bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-scenario genome-wide medical population genetics simulation framework
Authors: Mugo Jacquiline W , Geza Ephifania , Defo Joel , Elsheikh Samar S M , Mazandu Gaston K , Mulder Nicola J , Chimusa Emile R 
Published: June 2017

Abstract

Motivation
Recent technological advances in high-throughput sequencing and genotyping have facilitated an improved understanding of genomic structure and disease-associated genetic factors. In this context, simulation models can play a critical role in revealing various evolutionary and demographic effects on genomic variation, enabling researchers to assess existing and design novel analytical approaches. Although various simulation frameworks have been suggested, they do not account for natural selection in admixture processes. Most are tailored to a single chromosome or a genomic region, very few capture large-scale genomic data, and most are not accessible for genomic communities.

Results
Here we develop a multi-scenario genome-wide medical population genetics simulation framework called ‘FractalSIM’. FractalSIM has the capability to accurately mimic and generate genome-wide data under various genetic models on genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations. Moreover, the framework accounts for natural selection in both homogeneous and admixture processes. The outputs of FractalSIM have been assessed using popular tools, and the results demonstrated its capability to accurately mimic real scenarios. They can be used to evaluate the performance of a range of genomic tools from ancestry inference to genome-wide association studies.

Availability and implementation
The FractalSIM package is available at http://www.cbio.uct.ac.za/FractalSIM.

Supplementary information
Supplementary data are available at Bioinformatics online.
Vascularized Fibular Strut Autografts in Spinal Reconstruction after Resection of Vertebral Chordoma or Chondrosarcoma: A Retrospective Series
Authors: Yanamadala Vijay , Rozman Peter A. , Kumar Jay I. , Schwab Joseph H. , Lee Sang-Gil , Hornicek Francis J. , Curry William T. 
Published: June 2017

Abstract

BACKGROUND: Margin-free en bloc resection is the best medical practice for primary vertebral chordoma and chondrosarcoma. Spinal reconstruction following total spondylectomy requires reconstructive interbody graft (allograft, devascularized autograft, vascularized autograft, or cage constructs) and instrumentation. An important consideration when choosing grafts and instrumentation is the durability and the long-term success of the fusion without subsidence.

OBJECTIVE: To evaluate the potential use of vascularized fibular autograft as a reconstructive strategy after en bloc resection.

METHODS: We present a series of 16 patients who underwent spondylectomy for primary vertebral chordoma or chondrosarcoma with reconstruction using a vascularized fibular autograft and anterior/posterior instrumentation between January 2011 and April 2014. We report postoperative neurological outcome, 6-mo rates of fusion and graft subsidence, and other complications.

RESULTS: Two patients passed away prior to 6-mo follow-up, and 1 patient was lost to follow-up. The mean follow-up time for the remaining 13 patients was 32 mo. Of these patients, 9 (69%) had evidence of fusion on the 6-mo follow-up computed tomography (CT) scan. Of the 4 patients who did not fuse, 2 had undergone surgery for new tumor diagnoses, 1 for hardware failure, and 1 for graft nonunion. Two patients (15%) had eventual graft subsidence along with hardware failure.

CONCLUSIONS: Vascularized fibular strut grafts are a viable method for reconstruction following spondylectomy. We present the largest series of patients to date utilizing this technique. Further comparative studies examining vascularized grafts vs nonvascularized grafts or metallic cage constructs will be important in choosing the best reconstructive strategy.
FOREST unbiased Galactic plane imaging survey with the Nobeyama 45 m telescope (FUGIN). I. Project overview and initial results
Authors: Umemoto Tomofumi , Minamidani Tetsuhiro , Kuno Nario , Fujita Shinji , Matsuo Mitsuhiro , Nishimura Atsushi , Torii Kazufumi , Tosaki Tomoka , Kohno Mikito , Kuriki Mika , Tsuda Yuya , Hirota Akihiko , Ohashi Satoshi , Yamagishi Mitsuyoshi , Handa Toshihiro , Nakanishi Hiroyuki , Omodaka Toshihiro , Koide Nagito , Matsumoto Naoko , Onishi Toshikazu , Tokuda Kazuki , Seta Masumichi , Kobayashi Yukinori , Tachihara Kengo , Sano Hidetoshi , Hattori Yusuke , Onodera Sachiko , Oasa Yumiko , Kamegai Kazuhisa , Tsuboi Masato , Sofue Yoshiaki , Higuchi Aya E. , Chibueze James O. , Mizuno Norikazu , Honma Mareki , Muller Erik , Inoue Tsuyoshi , Morokuma-Matsui Kana , Shinnaga Hiroko , Ozawa Takeaki , Takahashi Ryo , Yoshiike Satoshi , Costes Jean , Kuwahara Sho 
Published: June 2017

Abstract
The FUGIN project is one of legacy projects using a new multi-beam FOREST (four-beam receiver system on the 45 m telescope). This project aims to simultaneously investigate the distribution, kinematics, and physical properties of both diffuse and dense molecular gases in the Galaxy by observing 12CO, 13CO, and C18O J = 1–0 lines simultaneously. Mapping regions are parts of the first quadrant (10° ≤ l ≤ 50°, |b| ≤ 1°) and the third quadrant (198° ≤ l ≤ 236°, |b| ≤ 1°) of the Galaxy, where spiral arms, bar structure, and the molecular gas ring are included. This survey achieves the highest angular resolution to date (∼20″) for the Galactic plane survey in the CO J = 1–0 lines, which makes it possible to find dense clumps located farther away than the previous surveys. FUGIN will provide us an invaluable dataset for investigating the physics of the Galactic interstellar medium (ISM), particularly the evolution of interstellar gas covering galactic-scale structures to the internal structures of giant molecular clouds, such as small filaments/clumps/cores. We present an overview of the FUGIN project, the observation plan and initial results. These results reveal wide-field and detailed structures of molecular clouds, such as entangled filaments that have not been obvious in previous surveys, and large-scale kinematics of molecular gas, such as spiral arms.
Improving heart failure patient outcomes utilizing guideline-directed therapy
Authors: Davidson Beth Towery , Allison Terri Lynn 
Published: June 2017

Abstract:
There is no fee for this activity. To receive credit after reading this CME/CE activity in its entirety, participants must complete the posttest and evaluation. The posttest and evaluation can be completed online at www.mlicme.org/P17039.html.
Heart failure (HF) prevalence continues to rise and remains a significant burden to patients, caregivers, providers, and the healthcare system. Guideline-directed medical therapy with standard neurohormonal blockade has been the cornerstone of medical management for many years. Despite aggressive utilization of angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, beta-blockers, and aldosterone antagonists, HF hospitalizations and readmissions are common and residual mortality remains high. With the development of two novel medical therapies (sacubitril/valsartan and ivabradine), the American College of Cardiology, American Heart Association, and Heart Failure Society of America released a pharmacologic update to provide guidelines for incorporation of these agents into clinical practice. Although effective via different mechanisms of action, both agents now have a prominent role in risk reduction. HF medical regimens often become quite complex, especially when associated with comorbid conditions, and require frequent follow-up. Providers must be proficient in patient monitoring, medication dose titration, and therapy optimization. Individualized patient care strategies such as guideline-directed therapy can promote long-term adherence and quality of life.
Performing pediatric eye exams in primary care
Authors: Martin Elaine F. 
Published: June 2017

Abstract:
Early vision care is critical for all children. If undetected, eye disorders such as amblyopia and strabismus may result in permanent vision loss. Vision exams should include a careful history and physical including fix and follow, red reflex, and cover/uncover testing. Photo screening and visual acuity exams should be administered whenever possible.
Cluster-like Headache Secondary to Focal Cervical Myelitis
Authors: Kim Dong-Eun , Park Ji-Yun , Ha Hyeonuk , Yoon Geum-Jin , Cho Bang-Hoon , Lee Seung-Han 
Published: June 2017

Background:
Cluster headache (CH) is characterized by attacks of severe periorbital pain associated with autonomic symptoms. As with other forms of primary headache, structural lesions should be excluded, particularly if the headache presents with an atypical pattern.

Case:
We report a 41-year-old woman who had no previous history of primary headache and showed a poor response to medication for CH. The patient was finally diagnosed as secondary headache with CH feature due to focal myelitis at the cervical level of the spinal cord. A strong positive Enzyme-linked Immunosorbent Assay test for Toxocara canis antibodies helped us to make a diagnosis of cervical Toxocara myelitis. After starting treatment with intravenous methylprednisolone and albendazole, her headache gradually improved with abortive and preventive treatment for CH.

Conclusions:
We suggest that neuroimaging of the upper cervical cord as well as the brain is important when CH is showing an atypical clinical course. Cervical Toxocara myelitis might be a possible cause of secondary headache with CH feature.
Corneal Nerve Morphology and Tear Film Substance P in Diabetes
Authors: Markoulli Maria , You Jingjing , Kim Juno , Duong Carmen L. , Tolentino Jonathan B. , Karras Joshua , Lum Edward 
Published: June 2017

ABSTRACT

Purpose
This work aims to characterize the relationship between tear film neuropeptide substance P and the structural integrity of the sub-basal nerve plexus in diabetes.

Methods
Seventeen healthy control participants and nine participants with diabetes were recruited in this cross-sectional study. Total protein content and substance P concentrations were determined in the flush tears of participants. Corneal nerve morphology was assessed by capturing the corneal sub-basal nerve plexus using the Heidelberg Retinal Tomograph II with the Rostock Corneal Module (Heidelberg Engineering GmbH, Heidelberg, Germany) in the central cornea. Corneal nerve fiber density (CNFD) was measured using ACCMetrics (M.A. Dabbah, Imaging Science and Biomedical Engineering, Manchester, UK) on eight captured images. Comparisons between groups were made using independent samples t-tests. Correlations between parameters were analyzed using Pearson’s correlations.

Results
Substance P concentrations were significantly higher in the tears of the control group compared to participants with diabetes (4150 ± 4752 and 1473 ± 1671 pg/mL, respectively, P = .047). There was no significant difference in total protein content between the groups (3.4 ± 1.8 and 2.6 ± 1.7 mg/mL in the control and diabetes groups, respectively, P = .262). CNFD was significantly lower in the participants with diabetes compared to the control group (16.1 ± 5.7 and 21.5 ± 7.0 mm/mm2, respectively, P = .041). There was a moderate correlation between substance P and CNFD (r = 0.48, P = .01).

Conclusions
Substance P is expressed at a significantly lower level in the tears of people with diabetes compared with healthy controls. The positive correlation between substance P and corneal nerve density indicates that substance P may be a potential biomarker for corneal nerve health.
Social Network Clustering and the Spread of HIV/AIDS Among Persons Who Inject Drugs in 2 Cities in the Philippines
Authors: Verdery Ashton M. , Siripong Nalyn , Pence Brian W. 
Published: June 2017

Introduction:
The Philippines has seen rapid increases in HIV prevalence among people who inject drugs. We study 2 neighboring cities where a linked HIV epidemic differed in timing of onset and levels of prevalence. In Cebu, prevalence rose rapidly from below 1% to 54% between 2009 and 2011 and remained high through 2013. In nearby Mandaue, HIV remained below 4% through 2011 then rose rapidly to 38% by 2013.

Objectives:
We hypothesize that infection prevalence differences in these cities may owe to aspects of social network structure, specifically levels of network clustering. Building on previous research, we hypothesize that higher levels of network clustering are associated with greater epidemic potential.

Methods:
Data were collected with respondent-driven sampling among men who inject drugs in Cebu and Mandaue in 2013. We first examine sample composition using estimators for population means. We then apply new estimators of network clustering in respondent-driven sampling data to examine associations with HIV prevalence.

Results:
Samples in both cities were comparable in composition by age, education, and injection locations. Dyadic needle-sharing levels were also similar between the 2 cities, but network clustering in the needle-sharing network differed dramatically. We found higher clustering in Cebu than Mandaue, consistent with expectations that higher clustering is associated with faster epidemic spread.

Conclusions:
This article is the first to apply estimators of network clustering to empirical respondent-driven samples, and it offers suggestive evidence that researchers should pay greater attention to network structure's role in HIV transmission dynamics.
Dexamethasone Prevents Lipopolysaccharide-Induced Epithelial Barrier Dysfunction in Rat Ileum
Authors: Ribeiro Aline Barbosa , Giusti Humberto , Souza Ana Paula Trevelin , Franci Celso Rodrigues , Saia Rafael Simone 
Published: June 2017

ABSTRACT
Inflammatory mediators have been postulated as elementary inducing factors to the disruption of the intestinal tight junctions (TJ) and consequently, gut permeability and bacterial translocation. Corticosteroids are considered the mainstay in the treatment of septic shock; however, the impact of this therapy on the intestinal epithelial barrier dysfunction during septic shock remains unknown. Our aims were to demonstrate the role of low dexamethasone (DEX) doses in modulation of the inflammatory response, as well as the expression and the arrangement of TJ proteins in endotoxemic rats. One hour before the endotoxemia induction by lipopolysaccharide (LPS) administration, rats were pretreated with DEX at two low-doses (0.1 and 1.0 mg/kg). The parameters assessed included intestinal permeability, bacterial translocation, cytokines production, histology injury, localization, and expression of TJ proteins. Endotoxemic rats displayed intestinal epithelial barrier dysfunction, characterized by increased permeability and bacterial translocation, TJ disruption (opening and changes to its constituent proteins expression) and hyperactivation of the inflammatory response. On the other hand, the pretreatment with DEX attenuated the systemic and mucosal production of inflammatory mediators and also reverted the LPS-induced ileal injuries, increasing the expression of occludin and claudin-1, but also reducing claudin-2. Moreover, the histological damages and the morphology of the TJ were preserved by the DEX administration, therefore reducing their LPS-induced opening. The present study sheds light on the fact that early DEX treatment breaks the vicious cycle of local gut inflammation and barrier dysfunction in endotoxemia, especially preserving an essential structure of this monolayer epithelium, the TJ.
Development and Validation of a Quantitative Measure of Adaptive Behaviors in Women With Pelvic Floor Disorders
Authors: Wei John T. , Dunn Rodney , Nygaard Ingrid , Burgio Kathryn , Lukacz Emily S. , Markland Alayne , Wren Patricia A. , Brubaker Linda , Barber Matthew D. , Jelovsek J. Eric , Spino Cathie , Meikle Susie , Janz Nancy 
Published: June 2017

Purpose
To establish validity for the Pelvic Floor Disorders Network (PFDN) self-administered Adaptive Behavior Index (ABI) and to assess whether ABI assesses known discordance between severity of pelvic floor symptoms and self-reported bother.

Methods
In addition to the ABI questionnaire, participants in 1 of 6 Pelvic Floor Disorders Network trials completed condition-specific measures of pretreatment symptom severity (including Pelvic Floor Distress Inventory; PFDI) and health-related quality of life (Pelvic Floor Impact Questionnaire; PFIQ). The final survey was developed from an iterative process using subject and expert endorsement, factor analyses, and response distributions. Domains were created using a development cohort (n = 304 women), reliability and validity were established using a validation cohort (n = 596 women), and test-retest reliability was assessed (n = 111 women).

Results
Factor analyses supported an 11-item avoidance domain and a 6-item hygiene domain. Cronbach' alphas were 0.88 and 0.68, respectively. Test-retest reliability was 0.84 for both domains. Construct validity was demonstrated in correlations between the ABI domains and baseline PFDI and PFIQ (r values, 0.43–0.79 with all P values <0.0001). Moreover, the ABI accounted for 8% to 26% of unexplained variance between the symptoms severity measure and the impact on health related quality of life. After treatment, avoidance domain scores improved for urinary and fecal incontinence groups and hygiene scores improved for the fecal incontinence group.

Conclusions
The ABI is a reliable and valid measure in women with pelvic floor disorders. Adaptive behaviors account in part for discordance between pelvic floor symptom severity and bother.
Preserving the Pancreas Graft: Outcomes of Surgical Repair of Duodenal Leaks in Enterically Drained Pancreas Allografts
Authors: Al-Adra David , McGilvray Ian , Goldaracena Nicolas , Spetzler Vinzent , Laurence Jerome , Norgate Andrea , Marquez Max , Greig Paul , Sapisochin Gonzalo , Schiff Jeffrey , Singh Sunita , Selzner Markus , Cattral Mark 
Published: June 2017

Background
Duodenal leak remains a major cause of morbidity and graft loss in pancreas transplant recipients. The role and efficacy of surgical and image-guided interventions to salvage enterically drained grafts with a duodenal leak has yet to be defined.

Methods
We investigated the incidence, treatment, and outcome of duodenal leak in 426 pancreas transplantation recipients from 2000 to 2015.

Results
Duodenal leak developed in 33 (7.8%) recipients after a median follow-up of 5.3 (range, 0.5-15.2) years. Most leaks occurred during the first year (n = 22; 67%), and most were located near the proximal and distal duodenal staple line. Graft pancreatectomy was performed in 8 patients as primary therapy because of unfavorable local and/or systemic conditions. Salvage was attempted in 25 patients using percutaneous drainage (n = 4), surgical drainage (n = 4), or surgical repair (n = 17). Percutaneous or surgical drainage failed to control the leak in 7 of these 8 patients, and all 7 ultimately required graft pancreatectomy for persistent leak and sepsis. Surgical repair salvaged 14 grafts, and 13 grafts continue to function after a median follow-up of 2.9 (range, 1.1-6.3) years after repair.

Conclusions
Our study shows that in selected patients a duodenal leak can be repaired successfully and safely in enterically drained grafts.
Deriving C4photosynthesis parameters by fitting intensive A/Cicurves
Authors: Zhou Haoran , Akçay Erol , Helliker Brent R. 
Published: June 2017

ABSTRACTMeasurements of photosynthetic assimilation rate as a function of intercellular CO2(A/Cicurves) are widely used to estimate photosynthetic parameters for C3species, yet few parameters have been reported for C4plants, because of a lack of estimation methods. Here, we extend the framework of widely-used estimation methods for C3plants to build estimation tools by exclusively fitting intensiveA/Cicurves (6-8 more sampling points) for C4using three versions of photosynthesis models with different assumptions about carbonic anhydrase processes and ATP distribution. We use simulation-analysis, out-of-sample tests, existing in vitro measurements and chlorophyll-fluorescence-measurements to validate the new estimation methods. Of the five/six photosynthetic parameters obtained, sensitivity analyses show that maximal-Rubisco-carboxylation-rate, electron-transport-rate, maximal-PEP-carboxylation-rate and carbonic-anhydrase were robust to variation in the input parameters, while day-respiration and mesophyll-conductance varied. Our method provides a way to estimate carbonic anhydrase activity, a new parameter, fromA/Cicurves, yet also shows that models that do not explicitly consider carbonic anhydrase yield approximate results. The two photosynthesis models, differing in whether ATP could freely transport between RuBP and PEP regeneration processes yielded consistent results under high light, but they may diverge under low light intensities. Modeling results show selection for Rubisco of low specificity and high catalytic rate, low leakage of bundle sheath and high PEPC affinity, which may further increase C4efficiency.
Characterising the short-term habituation of event-related evoked potentials
Authors: Mancini Flavia , Pepe Alessia , Bernacchia Alberto , Di Stefano Giulia , Mouraux André , Iannetti Gian Domenico 
Published: June 2017

AbstractFast-rising sensory events evoke a series of functionally heterogeneous event-related potentials (ERPs). Stimulus repetition at 1 Hz is known to induce a strong habituation of the largest ERP responses, the vertex waves, which are elicited by stimuli regardless of their modality7, provided that they are salient and behaviourally-relevant. In contrast, the effect of stimulus repetition on the earlier sensor)7components of ERl’s has been less explored, and the few existing results are inconsistent. To characterize how the different ERP waves habituate over time, we recorded the responses elicited by 60 identical somatosensory stimuli (activating either non-nociceptiveAβ or nociceptive A5 afferents), delivered at 1 Hz to healthy human participants. We show that the well-described spatiotemporal sequence of lateralised and vertex ERP components elicited by the first stimulus of the series is largely preserved in the smaller-amplitude, habituated response elicited by the last stimuli of the series. We also found that the earlier lateralised sensory waves habituate across the 60 trials following the same decay function of the vertex waves: this decay function is characterised by a large drop at the first stimulus repetition followed by smaller decreases at subsequent repetitions. Interestingly, the same decay functions described the habituation of ERPs elicited by repeated non-nociceptive and nociceptive stimuli. This study provides a neurophysiological characterization of the effect of prolonged and repeated stimulation on the main components of somatosensory ERPs. It also demonstrates that both lateralised waves and vertex waves are obligator}7components of ERPs elicited by non-nociceptive and nociceptive stimuli.Significance statementOur results provide a functional characterization of the decay of the different ERP components when identical somatosensory (nociceptive and non-nociceptive) stimuli are repeated at 1Hz. East-rising stimuli elicit ERPs obligator)7contributed by both early lateralised components and late vertex components, even when stimulus repetition minimizes stimulus relevance. This challenges the view that lateralised waves are not obligatorily elicited by nociceptive stimuli. Furthermore, the lateralised and vertex waves habituate to stimulus repetition following similar decay functions, which are unlikely explained in terms of fatigue or adaptation of skin receptors.