bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of Secondary Calvarial Defects with Ex Situ Split Calvarial Bone Grafts: Long-Term Evaluation of Outcomes
Authors: Frautschi Russell S. , Halasa Brianna , Kwiecien Grzegorz , Krebs Jillian , Recinos Violette , Onwuzulike Kaine , Rampazzo Antonio , Papay Francis , Zins James E. , Bassiri Gharb Bahar 
Published: December 2018

Background:
Autologous bone continues to represent the first choice for reconstruction of calvarial defects. However, unanswered questions remain on the natural history of the graft and the influence of patient-related risk factors. This study investigated the outcomes of skull reconstruction with split calvarial bone graft, examining the natural history and stratifying the risk of unfavorable results.

Methods:
Patients who underwent cranioplasty with split calvarial bone graft between 1982 and 2016 at the Cleveland Clinic were analyzed, recording demographics, comorbidities, indications, size and location of defect, and outcomes including complications and reoperations. Changes in graft thickness were analyzed using computed tomographic and magnetic resonance imaging scans.

Results:
Forty-one patients with an average age of 33.2 years, cranial defect size of 68 cm2, and mean follow-up of 28 months were included. The majority of patients (85 percent) had significant risk factors, with 43 percent suffering prior infection. Seventy-three percent of patients experienced successful restoration. A major complication was recorded in 26.8 percent; resorption occurred in 19.5 percent of patients (in 75 percent only at the recipient site), with 9.8 percent requiring reoperation. Patients with one or more risk factors or a smoking history were more likely to experience a complication. The mean ratio of the graft to the bicortical donor bone thickness was 0.48 ± 0.17 for the recipient site and 0.57 ± 0.10 for the donor site at an average radiographic follow-up of 11.9 ± 10.9 years.

Conclusions:
This study demonstrated a 73.2 percent first-attempt success rate in a high-risk population. The grafts maintain thickness over time, with no evidence of bone hypertrophy. Defect characteristics and patient systemic factors appear to be important variables influencing success.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Technological Advances in Lymphatic Surgery: Bringing to Light the Invisible
Authors: Singhal Dhruv , Tran Bao N. , Angelo Joseph P. , Lee Bernard T. , Lin Samuel J. 
Published: December 2018

Summary:Lymphatic surgery has become an integral and flourishing component of the field of plastic surgery. The diversity of ongoing technological innovations in perioperative imaging, including intraoperative dyes and cameras, allows plastic surgeons to work at the supermicrosurgical level. This study aims to highlight innovations that have shaped and will continue to revolutionize the perioperative management of the lymphatic surgery patient in the future. As additional advances emerge, we need a systematic and objective way to evaluate the efficacy and clinical integration readiness of such technologies. Undoubtedly, these technologies will help lymphatic surgery trend toward increasing objectivity, which will be critical for continued evolution and advancement.
Prepectoral Breast Reconstruction in the Setting of Postmastectomy Radiation Therapy: An Assessment of Clinical Outcomes and Benefits
Authors: Sbitany Hani , Gomez-Sanchez Clara , Piper Merisa , Lentz Rachel 
Published: December 2018

Background:
Prepectoral breast reconstruction following mastectomy has become a more widely performed technique in recent years because of its numerous benefits for women. These include full pectoralis muscle preservation, reduced loss of strength, reduced pain, and elimination of animation deformity. As with any breast reconstruction technique, widespread adoption is dependent on a low morbidity profile in the setting of postmastectomy radiation therapy, as this adjuvant therapy is routine in breast cancer treatment. The authors assess the clinical outcomes of patients undergoing postmastectomy radiation therapy following prepectoral breast reconstruction, and compare these to outcomes of patients undergoing postmastectomy radiation therapy with submuscular reconstruction.

Methods:
A single surgeon’s experience with immediate prepectoral breast reconstruction, followed by postmastectomy radiation therapy, from 2015 to 2017 was reviewed. Patient demographics and incidence of complications during the tissue expander stage were assessed. In addition, the morbidity profile of these patients was compared to that of patients undergoing submuscular/dual-plane reconstruction and postmastectomy radiation therapy over the same period.

Results:
Over 3 years, 175 breasts underwent immediate prepectoral reconstruction, and 236 breasts underwent immediate submuscular/dual-plane reconstruction. Overall rates of adjuvant radiation therapy (postmastectomy radiation therapy) were similar between prepectoral [26 breasts (14.9 percent)] and submuscular [31 breasts (13.1 percent)] (p = 0.6180) reconstruction. There were no significant differences in complication rates between the two reconstructive cohorts, in the setting of postmastectomy radiation therapy, including rates of explantation (15.4 percent versus 19.3 percent; p = 0.695).

Conclusions:
Prepectoral breast reconstruction is a safe and effective option in the setting of postmastectomy radiation therapy. The morbidity profile is similar to that encountered with submuscular reconstruction in this setting.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
A bird’s white-eye view on avian sex chromosome evolution
Authors: Leroy Thibault , Anselmetti Yoann , Tilak Marie-Ka , Bérard Sèverine , Csukonyi Laura , Gabrielli Maëva , Scornavacca Céline , Milá Borja , Thébaud Christophe , Nabholz Benoit 
Published: December 2018

ABSTRACTChromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, aZosterops borbonicus and a Z. pallidus. Then, we organized theZ. borbonicusscaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genusZosterops(1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms (πN/πS) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.
Direct Repeats Co-occur with Few Short Dispersed Repeats in Plastid Genome of A Spikemoss, Selaginella vardei (Selaginellaceae, Lycophyta)
Authors: Zhang Hong-Rui , Zhang Xian-Chun , Xiang Qiao-Ping 
Published: December 2018

AbstractBackgroundIt is hypothesized that the highly conserved inverted repeat (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organizations, whereas the mechanism of the occurrence and stability maintenance of the newly reported direct repeats (DR) structure was yet awaiting further exploration. Here we introduced the DR structure of plastome in Selaginella vardei (Selaginellaceae, Lycophyta), trying to elucidate the mechanism of DR occurrence and stability maintenance.ResultsThe plastome of S. vardei is 121,254 bp in length and encodes 76 different genes, of which 62 encode proteins, 10 encode tRNAs and four encode rRNAs. Unexpectedly, the two identical rRNA gene regions (13,893 bp) are arranged into DR, and a ca. 50-kb trnN-trnF inversion spanning one DR copy exists in S. vardei, comparing to the typical IR organization of Isoetes flaccida (Isoetaceae, Lycophyta). We find extremely rare short dispersed repeats (SDRs) in plastome of S. vardei and is confirmed in its closely related species S. indica. The occurrence time of DR in Selaginellaceae is estimated at late Triassic (ca. 215 Ma) based on the phylogenetic framework of land plants.ConclusionsWe propose that the unconventional DR structure, co-occurred with extremely few SDRs, plays key role in maintaining the stability of plastome, and reflects a relic of the environmental upheaval during extinction event. We suggest that the ca. 50-kb inversion resulted in the DR structure, and recombination between DR regions is confirmed to generate multipartite subgenomes and diverse multimers, which shed lights on the diverse structures in plastome of land plants.
Epistatic interactions can moderate the antigenic effect of substitutions in hemagglutinin of influenza H3N2 virus
Authors: Koel Björn F. , Burke David F. , der Vliet Stefan van , Bestebroer Theo M. , Rimmelzwaan Guus F. , Osterhaus Albert D.M.E. , Smith Derek J. , Fouchier Ron A.M. 
Published: December 2018

AbstractWe previously showed that single amino acid substitutions at seven positions in hemagglutinin determined major antigenic change of influenza H3N2 virus. Here, the impact of two such substitutions was tested in eleven representative H3 hemagglutinins to investigate context-dependence effects. The antigenic effect of substitutions introduced at hemagglutinin position 145 was fully independent of the amino acid context of the representative hemagglutinins. Antigenic change caused by substitutions introduced at hemagglutinin position 155 was variable and context-dependent. Our results suggest that epistatic interactions with contextual amino acids in the hemagglutinin can moderate the magnitude of antigenic change.
Cloud Bursting Galaxy: Federated Identity and Access Management
Authors: Jalili Vahid , Afgan Enis , Taylor James , Goecks Jeremy 
Published: December 2018

AbstractMotivationLarge biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users.ResultsWe have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g., username, password, API key), instead relying on automatically-generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use.Availability and ImplementationFreely available for academic and commercial use under the open-source Academic Free License (https://opensource.org/licenses/AFL-3.0) from the following Github repositories:https://github.com/galaxyproject/galaxyandhttps://github.com/galaxyproject/cloudauthzContactjalili@ohsu.edu,goecksj@ohsu.edu
Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers
Authors: Langelier Charles , Graves Michael , Kalantar Katrina , Caldera Saharai , Durrant Robert , Fisher Mark , Backman Richard , Tanner Windy , DeRisi Joseph L. , Leung Daniel T. 
Published: December 2018

AbstractWe engaged metagenomic next generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to understand global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion ofEscherichiaspecies within gut microbial communities without impacting diversity.
C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi’s Sarcoma Associated Herpesvirus (KSHV)
Authors: Rodriguez William , Srivastav Aman , Muller Mandy 
Published: December 2018

AbstractOne striking characteristic of certain herpesviruses is their ability to induce rapid and widespread RNA decay in order to gain access to host resources. This phenotype is induced by viral endoribonucleases, including SOX in KSHV, muSOX in MHV68, BGLF5 in EBV and vhs in HSV-1. Here, we performed comparative RNA-seq upon expression of these herpesviral endonucleases in order to characterize their effect on the host transcriptome. Consistent with previous reports, we found that approximately two thirds of transcripts are downregulated in cells expressing any of these viral endonucleases. Among transcripts spared from degradation, we uncovered a cluster of transcripts that systematically escape degradation from all tested endonucleases. Among these escapees, we identified C19ORF66 and reveal that like the previously identified escapees, this transcript is protected from degradation by its 3’UTR. We then show that C19ORF66, a known anti-viral protein, is a potent KSHV restriction factor, suggesting that its ability to escape viral cleavage may be an important component of the host response to viral infection. Collectively, our comparative approach is a powerful tool to pinpoint key regulators of the viral-host interplay and led us to uncover a novel KSHV regulator.
WITHDRAWN: The miR-338-3p involve in response to acute radiation syndrome by targeting DYRK2 in Tibet minipig
Authors: Yu-Jue Wang , Min Yue , Kai Guo , Shao-Jie Wu , Yu-Guang Tian 
Published: December 2018

Withdrawal statementThe authors have withdrawn this manuscript because the operation process of animal tumors does not comply with relevant ethical requirements. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
A Pivotal Role for Thiamine Deficiency in the Expression of Neuroinflammation Markers in Models of Alcohol‐Related Brain Damage
Authors: Toledo Nunes Polliana , Vedder Lindsey C. , Deak Terrence , Savage Lisa M. 
Published: December 2018

BackgroundAlcohol‐related brain damage (ARBD) is associated with neurotoxic effects of heavy alcohol use and nutritional deficiency, in particular thiamine deficiency (TD), both of which induce inflammatory responses in brain. Although neuroinflammation is a critical factor in the induction of ARBD, few studies have addressed the specific contribution(s) of ethanol (EtOH) versus TD.MethodsAdult rats were randomly divided into 6 conditions: chronic EtOH treatment (CET) where rats consumed a 20% v/v solution of EtOH for 6 months; CET with injections of thiamine (CET + T); severe pyrithiamine‐induced TD (PTD); moderate PTD; moderate PTD during CET; and pair‐fed controls. After the treatments, the rats were split into 3 recovery phase time points: the last day of treatment (time point 1), acute recovery (time point 2: 24 hours posttreatment), and delayed recovery (time point 3: 3 weeks posttreatment). At these time points, vulnerable brain regions (thalamus, hippocampus, frontal cortex) were collected and changes in neuroimmune markers were assessed using a combination of reverse transcription polymerase chain reaction and protein analysis.ResultsCET led to minor fluctuations in neuroimmune genes, regardless of the structure being examined. In contrast, PTD treatment led to a profound increase in neuroimmune genes and proteins within the thalamus. Cytokine changes in the thalamus ranged in magnitude from moderate (3‐fold and 4‐fold increase in interleukin‐1β [IL‐1β] and IκBα) to severe (8‐fold and 26‐fold increase in tumor necrosis factor‐α and IL‐6, respectively). Though a similar pattern was observed in the hippocampus and frontal cortex, overall fold increases were moderate relative to the thalamus. Importantly, neuroimmune gene induction varied significantly as a function of severity of TD, and most genes displayed a gradual recovery across time.ConclusionsThese data suggest an overt brain inflammatory response by TD and a subtle change by CET alone. Also, the prominent role of TD in the immune‐related signaling pathways leads to unique regional and temporal profiles of induction of neuroimmune genes.
Genetic Influences on the Amount of Cell Death in the Neural Tube of BXD Mice Exposed to Acute Ethanol at Midgestation
Authors: Théberge Emilie T. , Baker Jessica A. , Dubose Candis , Boyle Julia K. , Balce Kristina , Goldowitz Dan , Hamre Kristin M. 
Published: December 2018

BackgroundFetal alcohol spectrum disorders (FASD) have a strong genetic component although the genes that underlie this are only beginning to be elucidated. In the present study, one of the most common phenotypes of FASD, cell death within the early developing neural tube, was examined across a genetic reference population in a reverse genetics paradigm with the goal of identifying genetic loci that could influence ethanol (EtOH)‐induced apoptosis in the early developing neural tube.MethodsBXD recombinant inbred mice as well as the parental strains were used to evaluate genetic differences in EtOH‐induced cell death after exposure on embryonic day 9.5. Dams were given either 5.8 g/kg EtOH or isocaloric maltose‐dextrin in 2 doses via intragastric gavage. Embryos were collected 7 hours after the initial exposure and cell death evaluated via TUNEL staining in the brainstem and forebrain. Genetic loci were evaluated using quantitative trait locus (QTL) analysis at GeneNetwork.org.ResultsSignificant strain differences were observed in the levels of EtOH‐induced cell death that were due to genetic effects and not confounding variables such as differences in developmental maturity or cell death kinetics. Comparisons between the 2 regions of the developing neural tube showed little genetic correlation with the QTL maps exhibiting no overlap. Significant QTLs were found on murine mid‐chromosome 4 and mid‐chromosome 14 only in the brainstem. Within these chromosomal loci, a number of interesting candidate genes were identified that could mediate this differential sensitivity including Nfia (nuclear factor I/A) and Otx2 (orthodenticle homeobox 2).ConclusionsThese studies demonstrate that the levels of EtOH‐induced cell death occur in strain‐ and region‐dependent manners. Novel QTLs on mouse Chr4 and Chr14 were identified that modulate the differential sensitivity to EtOH‐induced apoptosis in the embryonic brainstem. The genes underlying these QTLs could identify novel molecular pathways that are critical in this phenotype.
Biomarker and Genomic Risk Factors for Liver Function Test Abnormality in Hazardous Drinkers
Authors: Whitfield John B. , Zhu Gu , Madden Pamela A. F. , Montgomery Grant W. , Heath Andrew C. , Martin Nicholas G. 
Published: December 2018

BackgroundAlcohol dependence and long‐term excessive alcohol use may cause liver damage, but only some patients develop cirrhosis. Similarly, high alcohol intake without evident liver disease often but not always produces abnormal enzymatic liver function tests (LFTs), particularly gamma‐glutamyl transferase (GGT). We postulate that the factors predisposing to cirrhosis in alcoholics and to liver enzyme abnormality in drinkers are similar, and that biochemical LFTs could therefore be useful as markers of risk of alcoholic liver disease in excessive drinkers.MethodsData from participants in twin and twin‐family studies on alcohol use and dependence were used to identify 1,003 people who had reported excessive alcohol intake (28 drinks or more per week). A total of 962 of these provided blood for biochemical tests at the same time. Body mass index (BMI) and biomarkers of metabolic syndrome, inflammation, and iron stores were used in logistic regression with abnormality in serum GGT, alanine aminotransferase (ALT), or aspartate aminotransferase (AST) as outcomes. We conducted genome‐wide association analyses for GGT, ALT, and AST separately in the group reporting excessive alcohol intake (N = 951) and a low‐intake group reporting 14 drinks or fewer per week (N = 8,716), and compared results.ResultsAbnormal GGT and ALT among excessive drinkers were associated with higher BMI, triglycerides, insulin, uric acid, C‐reactive protein, ferritin, and transferrin saturation; and with lower high‐density‐lipoprotein cholesterol. Abnormal AST was associated with triglycerides, ferritin, and transferrin saturation. ALT was significantly associated with variants at reported genetic loci for alcoholic liver disease (PNPLA3, rs738409, p = 0.0076; TM6SF2, rs10401969, p = 0.0076; HSD17B13, rs10433879, p = 0.0024).ConclusionsKnown risk factors for alcoholic cirrhosis including obesity and markers of metabolic syndrome, iron overload and inflammation are associated with liver enzyme abnormality in excessive drinkers.