bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steady progress toward a malaria vaccine
Authors: Lyke Kirsten E. 
Published: July 2017

Purpose of review
Great progress has been made in reducing malaria morbidity and mortality, yet the parasite continues to cause a startling 200 million infections and 500 000 deaths annually. Malaria vaccine development is pushing new boundaries by steady advancement toward a licensed product.

Recent findings
Despite 50 years of research, the complexity of Plasmoidum falciparum confounds all attempts to eradicate the organism. This very complexity has pushed the boundaries of vaccine development to new heights, yet it remains to be seen if an affordable vaccine can provide durable and high-level protection. Novel vaccines such as RTS,S/AS01E are on the edge of licensure, but old techniques have resurged with the ability to deliver vialed, whole organism vaccines. Novel adjuvants, multistage/multiantigen approaches and transmission blocking vaccines all contribute to a multipronged battle plan to conquer malaria.

Summary
Vaccines are the most cost-effective tools to control infectious diseases, yet the complexity of malaria has frustrated all attempts to develop an effective product. This review concentrates on recent advances in malaria vaccine development that lend hope that a vaccine can be produced and malaria eradicated.
Current perspectives on invasive nontyphoidal Salmonella disease
Authors: Haselbeck Andrea H. , Panzner Ursula , Im Justin , Baker Stephen , Meyer Christian G. , Marks Florian 
Published: July 2017

Purpose of review
We searched PubMed for scientific literature published in the past 2 years for relevant information regarding the burden of invasive nontyphoidal Salmonella disease and host factors associated with nontyphoidal Salmonella infection and discuss current knowledge on vaccine development. The following search terms were used: Salmonella, non typhoidal/nontyphoidal, NTS, disease, bloodstream infection, invasive, sepsis/septicaemia/septicemia, bacteraemia/bacteremia, gastroenteritis, incidence, prevalence, morbidity, mortality, case fatality, host/risk factor, vaccination, and prevention/control.

Recent findings
Estimates of the global invasive nontyphoidal Salmonella disease burden have been recently updated; additional data from Africa, Asia, and Latin America are now available. New data bridge various knowledge gaps, particularly with respect to host risk factors and the geographical distribution of iNTS serovars. It has also been observed that Salmonella Typhimurium sequence type 313 is emergent in several African countries. Available data suggest that genetic variation in the sequence type 313 strain has led to increased pathogenicity and human host adaptation. A bivalent efficacious vaccine, targeting Salmonella serovars Typhimurium and Enteritidis, would significantly lower the disease burden in high-risk populations.

Summary
The mobilization of surveillance networks, especially in Asia and Latin America, may provide missing data regarding the invasive nontyphoidal Salmonella disease burden and their corresponding antimicrobial susceptibility profiles. Efforts and resources should be directed toward invasive nontyphoidal Salmonella disease vaccine development.
Evaluation of Noninvasive Hemoglobin Monitoring in Trauma Patients with Low Hemoglobin Levels
Authors: Gamal Medhat , Abdelhamid Bassant , Zakaria Dina , Dayem Omnia Abd El , Rady Ashraf , Fawzy Maher , Hasanin Ahmed 
Published: July 2017

ABSTRACT

Objective:
Bleeding is a leading cause of death among trauma patients. Delayed assessment of blood hemoglobin level might result in either unnecessary blood transfusion in nonindicated patients or delayed blood transfusion in critically bleeding patients. In this study, we evaluate the precision of noninvasive hemoglobin monitoring in trauma patients with low hemoglobin levels.

Methods:
We included trauma patients with low hemoglobin levels (less than 8 g/dL) scheduled for surgical intervention. Blood samples were obtained on admission and after each blood unit with concomitant measurement of serum hemoglobin using radical-7 Masimo device. The change in blood hemoglobin after every transfused blood unit was also assessed by both methods (change in noninvasive Masimo hemoglobin [Delta-Sp-Hb] and change in laboratory hemoglobin [Delta-Lab-Hb]). The precision of Masimo hemoglobin level (Sp-Hb) compared with Laboratory hemoglobin level (Lab-Hb) was determined using both Bland–Altman and Pearson correlation analyses.

Results:
One hundred eighty-four time-matched samples were available for final analysis. Bland–Altman analysis showed excellent accuracy of Sp-Hb compared with Lab-Hb with mean bias of 0.12 g/dL and limits of agreement between −0.56 g/dL and 0.79 g/dL. Excellent correlation was reported between both measures with Pearson correlation coefficient of 0.872. Excellent agreement was also reported between both Delta-Sp-Hb and Delta-Lab-Hb with mean bias of −0.05 and limits of agreement from −0.62 to 0.51

Conclusions:
Sp-Hb showed accurate precision in both absolute values and trend values compared with Lab-Hb measurement in trauma patients with low hemoglobin levels.
Open Colectomies of Shorter Operative Time Do Not Result in Improved Outcomes Compared With Prolonged Laparoscopic Operations
Authors: Zettervall Sara L. , Haskins Ivy N. , Deery Sarah E. , Amdur Richard L. , Lin Paul P. , Vaziri Khashayar 
Published: July 2017

Background:
Laparoscopic colectomies are associated with reduced perioperative morbidity and mortality compared with open surgery. Nevertheless, many surgeons continue to utilize an open surgical approach due to the perceived benefits of shorter operative times. This study aims to compare the outcomes of laparoscopic versus open colectomies of equal or shorter operative duration.

Methods:
All patients undergoing elective laparoscopic or open colectomy in the American College of Surgeons National Surgical Quality Improvement Project (ACS-NSQIP) were identified from the years 2005 through 2012. Patients were stratified first by operative procedure including partial colectomy, total colectomy, or low anterior resection. Each surgical group was then divided into 4 groups according to operative time: <90 minutes, ≥90 minutes and <3 hours, ≥3 hours and <6 hours, and ≥6 hours. In total, 30-day outcomes were compared between laparoscopic operations and open procedures of shorter or equivalent durations within each surgical group. Multivariate logistic regression was utilized to account for differences in patient demographics and comorbidities between the surgical groups.

Results:
In total, 156,503 patients met inclusion criteria; 112,053 (71.6%) patients underwent a partial colectomy, 13,838 (8.8%) patients underwent a total colectomy, and 30,612 (19.6%) patients underwent a low anterior resection. A laparoscopic approach was used in 34% (37,789 patients) of the partial colectomies performed, 31% (4285 patients) of the total colectomies performed, and 45% (13,850 patients) of the low anterior resections performed. For all procedures, laparoscopic operations <6 hours were associated with superior outcomes compared with shorter open procedures. The benefit of laparoscopic operations was lost when operative time exceeded 6 hours.

Conclusions:
Laparoscopic colectomies are associated with improved outcomes compared with open operations that do not exceed an operative time of 6 hours. Given the potential to improve patient outcomes, consideration should be given to the laparoscopic approach for all colon surgeries expected to be completed in <6 hours.
Surgical Anatomy of the Uterosacral Ligament Colpopexy
Authors: Siff Lauren N. , Jallad Karl , Hickman Lisa C. , Walters Mark D. 
Published: July 2017

Objective
The aim of this study was to describe the relationship of the uterosacral ligament (USL) to the ureter and rectum along a surgeon's target location for suture placement under conditions simulating live surgery.

Methods
Dissections were performed in 11 unembalmed female cadavers. Steps were taken to identify the USL simulating USL colpopexy. Pins were placed in the midportion of the USL at the level of the IS, and at 1-cm, 2-cm, and 3-cm increments traveling proximally toward the sacrum (Fig. 1). We measured minimum distances from the USL to the ureter and rectum at each target location.

Results
In general, the ureters range from 1.3 to 2.0 cm lateral to the USLs along the target length. The rectum ranges from 1.9 to 2.6 cm from the right USL and remains 1.5 cm from the left USL. The mean change in distance between the ureter and USL for every 1 cm advanced toward the sacrum is 0.2 cm (95% confidence interval [CI], 0.19–0.24) on the right and 0.2 cm (95% CI, 0.18–0.27) on the left. The mean change in distance between the rectum and USL for every 1 cm advanced toward the sacrum is 0.2 cm (95% CI, 0.19–0.24) on the right and 0.0 cm (95% CI, 0–0) on the left.

Conclusions
For every centimeter traveled along the bilateral USLs from the IS toward the sacrum, the ureter moves 0.2 cm laterally away from the ligament, the rectum moves 0.2 cm medially away from the right USL, but maintains its position from the left USL.
Variables Affecting Intra-abdominal Pressure During Lifting in the Early Postpartum Period
Authors: Hsu Yvonne , Hitchcock Robert , Niederauer Stefan , Nygaard Ingrid E. , Shaw Janet M. , Sheng Xiaoming 
Published: July 2017

Objectives
Intra-abdominal pressure (IAP) may contribute to pelvic floor health, although the direction and magnitude of such an effect, if any, are not yet known. Identifying individual characteristics, and in particular modifiable factors, associated with higher IAP during recovery from vaginal childbirth might serve to mitigate early pelvic floor dysfunction. The aim of this study was to identify characteristics associated with maximal IAP during lifting in postpartum primiparous women who delivered vaginally.

Methods
At 6 to 10 weeks postpartum, we measured maximal IAP, assessed via an upper vaginal sensor, as participants (enrolled in an ongoing cohort study) lifted a weighted car seat (12.5 kg). We evaluated whether the following independent variables were associated with maximal IAP: age, ethnicity, body mass index, height, abdominal circumference, weight gain during pregnancy, lifting time, breath holding during lifting, lifting technique, measures of muscular fitness, and days since delivery.

Results
In the 206 participants, weight, waist circumference, body mass index, and days since delivery were positively associated with mean maximal IAP during lifting, whereas IAP decreased as height increased. As the duration of the lifting task increased, mean maximal IAP during lifting also increased, but there were no associations between lifting technique or breath holding during lifting and IAP. Neither pelvic floor muscle strength nor abdominal muscle endurance was associated with IAP during lifting.

Conclusions
Other than measures of body habitus and lifting duration, we did not identify modifiable factors that could mitigate maximal pressures experienced by the pelvic floor during the early postpartum period.
TDCPP exposure affects the concentrations of thyroid hormones in zebrafish
Authors: Song Jingxin 
Published: July 2017

AbstractPrevious studies show that TDCPP may interrupt the thyroid endocrine system, however, the potential mechanisms involved in these processes were largely unknown. In this study, zebrafish embryos/larvae were exposed to TDCPP until 120 hpf, by which time most of the organs of the larvae have completed development. In this study, the effects of TDCPP on HPT axis were examined and the thyroid hormone levels were measured after TDCPP treatment. Zebrafish (Danio rerio) embryos were treated with a series concentration of TDCPP (10, 20, 40, 80, 160 and 320 μg/L) from 1 day post-fertilization (dpf) to 5 dpf. Exposure concentrations of TDCPP were determined based on the survival rates in each group. Total mRNA were isolated, first-strand cDNA were synthesis and qPCR were performed to detect the mRNA expression levels in hypothalamic-pituitary-thyroid (HPT) axis. The mRNA expression levels of genes involved in thyroid hormone homeostasis were increased in the TDCPP-treated larvae. The mRNA levels of genes involved in thyroid hormone synthesis were also increased in the embryos treated with TDCPP. Furthermore, exposure to TDCPP led to a dose-dependent effect on zebrafish development, including diminished hatching and survival rates, increased malformation. TDCPP treatment significantly reduced the T4 concentration in the 5 dpf zebrafish larvae, but increased the concentration of T3, suggesting the function of thyroid endocrine were interrupted in the TDCPP-exposed zebrafish. Taken together, these data indicated that TDCPP affected the thyroid hormone levels in the zebrafish larvae and could increased the mRNA expression levels of genes related to HPT axis, which further impaired the endocrine homeostasis and thyroid system.
SnakeChunks: modular blocks to build Snakemake workflows for reproducible NGS analyses
Authors: Rioualen Claire , Charbonnier-Khamvongsa Lucie , Helden Jacques van 
Published: July 2017

AbstractSummaryNext-Generation Sequencing (NGS) is becoming a routine approach for most domains of life sciences, yet there is a crucial need to improve the automation of processing for the huge amounts of data generated and to ensure reproducible results. We present SnakeChunks, a collection of Snakemake rules enabling to compose modular and user-configurable workflows, and show its usage with analyses of transcriptome (RNA-seq) and genome-wide location (ChIP-seq) data.AvailabilityThe code is freely available (github.com/SnakeChunks/SnakeChunks), and documented with tutorials and illustrative demos (snakechunks.readthedocs.io).Contactclaire.rioualen@inserm.fr,jacques.van-helden@univ-amu.frSupplementary informationSupplementary data are available atBioinformaticsonline.
Orientation-dependentDxz4contacts shape the 3D structure of the inactive X chromosome
Authors: Bonora G. , Deng X. , Fang H. , Ramani V. , Qui R. , Berletch J. , Filippova G. N. , Duan Z. , Schendure J. , Noble W. S. , Disteche C. M. 
Published: July 2017

AbstractThe mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge we show that the conserved repeat locusDxz4alone is sufficient to maintain the bipartite structure and thatDxz4orientation controls the distribution of long-range contacts on the Xi. Frequent long-range contacts betweenDxz4and the telomeric superdomain are either lost after its deletion or shifted to the centromeric superdomain after its inversion. This massive reversal in contact distribution is consistent with the reversal of CTCF motif orientation atDxz4.De-condensation of the Xi afterDxz4deletion is associated with partial restoration of TADs normally attenuated on the Xi. There is also an increase in chromatin accessibility and CTCF binding on the Xi afterDxz4deletion or inversion, but few changes in gene expression, in accordance with multiple epigenetic mechanisms ensuring X silencing. We propose thatDxz4represents a structural platform for frequent long-range contacts with multiple loci in a direction dictated by the orientation of a bank of CTCF motifs atDxz4,which may work as a ratchet to form the distinctive bipartite structure of the condensed Xi.
Polygenic hazard score: an enrichment marker for Alzheimer’s associated amyloid and tau deposition
Authors: Tan Chin Hong , Fan Chun Chieh , Mormino Elizabeth C. , Sugrue Leo P. , Broce Iris J. , Hess Christopher P. , Dillion William P. , Bonham Luke W. , Yokoyama Jennifer S. , Karch Celeste M. , Brewer James B. , Rabinovici Gil D. , Miller Bruce L. , Schellenberg Gerald D. , Kauppi Karolina , Feldman Howard A. , Holland Dominic , McEvoy Linda K. , Hyman Bradley T. , Andreassen Ole A. , Dale Anders M. , Desikan Rahul S. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2017

ABSTRACTBackgroundThere is an urgent need for the early identification of nondemented individuals at the highest risk of progressing to Alzheimer’s disease (AD) dementia for early therapeutic interventions. Our goal was to evaluate whether a recently validated polygenic hazard score (PHS) can be integrated with knownin vivoCSF or PET biomarkers of amyloid or tau pathology to prospectively predict cognitive decline and clinical progression to AD dementia in nondemented older individuals.MethodsWe evaluated 347 cognitive normal (CN) and 599 mild cognitively impaired (MCI) individuals. We first investigated whether PHS can predict CSF or PET amyloid and tau deposition. We evaluated differences in positive and negative predictive values of biomarker status, as a function of PHS risk. Next, we used linear mixed-effects (LME) to examine if PHS and biomarker status in conjunction, best predict longitudinal cognitive and clinical progression. Lastly, we used survival analysis to investigate whether a combination of PHS and biomarker positivity predicts progression to AD dementia better than using PHS or biomarker positivity alone.FindingsIn CN and MCI individuals, we found that amyloid and total tau positivity systematically varies as a function of PHS. For individuals in greater than the 50thpercentile PHS, the positive predictive value for amyloid approached 100%. Similarly, for individuals in less than the 25thpercentile PHS, the negative predictive value for total tau approached 85%. BeyondAPOE, high PHS individuals with amyloid and tau pathology showed the fastest rate of longitudinal cognitive decline and time to AD dementia progression. Among the CN subgroup, we similarly found that PHS was strongly associated with amyloid positivity and the combination of PHS and biomarker status significantly predicted longitudinal clinical progression.InterpretationAmong asymptomatic and mildly symptomatic older individuals, PHS considerably improves the predictive value of CSF or PET amyloid and tau biomarkers. BeyondAPOE, PHS may be useful for risk stratification and cohort enrichment for MCI and preclinical AD therapeutic trials.
Improvement of Attention-Deficit/Hyperactivity Disorder (ADHD) Symptoms in School-Aged Children, Adolescents, and Young Adults With Autism via a Digital Smartglasses-Based Socioemotional Coaching Aid: An Efficacy Study
Authors: Vahabzadeh Arshya , Keshav Neha U. , Salisbury Joseph P. , Sahin Ned T. 
Published: July 2017

AbstractBackgroundPeople with autism spectrum disorder (ASD) commonly experience symptoms related to attention-deficit/hyperactivity disorder (ADHD), including hyperactivity, inattention, and impulsivity. One-third of ASD cases may be complicated by the presence of ADHD. Individuals with dual diagnoses face greater barriers to accessing treatment for ADHD and respond less positively to primary pharmacologic interventions. Nonpharmacologic technology-aided tools for hyperactivity and inattention in people with ASD are being developed, although research into their efficacy and safety remains limited.ObjectiveThe objective of this preliminary study was to describe the changes in ADHD-related symptoms in children, adolescents, and young adults with ASD after use of the Empowered Brain system, a behavioral and social communication aid for ASD running on augmented reality smartglasses.MethodsWe recruited 8 children, adolescents, and young adults with ASD (male to female ratio of 7:1, mean age 15 years, range 11.7-20.5 years) through a Web-based research signup form. The baseline score on the hyperactivity subscale of the Aberrant Behavioral Checklist (ABC-H), a measure of hyperactivity, inattention, and impulsivity, determined their classification into a high ADHD-related symptom group (n=4, ABC-H ≥13) and a low ADHD-related symptom group (n=4, ABC-H <13). All participants received an intervention with Empowered Brain, where they used smartglasses-based social communication and behavioral modules while interacting with their caregiver. We then calculated caregiver-reported ABC-H scores at 24 and 48 hours after the session.ResultsAll 8 participants were able to complete the intervention session. Postintervention ABC-H scores were lower for most participants at 24 hours (n=6, 75%) and for all participants at 48 hours (n=8, 100%). At 24 hours after the session, average participant ABC-H scores decreased by 54.9% in the high ADHD symptom group and by 20% in the low ADHD symptom group. At 48 hours after the session, ABC-H scores compared with baseline decreased by 56.4% in the high ADHD symptom group and by 66.3% in the low ADHD symptom group.ConclusionsThis study provides initial evidence for the efficacy of the Empowered Brain system in reducing ADHD-related symptoms, such as hyperactivity, inattention, and impulsivity, in school-aged children, adolescents, and young adults with ASD. This digital smartglasses intervention can potentially be targeted at a broader array of mental health conditions that exhibit transdiagnostic attentional and social communication deficits, including schizophrenia and bipolar disorder. Further research is required to understand the clinical importance of these observed changes and to conduct longitudinal studies on this intervention with larger sample sizes.
The electron transport chain sensitisesStaphylococcus aureusandEnterococcus faecalisto the oxidative burst
Authors: Painter Kimberley L. , Hall Alex , Ha Kam Pou , Edwards Andrew M. 
Published: July 2017

AbstractSmall colony variants (SCVs) ofStaphylococcus aureustypically lack a functional electron transport chain and cannot produce virulence factors such as leukocidins, hemolysins or the anti-oxidant staphyloxanthin. Despite this, SCVs are associated with persistent infections of the bloodstream, bones and prosthetic devices. The survival of SCVs in the host has been ascribed to intracellular residency, biofilm formation and resistance to antibiotics. However, the ability of SCVs to resist host defences is largely uncharacterised. To address this, we measured survival of wild-type and SCVS. aureusin whole human blood, which contains high numbers of neutrophils, the key defense against staphylococcal infection. Despite the loss of leukcocidin production and staphyloxanthin biosynthesis, SCVs defective for heme or menquinone biosynthesis were significantly more resistant to the oxidative burst than wild-type bacteria in a whole human blood model. Supplementation of the culture medium of the heme-auxotrophic SCV with heme, but not iron, restored growth, hemolysin and staphyloxanthin production, and sensitivity to the oxidative burst. SinceEnterococcus faecalisis a natural heme auxotroph and cause of bloodstream infection, we explored whether restoration of the electron transport chain in this organism also affected survival in blood. Incubation ofE. faecaliswith heme increased growth and restored catalase activity, but resulted in decreased survival in human blood via increased sensitivity to the oxidative burst. Therefore, the lack of functional electron transport chains in SCVS. aureusand wild-typeE. faecalisresults in reduced growth rate but provides resistance to a key immune defence mechanism.