bluuebunny/crossref_metadata_2025 huggingface dataset:
Pulsatile Flushing
Authors: Boord Christina
Published: December 2018

Flushing is an essential strategy in maintaining patency of a central vascular access device. However, there is no standard practice regarding flushing techniques. Pulsatile flushing has been discussed in the past based on the principles of fluid dynamics. Recently, in vitro studies regarding pulsatile flushing have shed light on the usefulness of this technique. A critique of the current literature regarding pulsatile flushing compared with standard continuous flushing is presented here.
Use of Asynchronous Audio Feedback in Discussion Boards With Online RN-BSN Students
Authors: London Julie
Published: December 2018

Background

Learning management systems are offering more complex technological tools to educators than ever before. One of these tools gaining interest is embedding audio files in discussion boards so the student can hear verbal feedback from the instructor. This study explored the effect of embedding audio feedback in discussion boards with RN-BSN students.

Purpose

The purpose of this research was to examine the instructional methodology of text-only versus audio-only feedback in discussion boards and the subsequent impact on teaching presence and sense of community in the course room.

Methods

A quasi-experimental posttest design with a comparison group was used to examine the impact of using audio-only compared with text-only feedback in discussion boards.

Results

Multiple regression statistics consistently indicated that text-only feedback was preferred by online RN-BSN students in discussion boards over audio-only feedback.

Conclusion

Use of text-only feedback in online course discussion boards increases the perception of teaching presence and sense of community.
SSTR2a Is a Useful Diagnostic Marker for Follicular Dendritic Cells and Their Related Tumors
Authors: Tao Li-Li , Huang Yu-Hua , Chen Yao-Li , Yu Guang-Yin , Yin Wei-Hua
Published: December 2018

SSTR2a, a member of the somatostatin receptor family, has been used as a diagnostic marker of meningioma. However, the expression of SSTR2a in follicular dendritic cells (FDCs) and their related tumors has been poorly characterized. This study aimed to assess the potential diagnostic utility of measuring SSTR2a immunohistochemically in FDCs and their related tumors. We evaluated whole-tissue sections from 182 cases including 83 lymphoid reactive follicular hyperplasias, 17 follicular lymphomas, 18 follicular dendritic cell sarcomas (FDCSs), 6 inflammatory pseudotumor-like FDCSs, and 58 other histologic mimics. Immunohistochemistry for SSTR2a and other FDC markers (CD21, CD23, CD35, clusterin, and podoplanin) were performed in all 182 cases. Diffuse membrane immunoreactivity for SSTR2a in FDCs was observed in 100% of follicular lymphoma and FDCS cases and in 96.4% of the reactive follicular hyperplasias cases. Notably, the positive rate of SSTR2a in FDCSs was higher than that of CD21 (88.9%), CD23 (77.8%), CD35 (94.4%), clusterin (55.6%), and podoplanin (94.4%). All inflammatory pseudotumor-like FDCSs were negative for SSTR2a. The histologic mimics were negative for SSTR2a, except for 1 leiomyosarcoma case that showed focal (~10%) positive expression for SSTR2a. Overall, our findings indicate that SSTR2a is a highly sensitive and diagnostically useful marker for FDCs and FDCSs. Furthermore, immunohistochemistry for SSTR2a may be helpful to distinguish FDCSs from inflammatory pseudotumor-like FDCSs and other histologic mimics. Moreover, our findings suggest that SSTR2a may be a potential therapeutic target for treatment of FDCSs.
Total Muscle Coverage versus AlloDerm Human Dermal Matrix for Implant-Based Breast Reconstruction
Authors: Ivey J. Simon , Abdollahi Hamid , Herrera Fernando A. , Chang Eric I.
Published: December 2018

Background:

Prosthetic breast reconstruction is the most common method for treatment of patients undergoing mastectomy. Acellular dermal matrix has become more popular in implant-based breast reconstruction.

Methods:

The authors conducted a retrospective review of all patients undergoing prosthetic breast reconstruction between August of 2002 and December of 2013. Patients were analyzed in terms of demographics, fill volumes, number of expansions, costs, and complications.

Results:

A total of 284 patients underwent mastectomy surgery with 481 implant-based breast reconstructions. Four hundred eight tissue expanders had total muscle coverage, whereas 73 had AlloDerm. The rate of overall complications and major complications was significantly higher in the AlloDerm group: 20.5 percent versus 8.8 percent (p = 0.005), and 13.7 percent versus 5.1 percent (p = 0.0001), respectively. The mean initial fill volume was significantly lower in the total muscle coverage group compared to the acellular dermal matrix group (54 ± 47 versus 167 ± 139; p = 0.00003), resulting in a higher number of expansions (8.1 versus 5.8; p = 0.000051) and longer time to full expansion (60.2 days versus 43.3 days; p = 0.0002). This did not translate into a faster time to expander exchange (162.4 days versus 162.3 days; p = 0.13). Use of AlloDerm added a mean cost of $2217 for each breast.

Conclusions:

Implant-based breast reconstruction has evolved with the advent of acellular dermal matrices. Although the use of acellular dermal matrix allows increased initial fill volumes and fewer total expansions, there is an increased risk of complications and increased costs, especially in patients undergoing bilateral reconstruction. Total muscle coverage remains an excellent option for providing quality breast reconstruction without increased complications.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
A New Method for Partial Breast Reconstruction: 3-Year New Zealand Experience
Authors: Harman John , Govender Stan , Simpson John , Benjamin Benji
Published: December 2018

In New Zealand, oncoplastic surgery is common, but partial breast reconstruction presents challenges for radiation therapy targeting. Tissue rearrangement creates ambiguity when targeting the tumor bed, with resultant overestimation of treatment volumes. Thus, adoption of advanced methods of radiation therapy have been hindered. This pilot study describes use of a novel three-dimensional implant that provides a scaffolding for tissue ingrowth during partial breast reconstruction and delineates the tumor bed more precisely to assist radiation planning and mammographic surveillance. After informed consent, 15 women were implanted with the three-dimensional bioabsorbable implant. The device was sutured to the tumor bed during lumpectomy, and tissue flaps were mobilized and attached to the implant. Visualization of the marker and radiation treatment volumes were recorded and compared. The implant provided volume replacement and helped to maintain breast contour. Cosmetic outcomes were excellent; no device- or radiation-related complications occurred. One patient had a postoperative hematoma that resolved after percutaneous drainage; there were no postoperative infections. Three-year follow-up shows no tumor recurrences and no untoward effects. When compared to conventional radiation targeting, use of the implant showed that a greater than 50 percent reduction in treatment volume was possible in some cases. Three-year mammograms show no significant artifact, normal tissue ingrowth, and minimal fibrosis. This study describes a method of oncoplastic breast reconstruction using an implantable device that marks the site of tumor excision and provides for volume replacement with tissue ingrowth. Patients tolerated it well, and radiation therapy planning, positioning, and treatment were facilitated.
Detailed Vascular Anatomy and Flap Harvest Technique of the Serratus Anterior/Rib Composite Flap
Authors: Matsumoto Hiroshi , Shinaoka Akira , Ohtsuka Aiji , Kimata Yoshihiro
Published: December 2018

Background:

The hemodynamics of blood flowing from the anterior serratus to the ribs has yet to be analyzed in detail in serratus anterior/rib composite flaps. The authors focused on new blood circulation, whereby the slip arteries branched from the serratus anterior branch, off the thoracodorsal artery and the intercostal arteries, directly through the interconnecting vessels (axial route). The authors analyzed in detail the hemodynamics of serratus anterior/rib composite flaps and developed a new method for flap elevation.

Methods:

The axial route was identified and analyzed by performing macroscopic autopsies of formalin perfusion-fixed cadavers involving three-dimensional computed tomographic angiography and vascular corrosion casting. Flap elevation was performed with new blood circulation, which included the axial route, and blood flow was evaluated using indocyanine green fluorescence angiography.

Results:

The interconnecting vessels penetrated the intercostal muscles at a mean distance of 4.5 cm from the anterior margin of the attachment sites of the serratus anterior muscle to the ribs and at a mean distance of 7.4 cm from the costochondral junction. The interconnecting vessels had a mean diameter of 0.5 mm. Vascular corrosion casting helped identify multiple capillaries that were distributed from the intercostal arteries to the periosteum of the ribs. In addition, intraoperative indocyanine green fluorescence angiography confirmed blood flow from the slip arteries to the intercostal arteries.

Conclusion:

Good blood flow in harvested graft tissue can be achieved by including the axial route with the periosteal blood circulation at the rib attachment sites of the serratus anterior in a serratus anterior/rib composite flap.
Baseline Lymphatic Dysfunction Amplifies the Negative Effects of Lymphatic Injury
Authors: Hespe Geoffrey E. , Ly Catherine L. , Kataru Raghu P. , Mehrara Babak J.
Published: December 2018

Background:

Genetic mutations and obesity increase the risk of secondary lymphedema, suggesting that impaired lymphatic function before surgical injury may contribute to disease pathophysiology. Previous studies show that obesity not only decreases lymphatic function, but also markedly increases pathologic changes, such as swelling, fibroadipose deposition, and inflammation. However, although these reports provide circumstantial evidence supporting the hypothesis that baseline lymphatic defects amplify the effect of lymphatic injury, the mechanisms regulating this association remain unknown.

Methods:

Baseline lymphatic morphology, leakiness, pumping, immune cell trafficking, and local inflammation and fibroadipose deposition were assessed in wild-type and Prox1-haploinsufficient (Prox1+/-) mice, which have previously been shown to have abnormal vasculature without overt evidence of lymphedema. In subsequent experiments, wild-type and Prox1+/- mice underwent popliteal lymph node dissection to evaluate the effect of lymphatic injury. Repeated testing of all variables was conducted 4 weeks postoperatively.

Results:

At baseline, Prox1+/- mice had dilated, leaky lymphatic vessels corresponding to low-grade inflammation and decreased pumping and transport function, compared with wild-type mice. Popliteal lymph node dissection resulted in evidence of lymphedema in both Prox1+/- and wild-type mice, but popliteal lymph node dissection–treated Prox1+/- mice had increased inflammation and decreased lymphatic pumping.

Conclusions:

Subclinical lymphatic dysfunction exacerbates the pathologic changes of lymphatic injury, an effect that is multifactorial and related to increased lymphatic leakiness, perilymphatic accumulation of inflammatory cells, and impaired pumping and transport capacity. These findings suggest that preoperative testing of lymphatic function may enable clinicians to more accurately risk-stratify patients and design targeted preventative strategies.
An Analysis of Differences in the Number of Children for Female and Male Plastic Surgeons
Authors: Furnas Heather J. , Li Alexander Y. , Garza Rebecca M. , Johnson Debra J. , Bajaj Anureet K. , Kalliainen Loree K. , Weston Jane S. , Song David H. , Chung Kevin C. , Rohrich Rod J.
Published: December 2018

Background:

Historically, the structure of surgical programs discourages women interested in both surgery and motherhood from pursuing a surgical career, and women plastic surgeons have been more likely than men to have no children or to have fewer, later in life. Female plastic surgery trainees now constitute over one-third of residents, and pregnancy rates can be expected to rise, but with women now a majority in medical schools, the specialty’s maternity policies may be deterring interested women from entering the specialty. A survey study was conducted to measure reproductive outcomes and to identify current disparities between women and men plastic surgeons.

Methods:

An anonymous electronic survey was distributed to American Society of Plastic Surgeons members and candidates, allowing comparisons of men’s and women’s responses. Differences were tested by the Fisher’s exact and chi-square tests.

Results:

Compared with male respondents, women were more likely than men to have no biological children (45.1 percent versus 23.1 percent). They were nearly twice as likely to delay having children because of the demands of training (72.6 percent versus 39.2 percent) and to experience infertility (26.3 percent versus 12.5 percent). Among the childless plastic surgeons, women were 11 times more likely to say they did not want children compared with men (20.1 percent versus 1.8 percent).

Conclusions:

Poor institutional maternity support results in a persistent, wide gap in reproductive outcomes between female and male plastic surgeons. Establishing a universal, comprehensive parental support policy is essential to closing that gap.
Pediatric Nasoorbitoethmoid Fractures: Cause, Classification, and Management
Authors: Lopez Joseph , Luck J. D. , Faateh Muhammad , Macmillan Alexandra , Yang Robin , Siegel Gabriel , Susarla Srinivas M. , Wang Howard , Nam Arthur J. , Milton Jacqueline , Grant Michael P. , Redett Richard , Tufaro Anthony P. , Kumar Anand R. , Manson Paul N. , Dorafshar Amir H.
Published: December 2018

Background:

Currently, there is a paucity of information on the presentation and proper management of pediatric nasoorbitoethmoid fractures. The purpose of this study was to examine the incidence, cause, associated injuries, and management of these fractures. Furthermore, the authors sought to assess outcomes after transnasal wiring or suture canthopexy for type III nasoorbitoethmoid fractures.

Methods:

A retrospective cohort review was performed of all patients with nasoorbitoethmoid fractures who presented to a Level I trauma center from 1990 to 2010. Charts and computed tomographic imaging were reviewed, and nasoorbitoethmoid fractures were labeled based on the Markowitz-Manson classification system. Patient fracture patterns, demographics, characteristics, and outcomes were recorded. Univariate and multivariate methods were used to compare groups.

Results:

A total of 63 pediatric patients were identified in the study period. The sample’s mean age was 8.78 ± 4.08 years, and 28.6 percent were girls. The sample included 18 type I injuries, 28 type II injuries, and 17 type III injuries. No significant demographic differences were found between patients with type I, II, and III fractures (p > 0.05). Operative intervention was pursued in 16.7, 46.4, and 82.4 percent of type I, II, and III nasoorbitoethmoid fractures, respectively. In patients with type III nasoorbitoethmoid fractures, no patients with transnasal wiring developed telecanthus.

Conclusions:

Pediatric nasoorbitoethmoid fractures are uncommon injuries. Type I fracture can often be treated with close observation. However, type II and III injury patterns should be evaluated for operative intervention. Transnasal wiring is an effective method to prevent traumatic telecanthus deformity in type III fracture patterns.
Botulinum Toxin versus Placebo: A Meta-Analysis of Prophylactic Treatment for Migraine
Authors: Bruloy Eva , Sinna Raphael , Grolleau, M.D. Jean-Louis , Bout-Roumazeilles Apolline , Berard Emilie , Chaput Benoit
Published: December 2018

Background:

The purpose of this study was to assess the efficacy of botulinum toxin in reducing the frequency of migraine headaches.

Methods:

The MEDLINE, Embase, and Cochrane Library databases were searched to identify randomized, double-blind, placebo-controlled trials that compared patients receiving botulinum toxin versus placebo injections in the head and neck muscles, for the preventive treatment of migraine. The primary outcome was change in the number of headache episodes per month from baseline to 3 months.

Results:

There were 17 studies including a total of 3646 patients. Overall analysis reported a tendency in favor of botulinum toxin over placebo at 3 months, with a mean difference in the change of migraine frequency of −0.23 (95 percent CI, −0.47 to 0.02; p = 0.08). The reduction in frequency of chronic migraines was significant, with a mean differential change of −1.56 (95 percent CI, −3.05 to −0.07; p = 0.04). Analysis of chronic migraine frequency was also significant after 2 months. The findings also highlighted an improvement of the patient’s quality of life at 3 months in the botulinum toxin group (p < 0.00001). Further adverse events were traced in the botulinum toxin type A group with a statistically significant risk ratio of 1.32 (p = 0.002).

Conclusions:

This meta-analysis reveals that botulinum toxin type A injections are superior to placebo for chronic migraines after 3 months of therapy. For the first time, a real benefit in patient quality of life is demonstrated with only few and mild adverse events.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, II.
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

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.
Consistency, Inconsistency and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome Scale Metabolic Modelling
Authors: Pham Nhung , Van Heck Ruben , van Dam Jesse , Schaap Peter , Saccenti Edoardo , Suarez-Diez Maria
Published: December 2018

Genome scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in eleven biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping.
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

ABSTRACT

Chromosomal 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

Background

It 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.

Results

The 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.

Conclusions

We 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

We 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.
From the inside out: An epibiotic Bdellovibrio predator with an expanded genomic complement
Authors: Deeg Christoph M , Le Tan T , Zimmer Matthias M , Suttle Curtis A
Published: December 2018

Bdellovibrio and like organisms are abundant environmental predators of prokaryotes that show a diversity of predation strategies, ranging from intra-periplasmic to epibiotic predation. The novel epibiotic predator Bdellovibrio qaytius was isolated from a eutrophic freshwater pond in British Columbia, where it was a continual part of the microbial community. Bdellovibrio qaytius was found to preferentially prey on the beta-proteobacterium Paraburkholderia fungorum. Despite its epibiotic replication strategy, B. qaytius encodes a complex genomic complement more similar to periplasmic predators as well as several biosynthesis pathways not previously found in epibiotic predators. Bdellovibrio qaytius is representative of a widely distributed basal cluster within the genus Bdellovibrio, suggesting that epibiotic predation might be a common predation type in nature and ancestral to the genus.
Cloud Bursting Galaxy: Federated Identity and Access Management
Authors: Jalili Vahid , Afgan Enis , Taylor James , Goecks Jeremy
Published: December 2018

Motivation

Large 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.

Results

We 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 Implementation

Freely 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/cloudauthz

Contact

jalili@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

We 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

One 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 statement

The 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.
MAVS polymers smaller than 80 nm induce mitochondrial membrane remodeling and interferon signaling
Authors: Hwang Ming-Shih , Boulanger Jerome , Howe Jonathan , Albecka Anna , Pasche Mathias , Muresan Leila , Modis Yorgo
Published: December 2018

Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Oligomerization of RIG-I-like receptors on cytosolic dsRNA nucleates self-assembly of the mitochondrial antiviral signaling protein (MAVS). In the current signaling model, the caspase recruitment domains of MAVS form helical fibrils that self-propagate like prions to promote signaling complex assembly. However, there is no conclusive evidence that MAVS forms fibrils in cells or with the transmembrane anchor present. We show here with super-resolution light microscopy that MAVS activation by dsRNA induces mitochondrial membrane remodeling. Quantitative image analysis at imaging resolutions as high as 32 nm shows that in the cellular context MAVS signaling complexes and the fibrils within them are smaller than 80 nm. The transmembrane domain of MAVS is required for its membrane remodeling, interferon signaling and proapoptotic activities. We conclude that membrane tethering of MAVS restrains its polymerization and contributes to mitochondrial remodeling and apoptosis upon dsRNA sensing.
HiCluster: A Robust Single-Cell Hi-C Clustering Method Based on Convolution and Random Walk
Authors: Zhou Jingtian , Ma Jianzhu , Chen Yusi , Cheng Chuankai , Bao Bokan , Peng Jian , Sejnowski Terrence , Dixon Jesse , Ecker Joseph
Published: December 2018

3D genome structure plays a pivotal role in gene regulation and cellular function. Single-cell analysis of genome architecture has been achieved using imaging and chromatin conformation capture methods such as Hi-C. To study variation in chromosome structure between different cell types, computational approaches are needed that can utilize sparse and heterogeneous single-cell Hi-C data. However, few methods exist that are able to accurately and efficiently cluster such data into constituent cell types. Here, we describe HiCluster, a single-cell clustering algorithm for Hi-C contact matrices that is based on imputations using linear convolution and random walk. Using both simulated and real data as benchmarks, HiCluster significantly improves clustering accuracy when applied to low coverage Hi-C datasets compared to existing methods. After imputation by HiCluster, structures similar to topologically associating domains (TADs) could be identified within single cells, and their consensus boundaries among cells were enriched at the TAD boundaries observed in bulk samples. In summary, HiCluster facilitates visualization and comparison of single-cell 3D genomes.
Salience-driven value construction for adaptive choice under risk
Authors: Spitmaan Mehran , Chu Emily , Soltani Alireza
Published: December 2018

Decisions we face in real life are inherently risky and can result in one of many possible outcomes. However, most of what we know about choice under risk is based on studies that use options with only two possible outcomes (simple gambles), so it remains unclear how the brain constructs reward values for more complex risky options faced in real life. To address this question, we combined experimental and modeling approaches to examine choice between pairs of simple gambles and pairs of three-outcome gambles in male and female human subjects. We found that subjects evaluated individual outcomes of three-outcome gambles by multiplying functions of reward magnitude and probability. To construct the overall value of each gamble, however, most subjects differentially weighted possible outcomes based on either reward magnitude or probability. These results reveal a novel dissociation between how reward information is processed when evaluating complex gambles: valuation of each outcome is based on an integrated value whereas combination of possible outcomes relies on a single piece of reward information. We show that differential weighting of possible outcomes enabled subjects to make decisions more easily and quickly. Together, these findings reveal a plausible mechanism for how salience, in terms of possible reward magnitude or probability, can influence the construction of subjective values for complex gambles. They also point to separable neural mechanisms for how reward value controls choice and attention in order to allow for more adaptive decision making.
Measuring urinary cortisol and testosterone levels in male Barbary macaques: A comparison of EIA and LC-MS
Authors: Rincon Alan , Ostner Julia , Heistermann Michael , Deschner Tobias
Published: December 2018

The development of methods to quantify hormones from non-invasively collected samples such as urine or feces has facilitated endocrinology research on wild-living animals. To ensure that hormone measurements are biologically meaningful, method validations are highly recommended for each new species or sample matrix. Our aim was to validate three commonly used enzyme immunoassays (EIA), one for analysis of cortisol and two for analysis of testosterone, to assess adrenocortical and gonadal activity, respectively, from the urine of male Barbary macaques. We compared EIA and liquid chromatography--mass spectrometry (LC-MS) results to determine if the EIA measurements truly reflect levels of the target hormone and to determine if cross-reactivities with other steroids were potentially confounding results. Furthermore, we conducted a biological validation of testosterone to ensure that both EIA and LC-MS were able to capture physiologically meaningful differences in hormone levels. We found that cortisol measured by EIA correlated strongly with cortisol measured by LC-MS in both adult and immature males, without the need for deconjugation of steroids in the urine. Both testosterone EIAs correlated strongly with LC-MS in adult males, but only if steroids in the urine were deconjugated by enzymatic hydrolysis prior to analysis. However, in immature males, EIA and LC-MS results did not correlate significantly. Further correlation analyses suggest this is likely due to cross-reactivity of the testosterone antibody with other adrenal steroids such as cortisol, DHEA, and likely others, which are present at much higher concentrations relative to testosterone in immature males. Testosterone levels were significantly higher in adult compared to immature males as measured by LC-MS but not as measured by EIA. Taken together, our results suggest that the testosterone EIAs are suitable to assess gonadal activity in adult but not immature males, and only if a hydrolysis of the urine is conducted prior to analysis.
Pupillary responses to affective words in bilinguals' first versus second language
Authors: Toivo Wilhelmiina , Scheepers Christoph
Published: December 2018

Late bilinguals often report less emotional involvement in their second language, a phenomenon called reduced emotional resonance in L2. The present study measured pupil dilation in response to high- versus low-arousing words (e.g., riot vs. swamp) in German-English and Finnish-English late bilinguals, both in their first and in their second language. A third sample of English monolingual speakers (tested only in English) served as a control group. To improve on previous research, we controlled for lexical confounds such as length, frequency, emotional valence, and abstractness – both within and across languages. Results showed no appreciable differences in post-trial word recognition judgements (98% recognition on average), but reliably stronger pupillary effects of the arousal manipulation when stimuli were presented in participants' first rather than second language. This supports the notion of reduced emotional resonance in L2. Our findings are unlikely to be due to differences in stimulus-specific control variables or to potential word-recognition difficulties in participants' second language. Linguistic relatedness between first and second language (German-English vs. Finnish-English) was also not found to have a modulating influence.
Co-allocation Action of Azospirillum brasilense Inoculation and Seed Priming for Improving Germination and Seedling Growth in Aged Grass Seeds
Authors: Liu Xu , Chen Zhao , Gao Yani , Liu Qian , Zhou Wennan , Zhao Tian , Jiang Wenbo , Cui Xuewen , Cui Jian , Wang Quanzhen
Published: December 2018

Germination of seeds during the transportation or after prolonged storage naturally and inevitably decreases because of ageing, but germination potential can be partially restored with seed priming treatments. A novel attempt was made to investigate the effects of combined treatments and to optimize the conditions for naturally aged seeds of tall fescue (Festuca arundinacea Schreb.), orchardgrass (Dactylis glomerata L.) and Russian wild rye (Psathyrostachys juncea (Fisch.) Nevski) using an orthogonal activity level experimental design [factor A: Azospirillum brasilense concentration, factor B: three seed priming treatments (H2O, MgSO4 and H2O2) and factor C: different priming times]. Multivariate regression model analysis was applied to determine the interactive effects of pairwise factors (A and C) and to optimize experimental conditions. The results showed that the mixed treatments positively affected seed germination and seedling growth. The three seed priming treatments were the dominant factors for germination promotion, whereas the bacterial concentration had the largest effect on seedling growth, especially root elongation. The combined results of all determined attributes showed that A. brasilense bio-priming with H2O2 priming constituted the optimal combination. The optimal bacterial concentration of A. brasilense and the time of seed priming were 52.3 × 106 colony forming units (CFU) mL-1 and 17.0 h, respectively. We also discussed the physiological mechanisms that could repair aged seeds: the malondialdehyde content and antioxidant enzyme (superoxide dismutase, peroxidase, catalase and ascorbate peroxidase) activities were affected.