bluuebunny/crossref_metadata_2025_split huggingface dataset:
The autoimmune ecology: an update
Authors: Anaya Juan-Manuel , Restrepo-Jiménez Paula , Ramírez-Santana Carolina 
Published: February 2018

Purpose of review
The autoimmune ecology refers to the interactions between individuals and their environment leading to a breakdown in immune tolerance and, therefore, to the development of one or more autoimmune diseases in such an individual. Herein, an update is offered on four specific factors associated with autoimmune diseases, namely, vitamin D, smoking, alcohol and coffee consumption from the perspective of exposome and metabolomics.

Recent findings
Smoking is associated with an increased risk for most of the autoimmune diseases. Carbamylation of proteins as well as NETosis have emerged as possible new pathophysiological mechanisms for rheumatoid arthritis. Low-to-moderate alcohol consumption seems to decrease the risk of systemic lupus erythematosus and rheumatoid arthritis, and studies of vitamin have suggested a beneficial effect on these conditions. Coffee intake appears to be a risk factor for type 1 diabetes mellitus and rheumatoid arthritis and a protective factor for multiple sclerosis and primary biliary cholangitis.

Summary
Recent studies support the previously established positive associations between environmental factors and most of the autoimmune diseases. Nevertheless, further studies from the perspective of metabolomics, proteomics and genomics will help to clarify the effect of environment on autoimmune diseases.
Noncoding RNAs in Calcific Aortic Valve Disease: A Review of Recent Studies
Authors: Ni Wen-Juan , Wu Ying-Zhong , Ma Dong-Hong , Leng Xiao-Min 
Published: February 2018

Abstract:
Calcific aortic valve disease (CAVD) is the most common heart valve disorder in human populations. Nevertheless, there are presently no effective means for its prevention and treatment. It is therefore critical to comprehensively define key mechanisms of the disease. A major focus of cardiovascular research has been characterization of how regulation of gene expression maintains healthy physiologic status of the component tissues of the system and how derangements of gene regulation may become pathological. Recently, substantial evidence has emerged that noncoding RNAs, which are an enormous and versatile class of regulatory elements, such as microRNAs and long noncoding RNAs, have roles in onset and prognosis of CAVD. Authors of the present report have therefore here provided a summary of the current understanding of contributions made by noncoding RNAs major features of CAVD. It is anticipated that this article will serve as a valuable guide to research strategy in this field and may additionally provide both researchers and clinicians with an expanded range of CAVD-associated biomarkers.
Corneal and Anterior Chamber Morphology in Human Immunodeficiency Virus-1–Infected Patients Without Opportunistic Infections
Authors: Cetin Ebru N. , Kutlu Selda Sayın , Parca Osman , Kutlu Murat , Pekel Gökhan 
Published: February 2018

Objectives:
To evaluate corneal and anterior chamber morphology as measured by Pentacam HR in human immunodeficiency virus (HIV)-infected patients without opportunistic infections and to search for signs of accelerated aging.

Methods:
This prospective study included 41 eyes of 41 HIV-1–infected patients (study group) and 50 eyes of 50 healthy subjects (control group). Specular microscope and Pentacam HR were used for corneal and anterior chamber morphology evaluation. Corneal endothelial cell density (CECD), hexagonal cell ratio, coefficient of variation, corneal thickness, density and volume, maximum keratometry, anterior chamber volume (ACV), and anterior chamber depth (ACD) measurements were recorded for analysis.

Results:
The mean CD4 count was 428.3±231.9 (36–950) cells/mL, and the time since diagnosis was 27.5±34.1 months in the study group. The difference in anterior segment parameters was not significantly different between the study and the control groups (P>0.05). Age significantly correlated with CECD (r=−0.436, P=0.004), ACV (r=−0.570, P<0.001), ACD (r=−0.471, P=0.002), and corneal density (r=0.424, P=0.006) in the study group, whereas it did not show a significant correlation with any ocular parameters in the control group (Pearson correlation).

Conclusion:
Corneal density, CECD, ACV, and ACD showed significant correlation with age in HIV-1–infected patients. Further studies are needed to show whether ocular parameters may serve as useful tools to monitor HIV-related accelerated aging.
Racial differences in presentations and predictors of acute pain after motor vehicle collision
Authors: Beaudoin Francesca L. , Gutman Roee , Zhai Wanting , Merchant Roland C. , Clark Melissa A. , Bollen Kenneth A. , Hendry Phyllis , Kurz Michael C. , Lewandowski Christopher , Pearson Claire , O'Neil Brian , Datner Elizabeth , Mitchell Patricia , Domeier Robert , McLean Samuel A. 
Published: February 2018

AbstractAfrican Americans experience a greater burden of acute pain than non-Hispanic white individuals across of variety of acute medical conditions, but it is unknown whether this is the case after trauma. We evaluated pain, pain-related characteristics (eg, peritraumatic distress), and analgesic treatment in 2 cohorts of individuals (African American [n = 931] and non-Hispanic white [n = 948]) presenting to the emergency department (ED) after a motor vehicle collision. We performed a propensity-matched analysis (n = 796 in each group) to assess racial differences in acute pain in the ED. In multivariable models conducted within the matched sample, race was associated with moderate to severe axial pain (odds ratio [OR] 3.2; 95% confidence interval [CI]: 2.1-5.0,P< 0.001) and higher average numerical rating scale scores (1.3; 95% CI: 1.1-1.6;P< 0.001). After adjustment for pain and other covariates, non-Hispanic white patients were more likely to receive an opioid analgesic in the ED (OR 2.0; 95% CI: 1.4-3.0,P< 0.001) or at discharge (OR 4.9; 95% CI: 3.4-7.1,P< 0.001) and also less likely to receive an NSAID in the ED (OR 0.54; 95% CI: 0.38-0.78;P= 0.001) or at discharge (0.31; 95% CI: 0.43-0.84). Racial differences in the severity of acute posttraumatic pain after a motor vehicle collision are not explained by factors such as socioeconomic status or crash characteristics. Despite a higher burden of acute pain, African Americans were less likely to receive opioid analgesics and more likely to receive NSAIDs. Further work is needed to understand the relationship between pain severity, disparities in analgesic treatment, and longer term outcomes, such as post–motor vehicle collision chronic pain.
Endothelial cell biology of Endoglin in hereditary hemorrhagic telangiectasia
Authors: Sugden Wade W. , Siekmann Arndt F. 
Published: February 2018

Purpose of reviewMutations in theEndoglin(Eng) gene, an auxiliary receptor in the transforming growth factor beta (TGFβ)-superfamily signaling pathway, are responsible for the human vascular disorder hereditary hemorrhagic telangiectasia (HHT) type 1, characterized in part by blood vessel enlargement. A growing body of work has uncovered an autonomous role forEngin endothelial cells. We will highlight the influence ofEngon distinct cellular behaviors, such as migration and shape control, which are ultimately important for the assignment of proper blood vessel diameters.Recent findingsHow endothelial cells establish hierarchically ordered blood vessel trees is one of the outstanding questions in vascular biology. Mutations in components of the TGFβ-superfamily of signaling molecules disrupt this patterning and cause arteriovenous malformations (AVMs).Engis a TGFβ coreceptor enhancing signaling through the type I receptorAlk1. Recent studies identified bone morphogenetic proteins (BMPs) 9 and 10 as the primary ligands forAlk1/Eng. Importantly,EngpotentiatedAlk1pathway activation downstream of hemodynamic forces. New results furthermore revealed howEngaffects endothelial cell migration and cell shape control in response to these forces, thereby providing new avenues for our understanding of AVM cause.SummaryWe will discuss the interplay ofEngand hemodynamic forces, such as shear stress, in relation toAlk1receptor activation. We will furthermore detail how this signaling pathway influences endothelial cell behaviors important for the establishment of hierarchically ordered blood vessel trees. Finally, we will provide an outlook how these insights might help in developing new therapies for the treatment of HHT.
Recent insights into vascular development from studies in zebrafish
Authors: Matsuoka Ryota L. , Stainier Didier Y.R. 
Published: February 2018

Purpose of reviewZebrafish has provided a powerful platform to study vascular biology over the past 25 years, owing to their distinct advantages for imaging and genetic manipulation. In this review, we summarize recent progress in vascular biology with particular emphasis on vascular development in zebrafish.Recent findingsThe advent of transcription activator-like effector nuclease and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome-editing technologies has dramatically facilitated reverse genetic approaches in zebrafish, as in other models. Here, we highlight recent studies on vascular development in zebrafish which mainly employed forward or reverse genetics combined with high-resolution imaging. These studies have advanced our understanding of diverse areas in vascular biology, including transcriptional regulation of endothelial cell differentiation, endothelial cell signaling during angiogenesis and lymphangiogenesis, vascular bed-specific developmental mechanisms, and perivascular cell recruitment.SummaryThe unique attributes of the zebrafish model have allowed critical cellular and molecular insights into fundamental mechanisms of vascular development. Knowledge acquired through recent zebrafish work further advances our understanding of basic mechanisms underlying vascular morphogenesis, maintenance, and homeostasis. Ultimately, insights provided by the zebrafish model will help to understand the genetic, cellular, and molecular underpinnings of human vascular malformations and diseases.
Contribution of resident and recruited macrophages in vascular physiology and pathology
Authors: Zhang Li 
Published: February 2018

Purpose of review
Macrophages are generally believed to originate entirely from the bone marrow; however, this paradigm is challenged by the discovery of yolk-sac-derived resident macrophages. Here, we provide an overview of recent advances in the ontogeny and function of resident macrophages.

Recent findings
Macrophage precursors from three distinct embryonic sources (yolk sac, fetal liver and bone marrow) are found to colonize various tissues via the blood circulation early during embryogenesis until shortly after birth. They differentiate into distinct long-lived resident macrophages in response to the expression of tissue-specific transcription factors. Resident macrophages are proficient at taking up tissue-specific cellular debris and consequently acquire tissue-specific imprints. They are primarily involved in homeostasis but can also support the functionality of various tissues. Under pathological settings, dysregulation of resident macrophages can promote disease progression.

Summary
Resident macrophages maintain themselves via in-situ proliferation under steady state. Following injury, bone marrow monocytes can contribute to the resident macrophage pool in adult animal. Embryonically and postnatally derived resident macrophages are similar but not identical: the former are more efficient at efferocytosis, whereas the latter are more competent at host defense. Thus, specific targeting of these two different resident macrophage populations may lead to better therapeutic strategies.
An Unusual Complication of Bone Wax Utilization
Authors: Fahradyan Artur , Ohanisian Levonti , Tsuha Michaela , Park Matthew J. , Hammoudeh Jeffrey A. 
Published: February 2018

Abstract
Bone wax is a commonly used hemostatic agent with minimal complications. Some of the known complications include inflammation, granuloma formation, infection, and impaired osteogenesis. Several clinical reports of bone wax migration have also been reported. In this paper, the authors present a rare patient of bone wax migration intracranially in a 6-year-old patient who initially underwent craniotomy for the evacuation of subdural hematoma and repair of depressed skull fracture. The patient then underwent craniotomy scalp scar revision several months later. Postoperatively he developed short-term memory loss, apraxia, and word finding difficulties. The imaging findings were consistent with the presence of a foreign body centered in the posterior aspect of the left middle temporal gyrus, which was surgically removed and found to be bone wax. The patient recovered well with complete improvement of his neurologic symptoms.
New Ways of “Seeing” the Mechanistic Heterogeneity of Multiple Sclerosis Plaque Pathogenesis
Authors: Meltzer Ethan I. , Costello Fiona E. , Frohman Elliot M. , Frohman Teresa C. 
Published: February 2018

Background:
Over the past few decades, we have witnessed a transformation with respect to the principles and pathobiological underpinnings of multiple sclerosis (MS). From the traditional rubric of MS as an inflammatory and demyelinating disorder restricted to central nervous system (CNS) white matter, our contemporary view has evolved to encompass a broader understanding of the variable mechanisms that contribute to tissue injury, in a disorder now recognized to affect white and grey matter compartments.

Evidence Acquisition:
A constellation of inflammation, ion channel derangements, bioenergetic supply: demand mismatches within the intra-axonal compartment, and alterations in the dynamics and oximetry of blood flow in CNS tissue compartments are observed in MS. These findings have raised questions regarding how histopathologic heterogeneity may influence the diverse clinical spectrum of MS; and, accordingly, how individual treatment needs vary from 1 patient to the next.

Results:
We are now on new scaffolding in MS; one that promises to translate key clinical and laboratory observations to the application of emerging patient-centered therapies.

Conclusions:
This review highlights our current knowledge of the underlying disease mechanisms in MS, explores the inflammatory and neurodegenerative consequences of tissue damage, and examines physiologic factors that contribute to bioenergetic homeostasis within the CNS of affected patients.
Effect of Fascia Penetration on Sensory Nerve Conduction in the Superficial Radial Nerve
Authors: Park Hye Jung , Yoon Joon Shik , Rhee Won Ihl , Kim Jea Won , Yang Seung Nam , Won Sun Jae 
Published: February 2018

Purpose:The aim of this study was to identify the effects of fascia penetration on superficial radial sensory nerve action potential amplitude.Methods:The penetration point (PP) at which the nerve penetrated the brachioradialis fascia and became superficial was observed using ultrasonography. The sensory nerve action potential amplitude was measured at five points: the penetration point, 2 and 4 cm proximal to the PP, and 2 and 4 cm distal to the PP.Results:The sensory nerve action potential amplitude at the penetration point and at 2 and 4 cm distal to the PP was significantly larger than that at 2 and 4 cm proximal to the PP. The largest amplitude was obtained 2 cm distal to the PP.Conclusions:The sensory nerve action potential of the superficial radial nerve changes significantly around the fascia penetration point.
Cost-effectiveness of a Ceramide-Infused Skin Barrier Versus a Standard Barrier
Authors: Berger Ariel , Inglese Gary , Skountrianos George , Karlsmark Tonny , Oguz Mustafa 
Published: February 2018

PURPOSE:
To assess the cost-effectiveness of a ceramide-infused skin barrier (CIB) versus other skin barriers (standard of care) among patients who have undergone ostomy creation.

DESIGN:
Cost-effectiveness analysis, based on a decision-analytic model that was estimated using data from the ADVOCATE (A Study Determining Variances in Ostomy Skin Conditions And The Economic Impact) trial, which investigated stoma-related healthcare costs over 12 weeks among patients who recently underwent fecal ostomy, and from other sources.

SUBJECTS AND SETTING:
Analysis was based on a hypothetical cohort of 1000 patients who recently underwent fecal ostomy; over a 1-year period, 500 patients were assumed to use CIB and 500 were assumed to use standard of care.

METHODS:
We adapted a previous economic model to estimate expected 1-year costs and outcomes among persons with a new ostomy assumed to use CIB versus standard of care. Outcomes of interest included peristomal skin complications (PSCs) (up to 2 during the 1-year period of interest) and quality-adjusted life days (QALDs); QALDs vary from 1, indicating a day of perfect health to 0, indicating a day with the lowest possible health (deceased). Subjects were assigned QALDs on a daily basis, with the value of the QALD on any given day based on whether the patient was experiencing a PSC. Costs included those related to skin barriers, ostomy accessories, and care of PSCs. The incremental cost-effectiveness of CIB versus standard of care was estimated as the incremental cost per PSC averted and QALD gained, respectively; net monetary benefit of CIB was also estimated. All analyses were run using the perspective of an Australian payer.

RESULTS:
On a per-patient basis, use of CIB was expected over a 1-year period to result in 0.16 fewer PSCs, an additional 0.35 QALDs, and a savings of A$180 (Australian dollars, US $137) in healthcare costs all versus standard of care. Management with CIB provided a net monetary benefit (calculated as the product of maximum willingness to pay for 1 QALD times additional QALDs with CIB less the incremental cost of CIB) of A$228 (US $174). Probabilistic sensitivity analysis was also completed; it revealed that 97% of model runs resulted in fewer expected PSCs with CIB; 92% of these runs resulted in lower expected costs with CIB.

CONCLUSIONS:
Findings suggest that the CIB is a cost-effective skin barrier for persons living with an ostomy.
Estimating sleep parameters using an accelerometer without sleep diary
Authors: van Hees V.T. , Sabia S. , Jones S.E. , Wood A.R. , Anderson K.N. , Kivimäki M. , Frayling T.M. , Pack A. I. , Bucan M , Trenell M.I. , Mazzotti Diego R. , Gehrman P. R. , Singh-Manoux B. A. , Weedon M. N. 
Published: February 2018

AbstractWrist worn raw-data accelerometers are used increasingly in large scale population research. We examined whether sleep parameters can be estimated from these data in the absence of sleep diaries. Our heuristic algorithm uses the variance in estimated z-axis angle and makes basic assumptions about sleep interruptions. Detected sleep period time window (SPT-window), was compared against sleep diary in 3752 participants (range=60-82years) and polysomnography in sleep clinic patients (N=28) and in healthy good sleepers (N=22). The SPT-window derived from the algorithm was 10.9 and 2.9 minutes longer compared with sleep diary in men and women, respectively. Mean C-statistic to detect the SPT-window compared to polysomnography was 0.86 and 0.83 in clinic-based and healthy sleepers, respectively. We demonstrated the accuracy of our algorithm to detect the SPT-window. The value of this algorithm lies in studies such as UK Biobank where a sleep diary was not used.
Quantitative understanding of molecular competition as a hidden layer of gene regulatory network
Authors: Yuan Ye , Wei Lei , Hu Tao , Li Shuailin , Cheng Tianrun , Lei Jinzhi , Xie Zhen , Zhang Michael Q. , Wang Xiaowo 
Published: February 2018

AbstractMolecular competition is ubiquitous, essential and multifunctional throughout diverse biological processes. Competition brings about trade-offs of shared limited resources among the cellular components, and it thus introduce a hidden layer of regulatory mechanism by connecting components even without direct physical interactions. By abstracting the analogous competition mechanism behind diverse molecular systems, we built a unified coarse-grained competition motif model to systematically compare experimental evidences in these processes and analyzed general properties shared behind them. We could predict in what molecular environments competition would reveal threshold behavior or display a negative linear dependence. We quantified how competition can shape regulator-target dose-response curve, modulate dynamic response speed, control target expression noise, and introduce correlated fluctuations between targets. This work uncovered the complexity and generality of molecular competition effect, which might act as a hidden regulatory mechanism with multiple functions throughout biological networks in both natural and synthetic systems.
Analysis of global and site-specific radiation damage in cryo-EM
Authors: Hattne Johan , Shi Dan , Glynn Calina , Zee Chih-Te , Gallagher-Jones Marcus , Martynowycz Michael W. , Rodriguez Jose A. , Gonen Tamir 
Published: February 2018

SummaryMicro-crystal electron diffraction (MicroED) is an emerging method in cryo-EM for structure determination using nanocrystals. It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
Dissection of the microProtein miP1 floral repressor complex in Arabidopsis
Authors: Rodrigues Vandasue L. , Dolde Ulla , Straub Daniel , Eguen Tenai , Botterweg-Paredes Esther , Sun Bin , Hong Shinyoung , Graeff Moritz , Li Man-Wah , Gendron Joshua M. , Wenkel Stephan 
Published: February 2018

SUMMARYMicroProteins have emerged as potent regulators of transcription factor activity. Here we use a combination of forward genetics and proteomics to dissect the miP1a/b microProtein complex that acts to delay the floral transition in Arabidopsis. The microProteins miP1a and miP1b can bridge an interaction between the flowering promoting factor CONSTANS (CO) and the TOPLESS (TPL) co-repressor protein to represses flowering. We find that the JUMONJI14 (JMJ14) histone demethylase is part of this repressor complex that can initiate chromatin changes in FLOWERING LOCUS T (FT) gene, the direct target of CO. Plants with mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on the activity of CO, supporting a role for CO in this repressive complex. When mis-expressed at the shoot apex, CO can induce early flowering only in the jmj14 background. Our results indicate that the repressor acts in the shoot apical meristem to keep it in an undifferentiated state until the leaf-derived florigen signal induces the conversion into a floral meristem.