bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective Evaluation of Health-Related Quality of Life following Lymphaticovenular Anastomosis for Upper and Lower Extremities Lymphedema
Authors: Salgarello Marzia , Mangialardi Maria , Pino Valentina , Gentileschi Stefano , Visconti Giuseppe 
Published: April 2018

Background Lymphedema is a progressive disease that negatively affects body image and physical, psychological, and social functions. There is lack of evidence in the present literature about the impact of super microsurgical lymphaticovenular anastomosis (LVA) on health-related quality of life (HRQoL). The aim of this prospective study is to report the outcomes of patients' HRQoL after LVA for lower and upper extremities lymphedema.
Methods Between September 2015 and February 2017, 74 patients with upper or lower limb lymphedema (ULL or LLL) underwent LVA at our center. Quality of life (QoL) was assessed by lymphedema QoL questionnaire (LyMQoL), which is a validated disease-specific instrument to measure the impact of lymphedema on patient's lives, covering four domains: function, body image, symptoms, and mood. All patients were evaluated preoperatively, 1 month after surgery, and every 3 months up to 1 year. Additionally, we evaluated the episodes of lymphangitis and the need for conservative therapy before and after surgery.
Results After a mean follow-up of 8.5 months (range: 2–21 months), we observed an increase of 2.3 points in the overall QoL average for upper limb and 2.6 points for lower limb (p  <  0.001). A statistically significant improvement in all four domains (p  <  0.01) was reported after surgery, being present from the first postoperative months for both upper and lower extremities.
Conclusion Our study shows that lymphaticovenular anastomosis improves HRQoL in patients affected by ULL and LLL. Additionally, both a reduction of episodes of lymphangitis and a decrease in the need of conservative therapy were observed in this cohort of patients.
Normal Cervical Effacement in Term Labor
Authors: Stout Molly , Woolfolk Candice , Tuuli Methodius , Macones George , Cahill Alison , Rhoades Janine 
Published: April 2018

Objective To estimate the natural history of cervical effacement in labor.
Study Design This is a retrospective cohort study of term, vertex, singletons who reached 10 cm of cervical dilation from 2010 to 2014. Interval-censored regression was used to estimate the median number of hours between changes in effacement (measured in centimeters of the residual cervix) and to estimate the median effacement at a given cervical dilation. Analysis was stratified by parity and labor type.
Results In total, 7,319 patients were included. Multiparas had faster effacement from 1 cm to complete effacement than nulliparas, but nulliparas were significantly more effaced at each cervical dilation. Patients in spontaneous labor had faster effacement and were significantly more effaced at each centimeter of cervical dilation than those who were induced or augmented. Once active labor was established (>6 cm of cervical dilation), 95% of patients had an effacement of 1 cm or less. By 8 cm of cervical dilation, 50% of all patients were completely effaced.
Conclusion There is a wide range in the normal length of time for the progression of cervical effacement. However, once a patient is in active labor, 95% of patients have effaced to 1 cm or less.
Gradual development of focus prosody and affect
prosody comprehension
Authors: Ito Kiwako 
Published: April 2018

Excellence in communication skills requires an ability to
appropriately represent the discourse structure including focus, as
well as good comprehension of speaker affect. Both focus and affect
are communicated in large part through prosody, so comprehension and
production of the accompanying prosody is essential. However, past
studies on focus prosody have been both theoretically and
methodologically separated from the research on affect prosody. (In
this chapter, I use the term ‘focus prosody’ to refer to prosodic
phenomena that are either produced or perceived as the cue to a
specific part of speech that conveys the focal content of a message.
This includes ‘narrow focus’, which is defined in terms of the
informational scope (e.g., answers to Wh-questions), and
‘contrastive focus’, which is a subtype of narrow focus that evokes
interpretational alternatives.) This chapter argues that the
suggested difference in the developmental trajectory (i.e., focus
prosody develops slower as compared to affect prosody) may be an
artifact of the perspective divergence, and points out that the
mastery of prosodic skills in both these domains must be necessarily
gradual – though they may not develop
hand-in-hand. A holistic approach that considers the interaction
between affect prosody and focus prosody is proposed as a future
direction of the research on prosodic development within and across
individuals.
Bilingual children’s prosodic development
Authors: Lleó Conxita 
Published: April 2018

This chapter focuses on various domains of prosodic development –
syllables, metrical feet, prosodic words, stress patterns,
phonological phrases, intonation and rhythm – as they are acquired
by bilingual children, exposed to two languages from birth: a
societal or majority language and a minority or heritage language.
The studies reviewed in this chapter discuss the bilingual
acquisition of these prosodic domains and the influence of one
language onto the other when children develop surrounded by two
languages in contact. The discussion deals with the various aspects
of the acquisition of prosody and prosodic structure described in
the main section of the chapter, and reports on the outcomes of
cross-language interaction: acceleration, delay, transfer, order of
acquisition, and fusion.
Effects of carbon dioxide on metabolite production and bacterial communities during kimchi fermentation
Authors: Park Doo Hyun 
Published: April 2018

Abstract
Bacterial communities and metabolites in kimchi fermented under conventional conditions (CC) compared to CO2-rich environments (CO2) were analyzed. After a 20-day fermentation, lactic and acetic acid productions were 54 and 69 mM under CC, and 19 and 12 mM under CO2, respectively. The final pH of kimchi fermented under CC (CC-fermenting) and CO2 (CO2-fermenting) were 4.1 and 4.7, respectively. For bacterial communities, OTU and Chao1 indices were both 35 in fresh kimchi, 10 and 15 in CC-fermenting kimchi, and 8 and 24 in CO2-fermenting kimchi, respectively. Shannon and Simpson indices were 3.47 and 0.93 in fresh kimchi, 1.87–0.06 and 0.46–0.01 in CC-fermenting kimchi, and 1.65–0.44 and 0.63–0.12 in CO2-fermenting kimchi, respectively. Non-lactic acid bacteria were eliminated in fermenting kimchi after 12 days under CC and 6 days under CO2. I conclude that carbon dioxide can alter bacterial communities, reduce metabolite production, and improve fermented kimchi quality.
Haplotype phasing in single-cell DNA-sequencing data
Authors: Satas Gryte , Raphael Benjamin J 
Published: April 2018

Abstract

Motivation
Current technologies for single-cell DNA sequencing require whole-genome amplification (WGA), as a single cell contains too little DNA for direct sequencing. Unfortunately, WGA introduces biases in the resulting sequencing data, including non-uniformity in genome coverage and high rates of allele dropout. These biases complicate many downstream analyses, including the detection of genomic variants.

Results
We show that amplification biases have a potential upside: long-range correlations in rates of allele dropout provide a signal for phasing haplotypes at the lengths of amplicons from WGA, lengths which are generally longer than than individual sequence reads. We describe a statistical test to measure concurrent allele dropout between single-nucleotide polymorphisms (SNPs) across multiple sequenced single cells. We use results of this test to perform haplotype assembly across a collection of single cells. We demonstrate that the algorithm predicts phasing between pairs of SNPs with higher accuracy than phasing from reads alone. Using whole-genome sequencing data from only seven neural cells, we obtain haplotype blocks that are orders of magnitude longer than with sequence reads alone (median length 10.2 kb versus 312 bp), with error rates &lt;2%. We demonstrate similar advantages on whole-exome data from 16 cells, where we obtain haplotype blocks with median length 9.2 kb—comparable to typical gene lengths—compared with median lengths of 41 bp with sequence reads alone, with error rates &lt;4%. Our algorithm will be useful for haplotyping of rare alleles and studies of allele-specific somatic aberrations.

Availability and implementation
Source code is available at https://www.github.com/raphael-group.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cluster Locator, online analysis and visualization of gene clustering
Authors: Pazos Obregón Flavio , Soto Pablo , Lavín José Luis , Cortázar Ana Rosa , Barrio Rosa , Aransay Ana María , Cantera Rafael 
Published: April 2018

Abstract

Summary
Genes sharing functions, expression patterns or quantitative traits are not randomly distributed along eukaryotic genomes. In order to study the distribution of genes that share a given feature, we present Cluster Locator, an online analysis and visualization tool. Cluster Locator determines the number, size and position of all the clusters formed by the protein-coding genes on a list according to a given maximum gap, the percentage of gene clustering of the list and its statistical significance. The output includes a visual representation of the distribution of genes and gene clusters along the reference genome.

Availability and implementation
Cluster Locator is freely available at http://clusterlocator.bnd.edu.uy/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Epidemiology and Risk Factors for Cryptosporidiosis in Children From 8 Low-income Sites: Results From the MAL-ED Study
Authors: Korpe Poonum S , Valencia Cristian , Haque Rashidul , Mahfuz Mustafa , McGrath Monica , Houpt Eric , Kosek Margaret , McCormick Benjamin J J , Penataro Yori Pablo , Babji Sudhir , Kang Gagandeep , Lang Dennis , Gottlieb Michael , Samie Amidou , Bessong Pascal , Faruque A S G , Mduma Esto , Nshama Rosemary , Havt Alexandre , Lima Ila F N , Lima Aldo A M , Bodhidatta Ladaporn , Shreshtha Ashish , Petri William A , Ahmed Tahmeed , Duggal Priya 
Published: April 2018

Abstract

Background
Cryptosporidium species are enteric protozoa that cause significant morbidity and mortality in children worldwide. We characterized the epidemiology of Cryptosporidium in children from 8 resource-limited sites in Africa, Asia, and South America.

Methods
Children were enrolled within 17 days of birth and followed twice weekly for 24 months. Diarrheal and monthly surveillance stool samples were tested for Cryptosporidium by enzyme-linked immunosorbent assay. Socioeconomic data were collected by survey, and anthropometry was measured monthly.

Results
Sixty-five percent (962/1486) of children had a Cryptosporidium infection and 54% (802/1486) had at least 1 Cryptosporidium-associated diarrheal episode. Cryptosporidium diarrhea was more likely to be associated with dehydration (16.5% vs 8.3%, P &lt; .01). Rates of Cryptosporidium diarrhea were highest in the Peru (10.9%) and Pakistan (9.2%) sites. In multivariable regression analysis, overcrowding at home was a significant risk factor for infection in the Bangladesh site (odds ratio, 2.3 [95% confidence interval {CI}, 1.2–4.6]). Multiple linear regression demonstrated a decreased length-for-age z score at 24 months in Cryptosporidium-positive children in the India (β = –.26 [95% CI, –.51 to –.01]) and Bangladesh (β = –.20 [95% CI, –.44 to .05]) sites.

Conclusions
This multicountry cohort study confirmed the association of Cryptosporidium infection with stunting in 2 South Asian sites, highlighting the significance of cryptosporidiosis as a risk factor for poor growth. We observed that the rate, age of onset, and number of repeat infections varied per site; future interventions should be targeted per region to maximize success.
Colonization With Levofloxacin-resistant Extended-spectrum β-Lactamase-producing Enterobacteriaceae and Risk of Bacteremia in Hematopoietic Stem Cell Transplant Recipients
Authors: Satlin Michael J , Chavda Kalyan D , Baker Thomas M , Chen Liang , Shashkina Elena , Soave Rosemary , Small Catherine B , Jacobs Samantha E , Shore Tsiporah B , van Besien Koen , Westblade Lars F , Schuetz Audrey N , Fowler Vance G , Jenkins Stephen G , Walsh Thomas J , Kreiswirth Barry N 
Published: April 2018

Abstract

Background
Bacteremia caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) is associated with inadequate empirical therapy and substantial mortality in neutropenic patients. Strategies are needed to identify neutropenic patients at high risk of these infections.

Methods
From April 2014 to September 2016, we collected perianal swabs, both at admission and weekly thereafter, from patients undergoing hematopoietic stem cell transplantation (HSCT). Patients received prophylactic levofloxacin while neutropenic. Swabs were plated onto selective agar, colonies were identified and underwent antimicrobial susceptibility testing, and phenotypic ESBL testing and polymerase chain reaction for β-lactamase genes were performed on ceftriaxone-resistant Enterobacteriaceae. We then determined the prevalence of pre-transplant ESBL-E colonization and risk of ESBL-E bacteremia. Colonizing and bloodstream isolates from patients with ESBL-E bacteremia underwent multilocus sequence typing and pulsed-field gel electrophoresis.

Results
We analyzed 312 patients, including 212 allogeneic and 100 autologous HSCT recipients. Ten percent (31/312) of patients had pre-transplant ESBL-E colonization. Susceptibility rates of colonizing ESBL-E were: levofloxacin, 25%; cefepime, 9%; piperacillin-tazobactam, 84%; and meropenem, 97%. Of 31 patients colonized with ESBL-E pre-transplant, 10 (32%) developed ESBL-E bacteremia during their transplant admission, compared to 1 (0.4%) of 281 patients not colonized with ESBL-E (P &lt; .001). All bloodstream ESBL-E were levofloxacin-resistant and colonizing and bloodstream isolates from individual patients had identical genotypic profiles.

Conclusions
HSCT recipients who are colonized with levofloxacin-resistant ESBL-E pre-transplant and receive levofloxacin prophylaxis have high rates of bacteremia from their colonizing strain during neutropenia. Assessing for ESBL-E colonization in neutropenic patients could lead to optimization of empirical antibacterial therapy.
The Economic and Social Burden of the 2014 Ebola Outbreak in West Africa
Authors: Huber Caroline , Finelli Lyn , Stevens Warren 
Published: April 2018

Abstract

Background
The 2014 Ebola virus disease (EVD) outbreak in West Africa was more devastating than all previous EVD outbreaks combined; however, many estimates of its economic burden did not capture its significant social costs. This study aimed to review all currently available estimates, identify social components missed by these estimates, and generate a comprehensive cost of the 2014 EVD outbreak.

Methods
We conducted a systematic review of the grey (reports produced by nonprofit or nongovernmental organizations, government, or industry) and published literature to identify current estimates of the burden of the outbreak. Based on the findings of this review, we identified 6 key areas absent or underestimated from previous estimates and calculated the underestimated social costs using estimates from the literature and extrapolation.

Results
Current estimates of the economic burden of the outbreak range from $2.8 to $32.6 billion in lost gross domestic product. We estimated the comprehensive economic and social burden from the 2014 EVD outbreak to be $53.19 billion (2014 USD). The most significant component, $18.8 billion, was deaths from non-Ebola causes.

Conclusions
A more complete understanding of the burden of the 2014 EVD outbreak underscores the value of interventions that can mitigate or reduce the severity of future outbreaks.
Decreased Rescue Analgesic Use with Elagolix Treatment in Women with Endometriosis-Associated Pain [35G]
Authors: Taylor Hugh S. , Diamond Michael , Surrey Eric , Schwefel Brittany , Snabes Michael , Peloso Paul 
Published: April 2018

INTRODUCTION:
Rescue analgesic use was evaluated in two phase 3 studies, wherein 6-months (M) of elagolix (an oral, non-peptide GnRH antagonist) treatment was associated with improved dysmenorrhea and nonmenstrual pelvic pain compared to placebo in women with endometriosis-associated pain.

METHODS:
Elaris EM-I (N=871) and Elaris EM-II (N=815) were randomized, double-blind, 6M, placebo-controlled phase 3 studies evaluating two elagolix doses (150mg once daily [QD] or 200mg twice daily [BID]) in women with moderate/severe endometriosis-associated pain. Women could use either naproxen and/or a single opioid as rescue analgesic (opioid varied by country). Daily pill counts were recorded in an electronic-diary.

RESULTS:
At baseline, the mean daily rescue analgesic pill count ranged 0.7-0.9 across studies/doses. The mean percent decrease from baseline in average daily rescue analgesic pill count (any analgesic) was significantly greater compared to placebo for elagolix 200mg BID at M3 in Elaris EM-I and M6 in both studies (M6-least-squares mean percent change; Elaris EM-I:placebo=-24.7%, 150mg QD=-40.3%, P=0.121, 200mg BID=-59.9%, P<0.001; Elaris EM-II:placebo=-23.1%, 150mg QD=-26.9%, P=0.810, 200mg BID=-75.3%, P<0.001). At M6 in each study, rescue analgesic use, based on percent change from baseline in average daily pill count, was significantly reduced compared to placebo for naproxen and opioid pill count in the 200mg BID dose group.

CONCLUSION:
It was previously shown that elagolix treatment (150mg QD and 200mg BID) decreased pain in women with moderate/severe endometriosis-associated pain at M3 and M6. The current analysis shows that women treated with elagolix 200mg BID had the greatest decrease in rescue analgesic use compared to placebo at M6.
Noninvasive Tracking of Anesthesia Neurotoxicity in the Developing Rodent Brain
Authors: Makaryus Rany , Lee Hedok , Robinson John , Enikolopov Grigori , Benveniste Helene 
Published: April 2018

Abstract

Background
Potential deleterious effect of multiple anesthesia exposures on the developing brain remains a clinical concern. We hypothesized that multiple neonatal anesthesia exposures are more detrimental to brain maturation than an equivalent single exposure, with more pronounced long-term behavioral consequences. We designed a translational approach using proton magnetic resonance spectroscopy in rodents, noninvasively tracking the neuronal marker N-acetyl-aspartate, in addition to tracking behavioral outcomes.

Methods
Trajectories of N-acetyl-aspartate in anesthesia naïve rats (n = 62, postnatal day 5 to 35) were determined using proton magnetic resonance spectroscopy, creating an “N-acetyl-aspartate growth chart.” This chart was used to compare the effects of a single 6-h sevoflurane exposure (postnatal day 7) to three 2-h exposures (postnatal days 5, 7, 10). Long-term effects on behavior were separately examined utilizing novel object recognition, open field testing, and Barnes maze tasks.

Results
Utilizing the N-acetyl-aspartate growth chart, deviations from the normal trajectory were documented in both single and multiple exposure groups, with z-scores (mean ± SD) of –0.80 ± 0.58 (P = 0.003) and –1.87 ± 0.58 (P = 0.002), respectively. Behavioral testing revealed that, in comparison with unexposed and single-exposed, multiple-exposed animals spent the least time with the novel object in novel object recognition (F(2,44) = 4.65, P = 0.015), traveled the least distance in open field testing (F(2,57) = 4.44, P = 0.016), but exhibited no learning deficits in the Barnes maze.

Conclusions
Our data demonstrate the feasibility of using the biomarker N-acetyl-aspartate, measured noninvasively using proton magnetic resonance spectroscopy, for longitudinally monitoring anesthesia-induced neurotoxicity. These results also indicate that the neonatal rodent brain is more vulnerable to multiple anesthesia exposures than to a single exposure of the same cumulative duration.
Assessment of Proximal Junctional Kyphosis and Shoulder Balance With Proximal Screws versus Hooks in Posterior Spinal Fusion for Adolescent Idiopathic Scoliosis
Authors: Pahys Joshua M. , Vivas Andrew C. , Samdani Amer F. , Cunn Gregory , Betz Randal R. , Newton Peter O. , Cahill Patrick J. 
Published: April 2018

Study Design.
A retrospective review of a prospectively collected multicenter database.

Objective.
To assess the effect of proximal hooks versus screws on proximal junctional kyphosis (PJK) as well as shoulder balance in otherwise all pedicle screw (>80%) posterior spinal fusion (PSF) constructs in adolescent idiopathic scoliosis (AIS).

Summary of Background Data.
Less rigid forms of fixation at the top of constructs in degenerative lumbar PSF have been postulated to decrease the risk of PJK.

Methods.
A multicenter AIS surgical database was reviewed to identify all patients who underwent PSF with all pedicle screw (>80%) constructs and minimum 2-year follow-up. Patients in the “hook” group had two hooks used at the top of the construct, whereas the “screw” group used only pedicle screws at all levels.

Results.
A total of 354 patients were identified, 274 (77%) in the screw group, and 80 (23%) in the hook group. There were no significant preoperative differences with regards to curve type, coronal/sagittal Cobb angle, or curve flexibility for either group. At 2 years post-op, the coronal Cobb correction was similar for both groups (60%). There was no difference in correction of shoulder asymmetry and T1 rib angle, including when the groups were matched for preoperative shoulder balance. PJK, defined as the sagittal Cobb angle between the uppermost instrumented and uninstrumented vertebrae, was similar for the screw versus hook group as well (7.1° vs. 6.2°, P = 0.2).

Conclusion.
The use of different anchors (pedicle screws vs. hooks) at the top of an otherwise all pedicle screw PSF construct for AIS did not have any significant bearing on the correction of shoulder asymmetry and coronal Cobb angle at 2 years postoperative. There was also no significant difference in the magnitude of PJK or incidence of marked PJK (>15°) between either group at 2 years.

Level of Evidence: 3