single-center cohort study with retrospective analysis of all of the treated patients.

SETTINGS:
Data were obtained from patient records and MRI reports, as well as follow-up telephone calls and clinical follow-up with endoanal ultrasonography.

PATIENTS:
All of the patients were treated for high transsphincteric and suprasphincteric anocutaneous fistulas at the Digestive Disease Center, Bispebjerg Hospital, between May 2013 and February 2015.

INTERVENTIONS:
All of the patients were treated with the nitinol proctology clip.

MAIN OUTCOME MEASURES:
Primary outcome was fistula healing after proctology clip placement, as evaluated through clinical examination, endoanal ultrasonography, and MRI.

RESULTS:
The fistula healing rate 1 year after the clip procedure was 54.3% (19 of 35 included patients). At the end of follow-up, 17 (49%) of 35 patients had persistent closure of the fistula tracks. No impairment of continence function was observed. Treatment outcome was not found to be statistically associated with any clinicopathological characteristics.

LIMITATIONS:
The study is limited by its retrospective and nonrandomized design. Selection bias may have occurred, because treatment options other than the clip were available during the study period. The small number of patients means that there is a nonnegligible risk of type II error in the conclusion, and the follow-up may be too short to have detected all of the failures.

CONCLUSIONS:
Healing rates were comparable with those of other noninvasive, sphincter-sparing techniques for high-complex anocutaneous fistulas, with no risk of incontinence. Predictive parameters for fistula healing using this technique remain uncertain. See Video Abstract at http://links.lww.com/DCR/A347.
ELLIPSOID ZONE MAPPING AND OUTER RETINAL ASSESSMENT IN STARGARDT DISEASE
Authors: Arepalli Sruthi , Traboulsi Elias I. , Ehlers Justis P. 
Published: June 2017

Purpose:
To quantify and correlate ellipsoid zone and photoreceptor outer segment changes with visual acuity in Stargardt disease.

Methods:
An institutional review board–approved study of 32 eyes with Stargardt disease was performed. After spectral domain optical coherence tomography, the macular cube was exported into a novel analysis tool and volumetric assessment from the ellipsoid zone to the retinal pigment epithelium was performed. Using this information, mapping was completed with en face representation of the height between the ellipsoid zone and retinal pigment epithelium. This analysis provided quantification of ellipsoid zone and photoreceptor outer segments, including atrophy (ellipsoid zone to retinal pigment epithelium thickness = 0 μm) and attenuation (ellipsoid zone to retinal pigment epithelium thickness <20 μm). These parameters were compared with visual acuity and controls (n = 12 eyes).

Results:
Visual acuity ranged from 20/30 to 20/250. The central foveal B-scan area of ellipsoid and photoreceptor outer segments was significantly less than controls (0.13 ± 0.05 mm2 vs. 0.17 ± 0.03 mm2, respectively, P = 0.0074). The central foveal B-scan mean thickness measured 22.52 ± 9.0 μm in Stargardt versus 30.0 ± 5.08 μm (P = 0.0096). Atrophy and attenuation were significantly higher in Stargardt patients (22% vs. 1%, P = 0.005 and 43% vs. 1%, P = 0.0002). Visual acuity directly correlated with ellipsoid zone/outer segment volume (R = 0.57, P < 0.005) and inversely correlated with attenuation and atrophy (R = −0.53 and −0.57; P < 0.005 for all).

Conclusion:
Eyes with Stargardt disease frequently have significant disruption of the ellipsoid zone and outer segments. This degenerative change was successfully quantified with a novel assessment platform and identified correlates with visual function. This software provides the opportunity for quantitative assessment and possible longitudinal surveillance.