bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indexed variation graphs for efficient and accurate resistome profiling
Authors: Rowe Will P M , Winn Martyn D 
Published: May 2018

Abstract

Motivation
Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the ‘resistome’) facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools.

Results
Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 min using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows.

Availability and implementation
GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license).

Supplementary information
Supplementary data are available at Bioinformatics online.
Hydrogen station technology development review through patent analysis
Authors: Wen Chengyu , He Guangli 
Published: May 2018

Abstract
This study is a review of hydrogen station patents using the Derwent Innovation system and also a secondary screening. This was undertaken by the researchers to better understand and identify hydrogen station trends. The review focuses on analyzing the developing trends of patent technologies associated with a hydrogen station. The results of the review indicated that the countries with the major distribution of patents were Japan, China, the USA and Europe. Japan is leading the developmental trajectory of hydrogen stations. The results of the analysis found the leading developers of these patented technologies are Kobe Steel, Nippon Oil, Toyota and Honda. Other active patent developers analyzed include Linde, Hyundai and Texaco. The review concludes with a suggestion that using a patent analysis methodology is a good starting point to identify, evaluate and measure the trend in hydrogen station commercial development.
Pregnancy Basics
Authors: Mathiesen Amber , Roy Kali 
Published: May 2018

Abstract
This chapter provides background on pregnancy concepts that are essential to understand when working in the perinatal setting. Topics include pregnancy timeline and duration, the difference between gestational and embryonic age, methods for establishing an expected due date, and tools for assisting with pregnancy dating, including pregnancy wheels and online tools. General pregnancy care topics are also addressed, including types of obstetric providers; common lab tests including the complete blood count, blood type, antibody testing, and HbA1C; and imaging including the first-, second-, and third-trimester ultrasounds as well as specialized evaluations such as a nuchal translucency and fetal magnetic resonance imaging (MRI). Last, there is a explanation with examples of how to document a pregnancy history by gravidity and parity.
Prenatal Screening
Authors: Mathiesen Amber , Roy Kali 
Published: May 2018

Abstract
This chapter provides information about a genetic counselor’s role in prenatal screening, including discussing and offering options to a patient, interpreting and providing results, or managing referrals based on abnormal results. It discusses how a screen is evaluated using sensitivity, specificity, positive predictive value, negative predictive value, and personal utility. It provides a detailed description of both maternal serum screening and cell-free DNA testing. The maternal serum screening discussion includes information on multiples of median, calculating risk, timing, pattern association, limitations, and follow-up. The review of cell-free DNA testing includes fetal fraction, methodology, test performance, limitations and considerations for testing, and follow-up. This chapter also provides a list of additional resources to use for cell-free DNA testing.
Hard state neutron star and black hole X-ray binaries in the radio:X-ray luminosity plane
Authors: Gallo Elena , Degenaar Nathalie , van den Eijnden Jakob 
Published: May 2018

ABSTRACT
Motivated by the large body of literature around the phenomenological properties of accreting black hole (BH) and neutron star (NS) X-ray binaries in the radio:X-ray luminosity plane, we carry out a comparative regression analysis on 36 BHs and 41 NSs in hard X-ray states, with data over 7 dex in X-ray luminosity for both. The BHs follow a radio to X-ray (logarithmic) luminosity relation with slope β = 0.59 ± 0.02, consistent with the NSs’ slope ($\beta =0.44^{+0.05}_{-0.04}$) within 2.5σ. The best-fitting intercept for the BHs significantly exceeds that for the NSs, cementing BHs as more radio loud, by a factor ∼22. This discrepancy cannot be fully accounted for by the mass or bolometric correction gap, or by the NS boundary layer contribution to the X-rays, and is likely to reflect physical differences in the accretion flow efficiency, or the jet powering mechanism. Once importance sampling is implemented to account for the different luminosity distributions, the slopes of the non-pulsating and pulsating NS subsamples are formally inconsistent (&gt;3σ), unless the transitional millisecond pulsars (whose incoherent radio emission mechanism is not firmly established) are excluded from the analysis. We confirm the lack of a robust partitioning of the BH data set into separate luminosity tracks.
Simulating the Role of the Parent: Promoting Family-Centered Nursing Care
Authors: Zimmermann Elizabeth , Alfes Celeste M. 
Published: May 2018

Abstract
Parents of hospitalized children need support to diminish their own fear and anxiety and provide safe and loving care for the child. Baccalaureate nursing students, who are rarely parents themselves, often find it difficult to understand the needs of parents. An innovative simulation strategy was created to enhance students’ understanding of the parent’s role and its effect on family-centered care. This article describes the development of pediatric simulation experiences that actively incorporate the role of a parent. Portraying the parent during the simulation increases students’ ability to be empathetic while providing safe family-centered care.
Variation in Neonate Swaddling Techniques
Authors: Fletcher Laura , Pham Tammy , Bar Sari , Li Diana , Spinazzola Regina , Papaioannou Helen , Milanaik Ruth 
Published: May 2018

Background:
It is common practice for healthcare practitioners to swaddle infants in newborn nursery and neonatal intensive care unit settings. Despite the widespread use of this practice, the American Academy of Pediatrics neither bans nor recommends swaddling. To date, there has been no standard protocol developed for either healthcare professionals or parents to establish optimal swaddling techniques in terms of infant arm positioning, infant leg positioning, and tightness of wrap.

Purpose:
To evaluate the variability in swaddling techniques used for infants in the newborn nursery and neonatal intensive care unit.

Methods:
Across 2 pediatric hospitals, the swaddling positioning of each open-crib infant in the newborn nursery and neonatal intensive care unit was examined. For each infant, the following data were collected: gender, left and right arm position, left and right leg position, and tightness of wrap.

Results:
In total, 132 swaddle observations were recorded. There was significant variability in swaddling positioning of arms and legs. The most common combination of arm/leg positioning was “mixed arm positioning” and “both legs flexed” (25.0% of all observations). In 9.1% of cases, tightness of wrap around chest was “tight,” and in 30.3% of cases, tightness of wrap around legs was “tight.”

Implications for Practice:
There was a large variability in swaddling positioning of both arms and legs. For such a widespread practice, the lack of medical guidelines results in inconsistent, and potentially harmful, positioning. Parents and healthcare professionals would benefit from specific, research-driven guidelines regarding proper swaddling techniques.

Implications for Research:
Different variations on swaddling should be evaluated for consideration of best practice swaddling.
Management of Labor and Delivery After Fetoscopic Repair of an Open Neural Tube Defect
Authors: Kohn Jaden R. , Rao Vibha , Sellner Allison A. , Sharhan Dina , Espinoza Jimmy , Shamshirsaz Alireza A. , Whitehead William E. , Belfort Michael A. , Sanz Cortes Magdalena 
Published: May 2018

OBJECTIVE:
To report labor, delivery, and neonatal outcomes in a cohort of women delivering neonates who had undergone fetoscopic neural tube defect repair.

METHODS:
We conducted a retrospective cohort study from April 2014 to January 2018. All patients met Management of Myelomeningocele Study eligibility criteria. We included patients with completed second-trimester fetoscopic neural tube defect repair (laparotomy, uterine exteriorization, and minimally invasive access through two or three uterine ports) followed by standardized management of labor and delivery at our institution. Outcomes included rates of vaginal delivery, term delivery, and intrapartum cesarean delivery as well as obstetric and neonatal outcomes after oxytocin. Complications of interest included preterm prelabor rupture of membranes, chorioamnionitis, uterine dehiscence or rupture, 5-minute Apgar score less than 7, and neonatal acidosis (umbilical artery pH less than 7.15).

RESULTS:
Thirty-four patients had fetoscopic repair, followed by 17 vaginal deliveries (50%, 95% CI 32–68%). Median gestational age was 38 1/7 weeks at vaginal delivery (range 26 0/7–40 2/7 weeks of gestation) and 37 1/7 weeks of gestation at cesarean delivery (range 25 5/7–40 5/7 weeks of gestation); 62% of deliveries occurred at term. Eight patients had prelabor cesarean delivery: three nonurgent and five urgent (for nonreassuring fetal heart tracings). Twenty-six patients labored; six were induced and 20 labored spontaneously. Of the latter, five were augmented. Of 26 laboring patients, 17 delivered vaginally and nine underwent urgent cesarean delivery (35%, 95% CI 17–56%; seven nonreassuring fetal heart tracings and two breech). There were no cases of uterine rupture or dehiscence. Most (94%, 95% CI 80–99%) had normal 5-minute Apgar scores; one neonate (3%, 95% CI 0–15%) had acidosis but normal Apgar scores.

CONCLUSION:
Our data regarding trial of labor, use of low-dose oxytocin, and vaginal delivery after prenatal fetoscopic neural tube defect repair are reassuring. Importantly, fetoscopic repair may permit delivery at advanced gestational ages.
Decreased Surgical Site Infection Rate in Hysterectomy
Authors: Andiman Sarah E. , Xu Xiao , Boyce John M. , Ludwig Elizabeth M. , Rillstone Heidi R. W. , Desai Vrunda B. , Fan Linda L. 
Published: May 2018

OBJECTIVE:
We implemented a hysterectomy-specific surgical site infection prevention bundle after a higher-than-expected surgical site infection rate was identified at our institution. We evaluate how this bundle affected the surgical site infection rate, length of hospital stay, and 30-day postoperative readmission rate.

METHODS:
This is a quality improvement study featuring retrospective analysis of a prospectively implemented, multidisciplinary team-designed surgical site infection prevention bundle that consisted of chlorhexidine-impregnated preoperative wipes, standardized aseptic surgical preparation, standardized antibiotic dosing, perioperative normothermia, surgical dressing maintenance, and direct feedback to clinicians when the protocol was breached.

RESULTS:
There were 2,099 hysterectomies completed during the 33-month study period. There were 61 surgical site infections (4.51%) in the pre–full bundle implementation period and 14 (1.87%) in the post–full bundle implementation period; we found a sustained reduction in the proportion of patients experiencing surgical site infection during the last 8 months of the study period. After adjusting for clinical characteristics, patients who underwent surgery after full implementation were less likely to develop a surgical site infection (adjusted odds ratio [OR] 0.46, P=.01) than those undergoing surgery before full implementation. Multivariable regression analysis showed no statistically significant difference in postoperative days of hospital stay (adjusted mean ratio 0.95, P=.09) or rate of readmission for surgical site infection-specific indication (adjusted OR 2.65, P=.08) between the before and after full-bundle implementation periods.

CONCLUSION:
The multidisciplinary implementation of a gynecologic perioperative surgical site infection prevention bundle was associated with a significant reduction in surgical site infection rate in patients undergoing hysterectomy.
Obstetric Management of Loeys-Dietz Syndrome
Authors: Russo Melissa L. , Sukhavasi Neelima , Mathur Veena , Morris Shaine A. 
Published: May 2018

BACKGROUND:
Loeys-Dietz syndrome is associated with arterial tortuosity and aortic dissection. Pregnancy may be a period of increased risk for aortic dissection.

CASE:
A 16-year-old primigravid girl was referred to our center with a family history of aortic dissection. Loeys-Dietz syndrome was suspected, and genetic testing confirmed the TGFβ2 (c.988C>T) mutation. A cesarean delivery was performed at 36 weeks of gestation, with no cardiovascular complications. In this case, the uterine vessels were significantly tortuous; this may be an additional finding in Loeys-Dietz syndrome.

CONCLUSION:
Women with Loeys-Dietz syndrome warrant special consideration in obstetric management secondary to the risk for aortic dissection. It is recommended that a multidisciplinary team with knowledge about connective tissue disorders and expertise in aortic surgery coordinate maternal obstetric and cardiovascular care.
Patterns of von Willebrand Disease Screening in Girls and Adolescents With Heavy Menstrual Bleeding
Authors: Jacobson Amanda E. , Vesely Sara K. , Koch Terah , Campbell Janis , O'Brien Sarah H. 
Published: May 2018

OBJECTIVE:
To estimate the frequency of von Willebrand disease screening and factors that affect screening frequency in a national sample of girls and adolescents with heavy menstrual bleeding.

METHODS:
In this retrospective cohort study, we used a national claims database for privately and publicly insured patients between 2011 and 2013 for girls aged 10–17 years. Diagnostic criteria of heavy menstrual bleeding were the presence of one inpatient or two outpatient International Classification of Diseases, 9th Revision codes for heavy menstrual bleeding. We defined severe heavy menstrual bleeding as heavy menstrual bleeding plus an inpatient stay for menstrual bleeding, iron deficiency anemia, or blood transfusion. To assess whether patient- or facility-level characteristics affected screening, we performed logistic regression analysis including patient age, health care provider type seen at first visit for menorrhagia, patient residence in a metropolitan statistical area (proxy for urban vs rural inhabitance), and approximate travel time to the nearest hemophilia treatment center.

RESULTS:
We identified 23,888 postpubertal girls and adolescents with heavy menstrual bleeding (986 with severe heavy menstrual bleeding). Von Willebrand disease screening was performed in 8% of females with heavy menstrual bleeding and 16% with severe heavy menstrual bleeding. Younger age at diagnosis, commercial insurance, and living within a metropolitan statistical area were associated with higher screening rates. Patients who underwent testing for iron deficiency anemia had the highest likelihood of undergoing screening (odds ratio 7.08, 95% CI 6.32–7.93). Among patients living in a metropolitan statistical area, those 60 minutes or more from a hemophilia treatment center were less likely to undergo screening.

CONCLUSION:
Despite recommendations by the American College of Obstetricians and Gynecologists for more than 15 years, fewer than 20% of postpubertal girls and adolescents with heavy menstrual bleeding underwent screening for von Willebrand disease in this cohort. Increased clinician awareness and adherence to recommended screening recommendations may increase diagnosis of von Willebrand disease.
Variation in the Nulliparous, Term, Singleton, Vertex Cesarean Delivery Rate
Authors: Pasko Daniel N. , McGee Paula , Grobman William A. , Bailit Jennifer L. , Reddy Uma M. , Wapner Ronald J. , Varner Michael W. , Thorp John M. , Leveno Kenneth J. , Caritis Steve N. , Prasad Mona , Saade George , Sorokin Yoram , Rouse Dwight J. , Blackwell Sean C. , Tolosa Jorge E. ,   for the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network
Published: May 2018

OBJECTIVE:
To estimate the contributions of patient and health care provider–hospital characteristics to the variation in the frequency of nulliparous, term, singleton, vertex cesarean delivery in a multi-institutional U.S. cohort.

METHODS:
We performed a secondary analysis of the multicenter Assessment of Perinatal Excellence cohort of 115,502 mother and neonatal pairs who were delivered at 25 hospitals between March 2008 and February 2011. Women met inclusion criteria if they were nulliparous and delivered a singleton in vertex presentation at term. Hospital ranks for nulliparous, term, singleton, vertex cesarean delivery frequency were determined after risk adjustment. The fraction of variation in nulliparous, term, singleton, vertex cesarean delivery frequency attributable to patient and health care provider–hospital characteristics was assessed using hierarchical logistic regression.

RESULTS:
Of the 115,502 deliveries in the initial cohort, 38,275 nulliparous, term, singleton, vertex deliveries met inclusion criteria. The median hospital nulliparous, term, singleton, vertex cesarean delivery frequency was 25.3% with a range from 15.0% to 35.2%. The majority of hospitals (16/25) changed rank quintiles after risk adjustment; overall the changes in rank were not statistically significant (P=.53). Patient characteristics accounted for 24% of the nulliparous, term, singleton, vertex cesarean delivery variation. The analyzed health care provider–hospital characteristics were not significantly associated with cesarean delivery frequency.

CONCLUSION:
Although patient characteristics accounted for some of the variation in nulliparous, term, singleton, vertex cesarean delivery frequency and accounting for case mix had implications for hospital cesarean delivery rankings, the majority of the variation was not explained by the characteristics evaluated. These findings emphasize the importance of continued efforts to understand aspects of obstetric care, including case mix, that contribute to cesarean delivery variation.
Clinical Comparison of Surgical Constructs for Anterior Cervical Corpectomy and Fusion in Patients With Cervical Spondylotic Myelopathy or Ossified Posterior Longitudinal Ligament
Authors: Niedzielak Timothy R. , Palmer Joseph , Malloy John P. 
Published: May 2018

Study Design:
This is a systematic review and meta-analysis.

Objective:
To examine the differences in outcomes among current constructs and techniques for anterior cervical corpectomy and fusion (ACCF) in patients with single or multiple level cervical myelopathy (CM) secondary to cervical spondylosis or ossified posterior longitudinal ligament.

Summary of Background Data:
The natural history of CM can be a progressive disease process. In such cases, where surgical decompression is indicated to halt the progression, ACCF is typically chosen for pathology located posterior to the vertebral body. Numerous studies have shown that decompression with appropriate stabilization not only halts progression, but also improves patient outcomes. However, several constructs are available for this procedure, all with variable outcomes.

Materials and Methods:
A systematic review was conducted using Cochrane Database, Medline, and PubMed. Only studies with a minimum patient population of 10, reporting on CM because of cervical spondylosis or ossified posterior longitudinal ligament were included; a minimum follow-up period of 12 months and 1 clinical and/or radiographic outcome were required. Studies examining patients with cervical trauma/fracture, tumor, and infection or revision cases were excluded. Data analysis was carried out with Microsoft Excel.

Results:
A total of 30 studies met the inclusion criteria for qualitative analysis, while 26 studies were included for quantitative analysis. Constructs that were reported in these studies included titanium mesh cages, nano-hydroxyapatite/polyamide 66 composite struts, bone graft alone, expandable corpectomy cages, and polyetheretherketone cages. Clinical outcomes included Japanese Orthopaedic Association and modified Japanese Orthopaedic Association scores, Visual Analog Scale scores, Neck Disability Index scores, and Nurick grades. Radiographic outcomes included C2–C7 and segmental Cobb angles and pseudarthrosis rates. Each construct type had variable and unique benefits and shortcomings.

Conclusions:
ACCF is a common surgical option for CM, despite carrying certain risks expected of any anterior cervical approach. Several constructs are available for ACCF, all with variable clinical and radiographic outcomes.