bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental constraints on size-dependent signaling affects mating and rival interactions
Authors: Smit Judith A H , Loning Hugo , Ryan Michael J , Halfwerk Wouter 
Published: February 2019

AbstractAdvertisement signals can convey information about a sender’s characteristics, such as body size. The reliability of signals, however, can be reduced when signal production is partially dependent on the environment. Here, we assess the effect of display-site properties on the production, attractiveness and honesty of sexual signals. We recorded male túngara frogs (Physalaemus pustulosus) while manipulating water levels in order to constrain calling. We found that water level affected male call properties in a size-dependent manner, with call amplitude being less affected in smaller males when forced to call in shallow water. Next, we tested how size-dependent and display-site-dependent signaling affected female choice and rival competition. Both males and females showed the strongest response to the call of a large male when he was calling at the deepest water levels. However, females showed no preference for large over small males when both were recorded in shallow water levels, or, depending on the call rate and timing of calls, even preferred small males. Likewise, males responded equally to large and small rivals recorded calling during shallow water level trials. Our experiments show that display-site properties can influence signal production and attractiveness in a size-dependent manner. These results can have important consequences for the evolution of signaling, as small males may be able to use their size to their advantage when selecting appropriate display sites and thereby outcompete large males.
IGLOSS: iterative gapless local similarity search
Authors: Rabar Braslav , Zagorščak Maja , Ristov Strahil , Rosenzweig Martin , Goldstein Pavle 
Published: February 2019

Abstract

Summary
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available sequences calls for novel methods to explore local sequence similarity. We have developed a new method for iterative motif scanning that will look for ungapped sequence patterns similar to a submitted query. Using careful parameter estimation and an adaptation of a fast string-matching algorithm, the method performs significantly better in this context than the existing software.

Availability and implementation
The IGLOSS web server is available at http://compbioserv.math.hr/igloss/.

Supplementary information
Supplementary data are available at Bioinformatics online.
G4Hunter web application: a web server for G-quadruplex prediction
Authors: Brázda Václav , Kolomazník Jan , Lýsek Jiří , Bartas Martin , Fojta Miroslav , Šťastný Jiří , Mergny Jean-Louis 
Published: February 2019

Abstract

Motivation
Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community.

Results
We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export.

Availability and implementation
G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz.

Supplementary information
Supplementary data are available at Bioinformatics online.
MicroRNAs in endometriosis: biological function and emerging biomarker candidates†
Authors: Bjorkman Sarah , Taylor Hugh S 
Published: February 2019

AbstractMicroRNAs (miRNAs), a class of small noncoding RNA molecules, have been recognized as key post-transcriptional regulators associated with a multitude of human diseases. Global expression profiling studies have uncovered hundreds of miRNAs that are dysregulated in several diseases, and yielded many candidate biomarkers. This review will focus on miRNAs in endometriosis, a common chronic disease affecting nearly 10% of reproductive-aged women, which can cause pelvic pain, infertility, and a myriad of other symptoms. Endometriosis has delayed time to diagnosis when compared to other chronic diseases, as there is no current accurate, easily accessible, and noninvasive tool for diagnosis. Specific miRNAs have been identified as potential biomarkers for this disease in multiple studies. These and other miRNAs have been linked to target genes and functional pathways in disease-specific pathophysiology. Highlighting investigations into the roles of tissue and circulating miRNAs in endometriosis, published through June 2018, this review summarizes new connections between miRNA expression and the pathophysiology of endometriosis, including impacts on fertility. Future applications of miRNA biomarkers for precision medicine in diagnosing and managing endometriosis treatment are also discussed.
Genetic transformation of Coniochaeta sp. 2T2.1, key fungal member of a lignocellulose-degrading microbial consortium
Authors: Nichols Nancy N , Hector Ronald E , Frazer Sarah E 
Published: February 2019

Abstract
Coniochaeta sp. strain 2T2.1 is a key member of a microbial consortium that degrades lignocellulosic biomass. Due to its ecological niche and ability to also grow in pure culture on wheat straw, protocols for transformation and antibiotic selection of the strain were established. Hygromycin was found to be a reliable selectable transformation marker, and the mammalian codon-optimized green fluorescent protein was expressed and used to visualize fluorescence in transformed cells of strain 2T2.1.
Biventricular repair after the hybrid Norwood procedure
Authors: Sojak Vladimir , Bokenkamp Regina , Kuipers Irene , Schneider Adriaan , Hazekamp Mark 
Published: February 2019

Abstract

OBJECTIVES
We analysed the outcomes of patients undergoing biventricular repair (BVR) after an initial hybrid Norwood approach as a salvage procedure in extremely sick infants; or as the initial palliation in patients with uncertain feasibility of single-stage BVR due to severe left ventricular outflow tract obstruction; or as part of a left ventricle (LV) recruitment strategy in patients with borderline LVs.

METHODS
Between September 2010 and July 2018, 26 patients underwent BVR after initial hybrid palliation at a median age of 13 days. The rationale for the hybrid approach was to promote the growth of the LV in 10 patients and that of the left ventricular outflow tract and/or aortic valve in 12 patients and to be a salvage procedure in 4 patients. Significant growth of the LV was noted during the interstage period, which had a median length of 65 days (P = 0.008). Fourteen patients underwent aortic arch repair, ventricular septal defect closure and relief of subaortic stenosis; 5 patients underwent the Yasui procedure; 4 patients had the Ross–Konno procedure; 2 patients had an arterial switch operation; and 1 patient had truncus arteriosus repair.

RESULTS
Twenty-two patients (84.6%) are alive at a median follow-up period of 1.8 (range 0.04–6.2) years. There were 2 early and 2 late deaths. Nineteen catheter-based reinterventions and 15 reoperations were performed after BVR.

CONCLUSIONS
The hybrid Norwood procedure permits stabilization of critical infants. It allows for growth of left ventricular structures in some patients with borderline left hearts and in those with severe left ventricular outflow tract obstruction. More patients may eventually have BVR than was thought during the newborn period.
Competition experiments betweenBrettanomyces bruxellensisstrains reveal specific adaptation to sulfur dioxide and complex interactions at intraspecies level
Authors: Avramova Marta , Grbin Paul , Borneman Anthony , Albertin Warren , Masneuf-Pomarède Isabelle , Varela Cristian 
Published: February 2019

ABSTRACTRecent studies have suggested a strong niche adaptation for Brettanomyces bruxellensis strains according to human-related fermentation environments, including beer, wine and bioethanol. This is further supported by a correlation between B. bruxellensis genetic grouping and tolerance to SO2, the main antimicrobial used in wine. The allotriploid AWRI1499-like cluster, in particular, shows high SO2 tolerance suggesting that the genetic configuration observed for these strains may confer a selective advantage in winemaking conditions. To test this hypothesis, we evaluated the relative selective advantage of representatives of the three main B. bruxellensis genetic groups in presence of SO2. As a proof-of-concept and using recently developed transformation cassettes, we compared strains under different SO2 concentrations using pairwise competitive fitness experiments. Our results showed that AWRI1499 is specifically adapted to environments with high SO2 concentrations compared to other B. bruxellensis wine strains, indicating a potential correlation between allotriploidisation origin and environmental adaptation in this species. Additionally, our findings suggest different types of competition between strains, such as coexistence and exclusion, revealing new insights on B. bruxellensis interactions at intraspecies level.
Hospitalization-Associated Change in Gait Speed and Risk of Functional Limitations for Older Adults
Authors: Duan-Porter Wei , Vo Tien N , Ullman Kristen , Langsetmo Lisa , Strotmeyer Elsa S , Taylor Brent C , Santanasto Adam J , Cawthon Peggy M , Newman Anne B , Simonsick Eleanor M , Waters Teresa M , Ensrud Kristine E 
Published: February 2019

Abstract

Background
Hospitalization-associated functional decline is a common problem for older adults, but it is unclear how hospitalizations affect physical performance measures such as gait speed. We sought to determine hospitalization-associated change in gait speed and likelihood of new limitations in mobility and activities of daily living (ADLs).

Methods
We used longitudinal data over 5 years from the Health, Aging and Body Composition Study, a prospective cohort of black and white community-dwelling men and women, aged 70–79 years, who had no limitations in mobility (difficulty walking 1/4 mile or climbing 10 steps) or ADLs (transferring, bathing, dressing, and eating) at baseline. Gait speed, and new self-reported limitations in mobility and ADLs were assessed annually. Selected participants (n = 2,963) had no limitations at the beginning of each 1-year interval. Hospitalizations were self-reported every 6 months and verified with medical record data. Generalized estimating equations were used to examine hospitalization-associated change in gait speed and odds of new limitations over each 1-year interval. Fully adjusted models included demographics, hospitalization within the past year, health conditions, symptoms, body mass index, and health-related behaviors.

Results
In fully adjusted models, any hospitalization was associated with decrease in gait speed (−0.04 m/s; 95% confidence interval [CI]: −0.05 to −0.03) and higher odds of new limitations in mobility or ADLs (odds ratio = 1.97, 95% CI: 1.70–2.28), and separately with increased odds of new mobility limitation (odds ratio = 2.22, 95% CI: 1.90–2.60) and new ADL limitations (odds ratio = 1.84, 95% CI: 1.53–2.21). Multiple hospitalizations within a year were associated with gait speed decline (−0.06 m/s; 95% CI: −0.08 to −0.04) and greater odds of new limitations in mobility or ADLs (odds ratio = 2.96, 95% CI: 2.23–3.95).

Conclusions
Functionally independent older adults experienced hospitalization-associated declines in gait speed and new limitations in mobility and ADLs.
Efficacy of Combination Antibiotic Therapy for Refractory Pediatric Inflammatory Bowel Disease
Authors: Breton Jessica , Kastl Arthur , Hoffmann Natalie , Rogers Rachel , Grossman Andrew B , Mamula Petar , Kelsen Judith R , Baldassano Robert N , Albenberg Lindsey 
Published: February 2019

Abstract

Background
Recent studies have shown that oral combination antibiotics may improve disease course in refractory inflammatory bowel disease (IBD). Here, we describe the use of combination oral antibiotics as salvage therapy in refractory ulcerative colitis (UC), Crohn’s colitis, and IBD-unclassified (IBD-U) at a large pediatric IBD center.

Methods
Clinical response, disease activity indices, adverse events, and clinical outcomes were measured up to 1 year after antibiotic treatment in this retrospective cohort study of children with medically refractory IBD colitis.

Results
Sixty-three patients with refractory UC, Crohn’s colitis, and IBD-U (median age [interquartile range {IQR}], 15.3 [11.2–16.5] years; median disease duration [IQR], 1.2 [0.41–4.6] years) received a combination of 3 or 4 oral antibiotics (most commonly amoxicillin, metronidazole, and either doxycycline or ciprofloxacin) for a median (IQR) of 29 (21–58) days. Thirty-four patients (54%) were deemed corticosteroid-refractory or -dependent, with the majority (62/63) having a previous or present loss of response or primary nonresponse to anti–tumor necrosis factor alpha (anti-TNFα) therapy. Use of combination antibiotics led to a significant decrease in median Pediatric Ulcerative Colitis Activity Index (PUCAI) score (IQR) from 55 (40–65) to 10 (0–40; P &lt; 0.0001) over 3 ± 1 weeks, with 25/63 (39.7%) patients achieving clinical remission (PUCAI &lt;10 points). The clinical benefits of oral antibiotics were independent of anti-TNFα therapy optimization. Among children entering clinical remission (n = 25), only 1 patient required surgery at 1-year follow-up, vs 10 patients in the nonresponder group. Negative predictors of response to combination antibiotics were exposure to doxycycline (odds ratio [OR], 0.25; 95% CI, 0.08–0.76) and PUCAI ≥65 at baseline (OR, 0.2; 95% CI, 0.05–0.74).

Conclusions
Oral combination antibiotics appears to be an effective rescue and steroid-sparing therapy to induce remission in the short term in patients failing a biologic.
Preexposure Prophylaxis for Mitigating Risk of HIV Transmission During HIV Cure–Related Clinical Trials With a Treatment Interruption
Authors: Lelièvre Jean-Daniel 
Published: February 2019

AbstractAnalytical treatment interruption performed during human immunodeficiency virus (HIV) cure–related clinical trials exposes sex partners of participants in these trials to a risk of HIV transmission. Preexposure prophylaxis (PrEP), which emerged in recent years as a key strategy for preventing HIV transmission, is often considered a useful tool to prevent this risk. This article supports offering PrEP to the stable sex partners of participants in these trials but also notes limitations that must be addressed. It concludes that PrEP cannot on its own eliminate the risk of secondary transmission in this context.
Asylum-seeking Parents’ Reports of Health Deterioration in Their Children since Fleeing Their Home Country
Authors: De Montgomery Christopher Jamil , Stathopoulou Theoni , Eikemo Terje Andreas 
Published: February 2019

Abstract
More than 50,000 asylum seekers scattered across Greece were waiting to have their cases processed in February 2016. Using unique survey data collected in six Greek refugee camps at the time, this article explores the health of asylum-seeking children as assessed by their parents. More than half of the parents reported that children’s health had deteriorated considerably or greatly since commencing their flight and the longer the time spent in Greece, the larger the share. The same tendency was found in a logistic regression model adjusting for educational level, sex and origin country. Feeling safe at the current location and access to basic amenities were alleviating factors. The results call for increased attention to the needs of asylum-seeking children in the Greek refugee camps and urgent action to alleviate potentially long-term impacts of the process of seeking asylum on these children.
Predicting multiple planet stability and habitable zone companions in the TESS era
Authors: Agnew Matthew T , Maddison Sarah T , Horner Jonathan , Kane Stephen R 
Published: February 2019

Abstract
We present an approach that is able to both rapidly assess the dynamical stability of multiple planet systems, and determine whether an exoplanet system would be capable of hosting a dynamically stable Earth-mass companion in its habitable zone (HZ). We conduct a suite of numerical simulations using a swarm of massless test particles (TPs) in the vicinity of the orbit of a massive planet, in order to develop a predictive tool which can be used to achieve these desired outcomes. In this work, we outline both the numerical methods we used to develop the tool, and demonstrate its use. We find that the TPs survive in systems either because they are unperturbed due to being so far removed from the massive planet, or due to being trapped in stable mean-motion resonant orbits with the massive planet. The resulting unexcited TP swarm produces a unique signature in (a, e) space that represents the stable regions within the system. We are able to scale and translate this stability signature, and combine several together in order to conservatively assess the dynamical stability of newly discovered multiple planet systems. We also assess the stability of a system’s HZ and determine whether an Earth-mass companion could remain on a stable orbit, without the need for exhaustive numerical simulations.
Delivering SaCas9 mRNA by lentivirus-like bionanoparticles for transient expression and efficient genome editing
Authors: Lu Baisong , Javidi-Parsijani Parisa , Makani Vishruti , Mehraein-Ghomi Farideh , Sarhan Walaa Mohamed , Sun Dongjun , Yoo Kyung Whan , Atala Zachary P , Lyu Pin , Atala Anthony 
Published: February 2019

Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system discovered using bacteria has been repurposed for genome editing in human cells. Transient expression of the editor proteins (e.g. Cas9 protein) is desirable to reduce the risk of mutagenesis from off-target activity. Using the specific interaction between bacteriophage RNA-binding proteins and their RNA aptamers, we developed a system able to package up to 100 copies of Staphylococcus aureus Cas9 (SaCas9) mRNA in each lentivirus-like bionanoparticle (LVLP). The SaCas9 LVLPs mediated transient SaCas9 expression and achieved highly efficient genome editing in the presence of guide RNA. Lower off-target rates occurred in cells transduced with LVLPs containing SaCas9 mRNA, compared with cells transduced with adeno-associated virus or lentivirus expressing SaCas9. Our LVLP system may be useful for efficiently delivering Cas9 mRNA to cell lines and primary cells for in vitro and in vivo gene editing applications.
Effectiveness of Cryopreserved Amniotic Membrane Transplantation in Corneal Ulceration: A Meta-Analysis
Authors: Liu Jinghua , Li Linghan , Li Xuan 
Published: February 2019

Purpose:
To evaluate the effectiveness of cryopreserved amniotic membrane transplantation (AMT) in corneal ulceration.

Methods:
The following electronic databases were searched: PubMed, EMBASE, and Cochrane Library. We evaluated the corneal epithelium healing rate (CEHR) and vision improvement rate (VIR) after AMT in the treatment of corneal ulceration. We analyzed the differences in the CEHR and VIR between the 2 groups of infective and noninfective corneal ulcerations. Subgroup analysis for the CEHR and VIR was performed based on the surgical methods. There were 3 subgroups: single-layered inlay, multilayered inlay, and sandwich (SAN). The differences were tested by referring to the Cochrane Handbook. Pooled estimates were determined with STATA software, version 15.

Results:
Eighteen eligible studies reporting the outcomes in 390 eyes of 385 patients were included. The results of the meta-analysis showed that the pooled CEHR was 97% (I2 = 37.9%, 95% confidence interval: 0.94–0.99, P = 0.089). The pooled VIR was 53% (I2 = 68.1%, 95% confidence interval: 0.42–0.65, P < 0.001). There were no significant differences in either the CEHR or the VIR between the 2 groups of infective and noninfective corneal ulcerations. Among the 3 subgroups of single-layered inlay, multilayered inlay, and SAN, the differences in both CEHR and VIR were statistically significant.

Conclusions:
Consistent with many published reports, this meta-analysis also concluded that AMT was effective in the treatment of corneal ulceration. The curative effect of AMT was not different between the infective and noninfective corneal ulcerations. The differences in both CEHR and VIR were statistically significant among the subgroups.
Effect of Anti–Vascular Endothelial Growth Factor Therapy on Corneal Nerves
Authors: Goldhardt Raquel , Batawi Hatim Ismail M. , Rosenblatt Mark , Lollett Ivonne V. , Park Jasmine J. , Galor Anat 
Published: February 2019

Purpose:
Vascular endothelial growth factor (VEGF) is a trophic factor for corneal nerves (CNs). Despite its widespread use to treat a variety of retinal diseases, the effect of repetitive intravitreal (IV) anti-VEGF injections on CN is not known.

Methods:
Retrospective case–control study. CN parameters were compared between eyes in 39 individuals who received anti-VEGF injections in one eye only. Next, we compared CN parameters between 50 eyes of 50 individuals with a history of IV anti-VEGF injections and 80 eyes of 80 individuals without a history of injection. In vivo confocal microscopic examination was conducted using the ConfoScan 4. Images were analyzed by the Corneal Nerve Analysis tool. Paired and independent t test methodologies were used to compare nerve parameters, and multivariable linear regression analysis was performed to control for potential confounders.

Results:
In 39 patients (own controls), eyes with a history of IV injection had lower CN length density, total length, nerve fibers, bifurcations, and branches (P < 0.005) compared to the fellow eyes without injection. Similar findings were seen in the eyes of 50 individuals with a history of injection compared to 80 individuals without injection. A history of IV injections and ethnicity remained significantly associated with the CN length density and explained 32% of the variability (R = 0.56).

Conclusions:
We found decreased CN parameters in eyes with a history of anti-VEGF injections compared to eyes without such a history.