bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of Orbital Floor With Auricular Concha
Authors: Seven Ergin , Tellioglu Ali Teoman , Inozu Emre , Ozakpinar Hulda Rifat , Horoz Ugur , Eryilmaz Avni Tolga , Karamursel Sebat 
Published: September 2017

Abstract
Orbital floor fractures of varying sizes commonly occur after orbital injuries and remain a serious challenge. Serious complications of such fractures include enopthalmos, restriction of extraocular movement, and diplopia. There is a dearth of literature that can be applied widely, easily, and successfully in all such situations, and therefore there is no consensus on the treatment protocol of this pathology yet. Autogenous grafts and alloplastic and allogenic materials with a wide variety of advantages and disadvantages have been discussed. The value of preoperative and postoperative ophthalmological examination should be standard of care in all orbital fracture patients. An ideal reconstructed orbital floor fracture should accelerate the restoration of orbital function with acceptable cosmetic results. Management parameters of orbital fractures such as timing of surgery, incision type, and implant materials, though widely discussed, remain controversial. In this study, 55 patients with orbital floor fractures surgically reconstructed with conchal cartilage grafts between 2008 and 2014 were retrospectively evaluated. Complications and long-time follow-up visit results have been reported with clinical and radiographic findings. The aim of this study was to present the authors’ clinical experiences of reconstruction of blow-out fractures with auricular conchal graft and to evaluate the other materials available for use.
Intraoperative Neurophysiologic Monitoring for Prediction of Postoperative Neurological Improvement in a Child With Chiari Type I Malformation
Authors: Kawasaki Yukari , Uchida Susumu , Onishi Kouhei , Toyokuni Masako , Okanari Kazuo , Fujiki Minoru 
Published: September 2017

Introduction:
Although many surgical treatment strategies for Chiari malformation type I (CM-I) have been reported, the most appropriate surgical technique remains controversial. It is wholly ascribable to the complicacy of pathological condition in CM-I. Recently, intraoperative neurophysiologic monitoring (INM) is becoming prevalent in spinal surgery. Indeed, motor-evoked potentials (MEPs) monitoring and somatosensory-evoked potentials (SSEPs) monitoring are standard tools to minimize the risk of neurologic injury and postoperative deficits. The most recent study suggested that multimodality INM can be beneficial in foramen magnum decompression surgery for CM-I patients for surgical positioning and planning. Various authors have investigated the consistency of intraoperative evoked potential changes that might aid the surgeon to determine the appropriate extent of decompression required for an individual patient.

Patient Description:
The authors report the case of a 7-year-old boy who had the signs of medullary and cerebellar dysfunction, clumsy hands, and ataxic gait. He underwent a surgery of foramen magnum decompression with tonsillectomy and duraplasty for CM-I with cervicomedullary compression. His intraoperative MEPs improved (indicated increased-amplitude and shortened-latency) both after craniotomy and durotomy, whereas SSEPs improved only after durotomy. Those results were correlated well with a functional improvement that was apparent in the immediate postoperative hospitalization.

Conclusions:
The authors’ data provides 1 possible interpretation of INM for safety aspect, but also which degree of decompression in each patient will require. The improvement in MEPs and SSEPs observed during decompression procedure may be a good indicator for the prediction of the clinical improvement seen postoperatively.
Olfactory Dysfunction Associated With Neuro-Behçet Disease
Authors: Doğan Remzi , Ertaş Burak , Özücer Berke , Birday Erkingul , Özturan Orhan , Veyseller Bayram 
Published: September 2017

Introduction:
Neurologic involvement associated with Behçet disease (BD) is defined as a different entity: Neuro-Behçet disease (NBD). Behçet disease presents with olfactory dysfunction. It is not known whether this is the consequence of mucosal involvement or neurologic involvement.

Objective:
The aim of this study was to investigate whether olfactory dysfunction was further aggravated as the result of neurologic involvement.

Methods:
Sixteen patients diagnosed with NBD and 16 healthy control patients with similar demographic characteristics were recruited as the healthy control group. Expanded Disability Status Scale (EDSS) scoring was used for quantification of neurological disability. All diagnoses were confirmed and categorized with magnetic resonance imaging studies in all patients individually: parenchymal or nonparenchymal. A well-established test of orthonasal olfaction developed at the CCCRC was used. Correlation analysis was carried out.

Results:
The mean CCCRC score of NBD patients was 4.60 out of 7, and this group was diagnosed to be moderately hyposmic, whereas the average score of the control group was 6.5; the difference was significant (P < 0.0001). CCCRC scores of NBD patients were significantly lower compared both healthy control patients and those of BD patients reported in the literature. Mean EDSS score of NBD patients was 1.75 ± 1.0 out of 10 (0—no neurologic disability and 10—worst neurologic disability). Magnetic resonance imaging of NBD patients revealed 4 nonparenchymal and 12 parenchymal patients. Neuro-Behçet disease patients with parenchymal involvement presented with (worse) EDSS scores. Mean olfactory CCCRC score of this group was 4.38 whereas the average olfactory score of the vascular group was 5.25 out 7. Average EDSS score of vascular group was 0.75, much better compared to higher average neurologic disability score of 2.08 for the parenchymal group. Significant correlation existed between the duration of NBD and both olfactory and neurologic dysfunction scores.

Conclusion:
Neuro-Behçet disease present with aggravated olfactory dysfunction compared to BD. Neurologic involvement—especially parenchymal involvement—seems to deteriorate the olfactory dysfunction. Duration of disease is correlated with this severity of dysfunction.
Early chemoprophylaxis is associated with decreased venous thromboembolism risk without concomitant increase in intraspinal hematoma expansion after traumatic spinal cord injury
Authors: Chang Ronald , Scerbo Michelle H. , Schmitt Karl M. , Adams Sasha D. , Choi Timothy J. , Wade Charles E. , Holcomb John B. 
Published: September 2017

BACKGROUND
After traumatic spinal cord injury (SCI), there is increased risk of venous thromboembolism (VTE), but chemoprophylaxis (PPX) may cause expansion of intraspinal hematoma (ISH).

METHODS
Single-center retrospective study of adult trauma patients from 2012 to 2015 with SCI. Exclusion criteria: VTE diagnosis, death, or discharge within 48 hours. Patients were dichotomized based on early (≤48 hours) heparinoid and/or aspirin PPX. Intraspinal hematoma expansion was diagnosed intraoperatively or by follow-up radiology. We used multivariable Cox proportional hazards to estimate the effect of PPX on risk of VTE and ISH expansion controlling for age, injury severity score (ISS), complete SCI, and mechanism as static covariates and operative spine procedure as a time-varying covariate.

RESULTS
Five hundred one patients with SCI were dichotomized into early PPX (n = 260 [52%]) and no early PPX (n = 241 [48%]). Early PPX patients were less likely blunt injured (91% vs 97%) and had fewer operative spine interventions (65% vs 80%), but age (median, 43 vs 49 years), ISS (median 24 vs 21), admission ISH (47% vs 44%), and VTE (5% vs 9%) were similar. Cox analysis found that early heparinoids was associated with reduced VTE (hazard ratio [HR], 0.37; 95% confidence interval [CI], 0.16–0.84) and reduced pulmonary embolism (PE) (HR, 0.20; 95% CI, 0.06–0.69). The estimated number needed to treat with heparinoids was 10 to prevent one VTE and 13 to prevent one PE at 30 days. Early aspirin was not associated with reduced VTE or PE. Seven patients (1%) had ISH expansion, of which four were on PPX at the time of expansion. Using heparinoid and aspirin as time-varying covariates, neither heparinoids (HR, 1.90; 95% CI, 0.32–11.41) nor aspirin (HR, 3.67; 95% CI, 0.64–20.88) was associated with ISH expansion.

CONCLUSION
Early heparinoid therapy was associated with decreased VTE and PE risk in SCI patients without concomitant increase in ISH expansion.

LEVEL OF EVIDENCE
Therapeutic, level IV.
The prevalence of chronic deep venous thrombosis in trauma: Implications for hospitals and patients
Authors: Cannon Kathleen A. , Badiee Jayraan , Wallace James D. , Brill Jason B. , Sise Michael J. , Bansal Vishal , Sise C. Beth , Shackford Steven R. 
Published: September 2017

INTRODUCTION
Deep venous thrombosis (DVT) is considered a preventable complication in trauma patients. Hospitals risk financial penalties for DVT rates above accepted benchmarks. These penalties do not apply to chronic DVT, which develops before admission. Lower-extremity duplex ultrasound (LEDUS) can detect characteristics of thrombus chronicity, allowing differentiation of chronic from acute DVT. The objective of this study was to determine the prevalence of chronic DVT in hospitalized trauma patients.

METHODS
We performed a retrospective review of trauma patients admitted to our Level I trauma center between July 1, 2006 and October 31, 2016 who had a DVT on initial screening LEDUS. Our center utilizes screening and surveillance LEDUS for patients admitted more than 48 hours. Definitions for chronic and acute DVT were extracted from existing literature. Patients with DVT on initial LEDUS underwent review of that LEDUS to assess clot chronicity and were classified as having acute DVT, chronic DVT, or DVT of indeterminate age. Demographic data, medical history, and injury characteristics were collected. Patients with acute DVT and those with chronic DVT were compared.

RESULTS
The prevalence of chronic DVT among patients with a DVT on initial LEDUS was 29.9%. Chronic DVT occurred in patients who were older and less severely injured. An above-knee component was significantly more common in chronic DVT (65%). Only 34 (41%) of those with chronic DVT reported a history of DVT. Among the patients with chronic DVT, 44 (53%) had a subsequent LEDUS, of whom 4 (9%) showed thrombus progression and 6 (14%) formed a new DVT.

CONCLUSION
Lower-extremity duplex ultrasound can identify chronic DVT, which represents nearly 30% of all DVT found on initial screening LEDUS in trauma patients. Those with chronic DVT should receive pharmacologic and mechanical prophylaxis because of the incidence of progression and new acute DVT. They should also be counseled regarding the possibilities of recurrence and chronic venous insufficiency.

LEVEL OF EVIDENCE
Diagnostic study, level III.
Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking
Authors: Capella-Gutierrez Salvador , Iglesia Diana de la , Haas Juergen , Lourenco Analia , Fernández José María , Repchevsky Dmitry , Dessimoz Christophe , Schwede Torsten , Notredame Cedric , Gelpi Josep Ll , Valencia Alfonso 
Published: September 2017

AbstractThe dependence of life scientists on software has steadily grown in recent years. For many tasks, researchers have to decide which of the available bioinformatics software are more suitable for their specific needs. Additionally researchers should be able to objectively select the software that provides the highest accuracy, the best efficiency and the highest level of reproducibility when integrated in their research projects.Critical benchmarking of bioinformatics methods, tools and web services is therefore an essential community service, as well as a critical component of reproducibility efforts. Unbiased and objective evaluations are challenging to set up and can only be effective when built and implemented around community driven efforts, as demonstrated by the many ongoing community challenges in bioinformatics that followed the success of CASP. Community challenges bring the combined benefits of intense collaboration, transparency and standard harmonization. Only open systems for the continuous evaluation of methods offer a perfect complement to community challenges, offering to larger communities of users that could extend far beyond the community of developers, a window to the developments status that they can use for their specific projects. We understand by continuous evaluation systems as those services which are always available and periodically update their data and/or metrics according to a predefined schedule keeping in mind that the performance has to be always seen in terms of each research domain.We argue here that technology is now mature to bring community driven benchmarking efforts to a higher level that should allow effective interoperability of benchmarks across related methods. New technological developments allow overcoming the limitations of the first experiences on online benchmarking e.g. EVA. We therefore describe OpenEBench, a novel infra-structure designed to establish a continuous automated benchmarking system for bioinformatics methods, tools and web services.OpenEBench is being developed so as to cater for the needs of the bioinformatics community, especially software developers who need an objective and quantitative way to inform their decisions as well as the larger community of end-users, in their search for unbiased and up-to-date evaluation of bioinformatics methods. As such OpenEBench should soon become a central place for bioinformatics software developers, community-driven benchmarking initiatives, researchers using bioinformatics methods, and funders interested in the result of methods evaluation.
Gene expression drives the evolution of dominance
Authors: Huber Christian D. , Durvasula Arun , Hancock Angela M. , Lohmueller Kirk E. 
Published: September 2017

AbstractDominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, and complex traits. However, despite its importance, the degree of dominance has yet to be quantified in natural populations. Here, we leverage multiple mating systems in natural populations ofArabidopsisto co-estimate the distribution of fitness effects and dominance coefficients of new amino acid changing mutations. We find that more deleterious mutations are more likely to be recessive than less deleterious mutations. Further, this pattern holds across gene categories, but varies with the connectivity and expression patterns of genes. Our work argues that dominance arose as the inevitable consequence of the functional importance of genes and their optimal expression levels.One sentence summaryWe use population genomic data to characterize the degree of dominance for new mutations and develop a new theory for its evolution.
Comparison of single genome and allele frequency data reveals discordant demographic histories
Authors: Beichman Annabel C. , Phung Tanya N. , Lohmueller Kirk E. 
Published: September 2017

ABSTRACTInference of demographic history from genetic data is a primary goal of population genetics of model and non-model organisms. Whole genome-based approaches such as the Pairwise/Multiple Sequentially Markovian Coalescent (PSMC/MSMC) methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba (YRI), descendants of northwest-Europeans (CEU), and Han Chinese (CHB)) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.
Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter fromSorghum bicolor
Authors: Doshi Rupak , McGrath Aaron P. , Piñeros Miguel , Szewczyk Paul , Garza Denisse M. , Kochian Leon V. , Chang Geoffrey 
Published: September 2017

ABSTRACTAbout 50% of the world’s arable land is strongly acidic (soil pH < 5). The low pH of these soils solubilizes root-toxic ionic aluminium (Al3+) species from clay minerals, driving the evolution of various counteractive adaptations in cultivated crops. The food cropSorghum bicolor, for example, upregulates the membrane-embedded transporter protein SbMATE in its roots. SbMATE mediates efflux of the anionic form of the organic acid, citrate, into the soil rhizosphere, chelating Al3+ions and thereby imparting Al-resistance based on excluding Al+3from the growing root tip. Here, we use electrophysiological, radiolabeled, and fluorescence-based transport assays in two heterologous expression systems to establish a broad substrate recognition profile of SbMATE, showing the transport of14C- citrate anion, as well as the organic monovalent cation, ethidium, but not the divalent ethidium-derivative, propidium. The transport cycle is proton and/or sodium-driven, and shares certain molecular mechanisms with bacterial MATE-family transporters. We further complement our transport assays by directly measuring substrate binding to detergent-purified SbMATE protein. Finally, we use the functionally-folded, purified membrane protein as an antigen to discover high-affinity, native conformation-binding and transport function-altering nanobodies using an animal-free, mRNA/cDNA display technology. Our results demonstrate the utility of usingPichia pastorisas an efficient eukaryotic host to express large quantities of functional plant transporter proteins forin vitrocharacterization. The nanobody discovery approach is applicable to other low immunogenic plant proteins.
Streptolysin-induced endoplasmic reticulum stress promotes group A streptococcalin vivobiofilm formation and necrotizing fasciitis
Authors: Vajjala Anuradha , Biswas Debabrata , Long Chong Kelvin Kian , Tay Wei Hong , Hanski Emanuel , Kline Kimberly A 
Published: September 2017

AbstractGroup AStreptococcus(GAS) is a human pathogen that causes infections ranging from mild to fulminant and life-threatening. Biofilms have been implicated in acute GAS soft-tissue infections such as necrotizing fasciitis (NF). However, mostin vitromodels used to study GAS biofilms have been designed to mimic chronic infections and insufficiently recapitulatein vivoconditions and the host-pathogen interactions that might influence biofilm formation. Here we establish and characterize anin vitromodel of GAS biofilm development on mammalian cells that simulates microcolony formation observed in a murine model of human NF. We show that on mammalian cells, GAS forms dense aggregates that display hallmark biofilm characteristics including a three-dimensional architecture and enhanced tolerance to antibiotics. In contrast to abiotic-grown biofilms, host-associated biofilms require the expression of secreted GAS streptolysins O and S (SLO, SLS) resulting in the release of a host-associated biofilm promoting-factor(s). Supernatants from GAS-infected mammalian cells or from cells treated with endoplasmic reticulum (ER) stressors restore biofilm formation to an SLO and SLS null mutant that is otherwise attenuated in biofilm formation on cells, together suggesting a role for streptolysin-induced ER stress in this process. In an in vivomouse model, the streptolysin-null mutant is attenuated in both microcolony formation and bacterial spread, but pre-treatment of softtissue with an ER-stressor restores the ability of the mutant to form wild type like microcolonies that disseminate throughout the soft tissue. Taken together, we have identified a new role of streptolysin-driven ER stress in GAS biofilm formation and NF disease progression.Significance StatementAlthough it is well-accepted that bacterial biofilms are associated with many chronic infections, little is known about the mechanisms by which group AStreptococcus(GAS) biofilms contribute to acute soft tissue-invasive diseases like necrotizing fasciitis (NF). In this study, we establish a physiologically relevantin vitromodel to study GAS biofilm formation on mammalian cells and validate our findings in a mouse model that mimics human NF. This study demonstrates a novel role of GAS streptolysin-mediated ER stress in the development and spread of GAS biofilms in acute softtissue infections. We also show that biofilm formation depends on the release of a host-associated factor that promotes microcolony formation and GAS disseminationin vivo.
Conserving amphibians in the face of land development: integrating field experiments as a planning tool
Authors: Felson Alexander J. 
Published: September 2017

AbstractRegulations designed to guide development practices inadequately reflect ecological understanding and fall short of preserving viable habitats. Environmental consultants use rapid assessments and monitoring on individual ponds to rank pond habitat quality, relying on coarse proxies, including vegetative indicators, soil characteristics, hydroperiod, and breeding evidence in obligate species. Planners incorporate these rankings to inform the layout of neighborhoods, roadways, infrastructure and housing. However, important drivers of amphibian survival and fecundity—including metapopulation dynamics, habitat connectivity, watershed health, terrestrial density dependence, and environmental gradients—are often poorly measured and regulated. Given that development proceeds regardless, what options exists improve land development practices?Integrating experimentation into the planning process can inform land development and improve amphibian conservation. Working as part of the design team we employed an adaptive approach calleddesigned experimentto inform development practices. We manipulatedAmbystoma opacumlarvae within enclosures to test the effects of inter-pond conditions (versus intra-pond density dependence) on the survival and fecundity of conspecifics,Rana sylvatica and Ambystoma maculatum. While the A. maculatum populations were decimated with only 1.5 % survival. ForA. opacumandR. sylvaticaresults indicate habitat variation between ponds accounted for 63.7% and 50.3% of the variance in survival rates of larvae, respectively, and are not predicted by the presence and abundance of egg masses, while density effects accounted for 3.5% and 2.8% of the variation in survival. The results suggest that ponds ranked as high value based on egg mass counts may actually function as habitat sinks. This study illustrates the potential value of assessment approaches that emphasize habitat quality across pond clusters to guide mitigation, conservation, regulations, and to establish sites and funding for ecological research.