bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Revision Rates of Anterior- and Posterior-Approach Ptosis Surgery: A Retrospective Review of 1519 Cases
Authors: Chou Eva , Liu Jun , Seaworth Cathleen , Furst Meredith , Amato Malena M. , Blaydon Sean M. , Durairaj Vikram D. , Nakra Tanuj , Shore John W. 
Published: June 2017

Purpose:
To compare revision rates for ptosis surgery between posterior-approach and anterior-approach ptosis repair techniques.

Methods:
This is the retrospective, consecutive cohort study. All patients undergoing ptosis surgery at a high-volume oculofacial plastic surgery practice over a 4-year period. A retrospective chart review was conducted of all patients undergoing posterior-approach and anterior-approach ptosis surgery for all etiologies of ptosis between 2011 and 2014. Etiology of ptosis, concurrent oculofacial surgeries, revision, and complications were analyzed. The main outcome measure is the ptosis revision rate.

Results:
A total of 1519 patients were included in this study. The mean age was 63 ± 15.4 years. A total of 1056 (70%) of patients were female, 1451 (95%) had involutional ptosis, and 1129 (74.3%) had concurrent upper blepharoplasty. Five hundred thirteen (33.8%) underwent posterior-approach ptosis repair, and 1006 (66.2%) underwent anterior-approach ptosis repair. The degree of ptosis was greater in the anterior-approach ptosis repair group. The overall revision rate for all patients was 8.7%. Of the posterior group, 6.8% required ptosis revision; of the anterior group, 9.5% required revision surgery. The main reason for ptosis revision surgery was undercorrection of one or both eyelids. Concurrent brow lifting was associated with a decreased, but not statistically significant, rate of revision surgery. Patients who underwent unilateral ptosis surgery had a 5.1% rate of Hering’s phenomenon requiring ptosis repair in the contralateral eyelid. Multivariable logistic regression for predictive factors show that, when adjusted for gender and concurrent blepharoplasty, the revision rate in anterior-approach ptosis surgery is higher than posterior-approach ptosis surgery (odds ratio = 2.08; p = 0.002).

Conclusions:
The overall revision rate in patients undergoing ptosis repair via posterior-approach or anterior-approach techniques is 8.7%. There is a statistically higher rate of revision with anterior-approach ptosis repair.
Critical care ultrasonography in circulatory shock
Authors: Koster Geert , van der Horst Iwan C.C. 
Published: June 2017

Purpose of review
The objective was to define the role of ultrasound in the diagnosis and the management of circulatory shock by critical appraisal of the literature.

Recent findings
Assessment of any patient's hemodynamic profile based on clinical examination can be sufficient in several cases, but many times unclarities remain. Arterial catheters and central venous lines are commonly used in critically ill patients for practical reasons, and offer an opportunity for advanced hemodynamic monitoring. Critical care ultrasonography may add to the understanding of the hemodynamic profile at hand. Improvements in ultrasound techniques, for example, smaller devices and improved image quality, may reduce limitations and increase its value as a complementary tool. Critical care ultrasonography has great potential to guide decisions in the management of shock, but operators should be aware of limitations and pitfalls as well. Current evidence comes from cohort studies with heterogeneous design and outcomes.

Summary
Use of ultrasonography for hemodynamic monitoring in critical care expands, probably because of absence of procedure-related adverse events. Easy applicability and the capacity of distinguishing different types of shock add to its increasing role, further supported by consensus statements promoting ultrasound as the preferred tool for diagnostics in circulatory shock.
Development of Nerve Fibre Diameter in Young Infants With Hirschsprung Disease
Authors: Janssen Lok Maarten , Rassouli‐Kirchmeier Roxana , Köster Nils , Kusters Benno , de Blaauw Ivo 
Published: June 2017

ABSTRACTObjectives:Finding thickened nerve fibres is one of the key elements in the diagnosis of Hirschsprung disease (HD); however, its value at different ages remains uncertain. Nerve fibre diameters <40 μm can be observed in infants younger than 8 weeks, despite the presence of HD. The aim of this study was to identify a change in maximum nerve fibre diameter in HD patients, measured before and after 8 weeks of age.Methods:Nerve fibre diameter was retrospectively evaluated in tissue of 20 infants treated for definite HD. Rectal suction biopsies (RSBs) obtained within the first 8 weeks of life (T1) and resected bowel obtained during primary surgery at an average of 24.7 weeks (T2), were assessed. The 2 thickest nerve fibre diameter recordings at T1 and T2 were compared in each subject, to examine changes in nerve trunk diameter with increasing age.Results:In 13 cases (65%), nerve fibre diameters were ≥40 μm at T1 and T2. Six subjects (30%) had nerve trunk diameters <40 μm at T1; however, they experienced diameter increases to ≥40 μm by T2. Thus, at T2, 19 subjects (95%) had diameter recordings ≥40 μm. Nerve fibre diameter in the remaining case (5%) stayed consistent at <40 μm at T1 and T2, despite the presence of HD.Conclusions:After the first 8 weeks of life, nerve fibre measurements appear to be associated with HD. Measuring the 2 thickest nerve fibres can support typical HD diagnosis criteria beyond 8 weeks of age, but is not superior to histopathological confirmation of aganglionosis.
Simulation-Based Assessment Identifies Longitudinal Changes in Cognitive Skills in an Anesthesiology Residency Training Program
Authors: Sidi Avner , Gravenstein Nikolaus , Vasilopoulos Terrie , Lampotang Samsun 
Published: June 2017

Objectives
We describe observed improvements in nontechnical or “higher-order” deficiencies and cognitive performance skills in an anesthesia residency cohort for a 1-year time interval. Our main objectives were to evaluate higher-order, cognitive performance and to demonstrate that simulation can effectively serve as an assessment of cognitive skills and can help detect “higher-order” deficiencies, which are not as well identified through more traditional assessment tools. We hypothesized that simulation can identify longitudinal changes in cognitive skills and that cognitive performance deficiencies can then be remediated over time.

Methods
We used 50 scenarios evaluating 35 residents during 2 subsequent years, and 18 of those 35 residents were evaluated in both years (post graduate years 3 then 4) in the same or similar scenarios. Individual basic knowledge and cognitive performance during simulation-based scenarios were assessed using a 20- to 27-item scenario-specific checklist. Items were labeled as basic knowledge/technical (lower-order cognition) or advanced cognitive/nontechnical (higher-order cognition). Identical or similar scenarios were repeated annually by a subset of 18 residents during 2 successive academic years. For every scenario and item, we calculated group error scenario rate (frequency) and individual (resident) item success. Grouped individuals’ success rates are calculated as mean (SD), and item success grade and group error rates are calculated and presented as proportions. For all analyses, α level is 0.05.

Results
Overall PGY4 residents’ error rates were lower and success rates higher for the cognitive items compared with technical item performance in the operating room and resuscitation domains. In all 3 clinical domains, the cognitive error rate by PGY4 residents was fairly low (0.00–0.22) and the cognitive success rate by PGY4 residents was high (0.83–1.00) and significantly better compared with previous annual assessments (P < 0.05). Overall, there was an annual decrease in error rates for 2 years, primarily driven by decreases in cognitive errors. The most commonly observed cognitive error types remained anchoring, availability bias, premature closure, and confirmation bias.

Conclusions
Simulation-based assessments can highlight cognitive performance areas of relative strength, weakness, and progress in a resident or resident cohort. We believe that they can therefore be used to inform curriculum development including activities that require higher-level cognitive processing.
Fine-mapping the Favored Mutation in a Positive Selective Sweep
Authors: Akbari Ali , Vitti Joseph J. , Iranmehr Arya , Bakhtiari Mehrdad , Sabeti Pardis C. , Mirarab Siavash , Bafna Vineet 
Published: June 2017

AbstractMethods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and in human populations from the 1000 Genomes Project, at 22 loci with previously characterized selective sweeps. For 14 of the 22 loci, iSAFE ranked the previously characterized candidate mutation among the 13 highest scoring (out of ∼ 21, 000 variants). Three loci did not show a strong signal. For the remaining loci, iSAFE identified previously unreported mutations as being favored. In these regions, all of which involve pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection. The iSAFE software can be downloaded fromhttps://github.com/alek0991/iSAFE.
Accurate and Fast feature selection workflow for high-dimensional omics data
Authors: Perez-Riverol Yasset , Kun Max , Vizcaíno Juan Antonio , Hitz Marc-Phillip , Audain Enrique 
Published: June 2017

AbstractWe are moving into the age of ‘Big Data’ in biomedical research and bioinformatics. This trend could be encapsulated in this simple formula: D = S × F, where the volume of data generated (D) increases in both dimensions: the number of samples (S) and the number of sample features (F). Frequently, a typical bioinformatics problem (e.g. classification) includes redundant and irrelevant features that can result, in the worst-case scenario, in false positive results. Then, Feature Selection (FS) constitutes an enormous challenge. Despite the number and diversity of algorithms available, the proper choice of an approach for facing a specific problem often falls in a ‘grey zone’. In this study, we select a subset of FS methods to develop an efficient workflow and an R package for bioinformatics machine learning problems. We cover relevant issues concerning FS, ranging from domain’s problems to algorithm solutions and computational tools. Finally, we use seven different proteomics and gene expression datasets to evaluate the workflow and guide the FS process.
Pathogen dependent phenotypic but no genetic correlation between sexual activity and 3 immunity in maleDrosophila melanogastersubjected to differential sexual selection
Authors: Syed Zeeshan Ali , Gupta Vanika , Samant Manas Arun , Dhiman Aatashi , Prasad Nagaraj Guru 
Published: June 2017

AbstractThe theory of trade-off suggest that limited resources should lead to trade-off in resource intensive traits such as immunity related and sexually selected traits in males. Alternatively, sexual exaggerations can also act as an honest indicator of underlying immunocompetence, leading to positive correlations between these traits. Several studies have addressed this question using experimental evolution. However, they have rarely used ecologically relevant pathogens and fitness measurement (e.g., measuring post-infection survivorship) to find correlations between sexual selection and immunity. Here we attempt to address this caveat by evolving populations ofDrosophila melanogasterunder differential sexual selection. After more than hundred generations, we infected virgin and mated males from each population with three pathogenic bacteria:Pseudomonas entomophila(Pe),Staphylococcus succinus(Ss) andProvidentia rettgeri(Pr). Fitness was measured as either post-infection survivorship (Pe and Ss) or bacterial clearance ability (Pr). Contrary to expectations, sexual selection had no evolutionary effect on male fitness against any of the pathogens. Moreover, mating had a beneficial effect against Pe and Pr, but no effect against Ss, suggesting pathogen specific phenotypic correlations between mating and immunity. Following these results, we discuss the significance of using ecologically relevant pathogens and quantifying host fitness while studying sexual selection-immunity correlations.
Advances and perspectives in tissue clearing using CLARITY
Authors: Reveles Jensen Kristian H. , Berg Rune W. 
Published: June 2017

AbstractCLARITY is a tissue clearing method, which enables immunostaining and imaging of large volumes for 3Dreconstruction. The method was initially time-consuming, expensive and relied on electrophoresis to remove lipids to make the tissue transparent. Since then several improvements and simplifications have emerged, such as passive clearing (PACT) and methods to improve tissue staining. Here, we review advances and compare current applications with the aim of highlighting needed improvements as well as aiding selection of the specific protocol for use in future investigations.
pals-22, a member of an expandedC. elegansgene family, controls silencing of repetitive DNA
Authors: Leyva-Díaz Eduardo , Stefanakis Nikolaos , Carrera Inés , Glenwinkel Lori , Wang Guoqiang , Driscoll Monica , Hobert Oliver 
Published: June 2017

ABSTRACTRepetitive DNA sequences are subject to gene silencing in various animal species. Under specific circumstances repetitive DNA sequences can escape such silencing. For example, when exogenously added, extrachromosomal DNA sequences that are stably inherited in multicopy repetitive arrays in the nematodeC. elegansare frequently silenced in the germline, whereas such silencing often does not occur in the soma. This indicates that somatic cells might utilize factors that prevent repetitive DNA silencing. Indeed, such “anti-silencing” factors have been revealed through genetic screens that identified mutant loci in which repetitive transgenic arrays are aberrantly silenced in the soma. We describe here a novel locus,pals-22(forprotein containingALS2CR12 domain), required to prevent silencing of repetitive transgenes in neurons and other somatic tissue types.pals-22deficiency also severely impacts animal vigor and confers phenotypes reminiscent of accelerated aging. We find thatpals-22is a member of a large family of divergent genes (39 members), defined by the presence of an ALS2CR12 domain. While gene family members are highly divergent, they show striking patterns of genomic clustering. The family expansion appearsC. elegans-specific and has not occurred to the same extent in other nematode species. Previous transcriptome analysis has revealed that most of thepalsgenes are induced under stress conditions or upon infection by intracellular parasites. The transgene silencing phenotype observed upon loss of cytoplasmically localized PALS-22 protein depends on the biogenesis of small RNAs, since silencing is abolished in the RNAi defective mutantrde-4, suggesting thatpals-22might regulate RNAi dependent silencing in the cytoplasm of neurons and other tissues. We speculate that thepalsgene family may be part of a species-specific cellular defense mechanism.
Detecting local Zika virus transmission in the continental United States: a comparison of surveillance strategies
Authors: Russell Steven P , Ryff Kyle R , Gould Carolyn V , Martin Stacey W , Johansson Michael A 
Published: June 2017

AbstractIntroductionThe 2015-2017 Zika virus (ZIKV) epidemic in the Americas has driven efforts to strengthen surveillance systems and to develop interventions, testing, and travel recommendations. In the continental U.S. and Hawaii, where limited transmission has been observed, detecting local transmission is a key public health objective. We assessed the effectiveness of three general surveillance strategies for this situation: testing all pregnant women twice during pregnancy, testing blood donations, and testing symptomatic people who seek medical care in an emergency department (ED).MethodsWe developed a simulation model for each surveillance strategy and simulated different transmission scenarios with varying population sizes and infection rates. We then calculated the probability of detecting transmission, the number of tests needed, and the number of false positive test results.ResultsThe probability of detecting ZIKV transmission was highest for testing ED patients with Zika symptoms, followed by pregnant women and blood donors, in that order. The magnitude of the difference in probability of detection between strategies depended on the incidence of infection. Testing ED patients required fewer tests and resulted in fewer false positives than surveillance among pregnant women. The optimal strategy identified was to test ED patients with at least two Zika virus disease symptoms. This case definition resulted in a high probability of detection with relatively few tests and false positives.DiscussionIn the continental U.S. and Hawaii, where local ZIKV transmission is rare, optimizing the probability of detecting infections while minimizing resource usage is particularly important. Local surveillance strategies will be influenced by existing public health system infrastructure, but should also consider the effectiveness of different approaches. This analysis demonstrated differences across strategies and indicated that testing symptomatic ED patients is generally a more efficient strategy for detecting transmission than routine testing of pregnant women or blood donors.
Massive variation of short tandem repeats with functional consequences across strains ofArabidopsis thaliana
Authors: Press Maximilian O. , McCoy Rajiv C. , Hall Ashley N. , Akey Joshua M. , Queitsch Christine 
Published: June 2017

AbstractShort tandem repeat (STR) mutations may be responsible for more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assess the scope of this contribution across a collection of 96 strains ofArabidopsis thalianaby massively parallel STR genotyping. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR in these strains. Modest STR expansions are found in most strains, some of which have evident functional effects. For instance, three of six intronic STR expansions are associated with intron retention. Coding STRs are depleted of variation relative to non-coding STRs, consistent with the action of purifying selection, and some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detect dozens of novel STR-phenotype associations that could not be detected with SNPs alone, validating several with follow-up experiments. Our results demonstrate that STRs comprise a large, unascertained reservoir of functionally relevant genomic variation.
Genetically modified human type II collagen for N- and C-terminal covalent tagging
Authors: Wieczorek Andrew , Chan Clara K. , Kovacic Suzana , Li Cindy , Dierks Thomas , Forde Nancy R. 
Published: June 2017

AbstractCollagen is the predominant structural protein in vertebrates, where it contributes to connective tissues and the extracellular matrix; it is also widely used in biomaterials and tissue engineering. Dysfunction of this protein and its processing can lead to a wide variety of developmental disorders and connective tissue diseases. Recombinantly engineering the protein is challenging due to posttranslational modifications generally required for its stability and secretion from cells. Introducing end labels into the protein is problematic, because the N- and C-termini of the physiologically relevant tropocollagen lie internal to the initially flanking N- and C-propeptide sequences. Here, we introduce mutations into human type II procollagen in a manner that address these concerns, and purify the recombinant protein from a stably transfected HT1080 human fibrosarcoma cell line. Our approach introduces chemically addressable groups into the N- and Ctelopeptide termini of tropocollagen. Simultaneous overexpression of formylglycine generating enzyme (FGE) allows the endogenous production of an aldehyde tag in a defined, substituted sequence in the N-terminus of the mutated collagen, while the C-terminus of each chain presents a sulfhydryl group from an introduced cysteine. These modifications are designed to enable specific covalent end-labelling of collagen. We find that the doubly-mutated protein folds and is secreted from cells, while higher-order assembly into well-ordered collagen fibrils is demonstrated through transmission electron microscopy. Chemical tagging of thiols is successful, however background from endogenous aldehydes present in wildtype collagen has thus far obscured the desired specific N-terminal labelling. Strategies to overcome this challenge are proposed.
Sexual imprinting and speciation in twoPeromyscusspecies
Authors: Delaney E.K. , Hoekstra H.E. 
Published: June 2017

AbstractSexual isolation, a reproductive barrier, can prevent interbreeding between diverging populations or species. Sexual isolation can have a clear genetic basis; however, it may also result from learned mate preferences that form via sexual imprinting. Here, we demonstrate that two sympatric species of mice—the white-footed mouse (Peromyscus leucopus) and its sister species, the cotton mouse (P. gossypinus)—hybridize only rarely in the wild despite co-occurrence in the same habitat and lack of any measurable intrinsic postzygotic barriers in laboratory crosses. We present evidence that strong conspecific mating preferences in each species result in significant sexual isolation. We find that these preferences are learned in at least one species:P. gossypinussexually imprints on its parents, but inP. leucopus,additional factors influence mating preferences. Our study demonstrates that sexual imprinting contributes to reproductive isolation that reduces hybridization between otherwise interfertile species, supporting the role for learning in mammalian speciation.
Genetic identification Of brain cell types underlying schizophrenia
Authors: Skene Nathan G. , Bryois Julien , Bakken Trygve E. , Breen Gerome , Crowley James J , A Gaspar Héléna , Giusti-Rodriguez Paola , Hodge Rebecca D , Miller Jeremy A. , Muñoz-Manchado Ana , O’Donovan Michael C , Owen Michael J , Pardiñas Antonio F , Ryge Jesper , Walters James T R , Linnarsson Sten , Lein Ed S. ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sullivan Patrick F , Hjerling-Leffler Jens 
Published: June 2017

AbstractWith few exceptions, the marked advances in knowledge about the genetic basis for schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. Applying knowledge of the cellular taxonomy of the brain from single-cell RNA-sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. The common variant genomic results consistently mapped to pyramidal cells, medium spiny neurons, and certain interneurons but far less consistently to embryonic, progenitor, or glial cells. These enrichments were due to distinct sets of genes specifically expressed in each of these cell types. Many of the diverse gene sets associated with schizophrenia (including antipsychotic targets) implicate the same brain cell types. Our results provide a parsimonious explanation: the common-variant genetic results for schizophrenia point at a limited set of neurons, and the gene sets point to the same cells. While some of the genetic risk is associated with GABAergic interneurons, this risk largely does not overlap with that from projecting cells.