bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoumbilicoplasty with a Superiorly Based Abdominal Skin Flap
Authors: Tessler Oren , Bourn Lynn , Khoobehi Kamran , Walters Jules , Jansen David 
Published: April 2018

Summary:
We propose a neoumbilicoplasty technique that can be applied when the umbilical stalk becomes disrupted during an abdominoplasty. This case used surgical concepts that involved progressive thinning of the flap in a 3-cm radius around the neoumbilicus, with increased thinning toward the neoumbilical position. This was followed with suture tacking of the thinned abdominal flap to create a concavity around the neoumbilicus. A longer “U” shaped incision was created and also sutured down to abdominal wall to recreate an umbilical “floor” with the adjacent skin sutured to the superior-based flap to construct the walls of the neoumbilicus. An aesthetically pleasing umbilicus resulted with high patient satisfaction and a lack of postoperative complications. There were no additional scars extending beyond the umbilical region.
Proceedings of the 2017 International Forum on Gonococcal Infections and Resistance in Shenzhen, China
Authors: Chen Xiang-Sheng 
Published: April 2018

Abstract
The 2017 International Forum on Gonococcal Infections and Resistance (2017 IFGIR) was held at Shenzhen, China from September 17, 2017, to September 19, 2017. The key objectives of the conference were to review and analyze the epidemiological profiles of gonococcal infections and antimicrobial resistance (AMR) at global, regional, and national levels; to share and discuss findings from ongoing and completed research studies; and to identify research needs to respond to the spread of gonococcal infections and AMR. The following contents were presented at the conference: global estimates of infections with Neisseria gonorrhoeae; global, regional and country status of gonococcal AMR; molecular techniques for predicting gonococcal AMR and the use of these technologies to enhance gonococcal AMR surveillance and clinical management; and updates on therapeutic approaches to gonococcal AMR.
Do-Not-Resuscitate Orders in the Neonatal ICU: Experiences and Beliefs Among Staff*
Authors: Arzuaga Bonnie H. , Wraight C. Lydia , Cummings Christy L. , Mao Wenyang , Miedema David , Brodsky Dara D. 
Published: April 2018

Objectives:
Studies in adult patients have shown that do-not-resuscitate orders are often associated with decreased medical intervention. In neonatology, this phenomenon has not been investigated, and how do-not-resuscitate orders potentially affect clinical care is unknown.

Design:
Retrospective medical record data review and staff survey responses about neonatal ICU do-not-resuscitate orders.

Setting:
Four academic neonatal ICUs.

Subjects:
Clinical staff members working in each neonatal ICU.

Interventions:
Survey response collection and analysis.

Measurements and Main Results:
Participating neonatal ICUs had 14–48 beds and 120–870 admissions/yr. Frequency range of do-not-resuscitate orders was 3–11 per year. Two-hundred fifty-seven surveys were completed (46% response). Fifty-nine percent of respondents were nurses; 20% were physicians. Over the 5-year period, 44% and 17% had discussed a do-not-resuscitate order one to five times and greater than or equal to 6 times, respectively. Fifty-seven percent and 22% had cared for one to five and greater than or equal to 6 patients with do-not-resuscitate orders, respectively. Neonatologists, trainees, and nurse practitioners were more likely to report receiving training in discussing do-not-resuscitate orders or caring for such patients compared with registered nurses and respiratory therapists (p < 0.001). Forty-one percent of respondents reported caring for an infant in whom interventions had been withheld after a do-not-resuscitate order had been placed without discussing the specific withholding with the family. Twenty-seven percent had taken care of an infant in whom interventions had been withdrawn under the same circumstances. Participants with previous experiences withholding or withdrawing interventions were more likely to agree that these actions are appropriate (p < 0.001).

Conclusions:
Most neonatal ICU staff report experience with do-not-resuscitate orders; however, many, particularly nurses and respiratory therapists, report no training in this area. Variable beliefs with respect to withholding and withdrawing care for patients with do-not-resuscitate orders exist among staff. Because neonatal ICU patients with do-not-resuscitate orders may ultimately survive, withholding or withdrawing interventions may have long-lasting effects, which may or may not coincide with familial intentions.
Alkaline Phosphatase Activity and Endotoxemia After Infant Cardiothoracic Surgery
Authors: Davidson Jesse A. , Urban Tracy T. , Tong Suhong , Maddux Aline , Hill Gerald , Frank Benjamin S. , Watson John D. , Jaggers James , Simões Eric A. F. , Wischmeyer Paul 
Published: April 2018

ABSTRACT

Objective:
Infant cardiopulmonary bypass (CPB) increases intestinal permeability leading to endotoxemia. Alkaline phosphatase (AP) reduces endotoxin toxicity in vitro but its effects on endotoxemia in human disease are poorly understood. We assessed the association between serum AP activity and endotoxemia in infants undergoing CPB and determined the effect of ex vivo addition of AP on endotoxemia.

Methods:
Prospective cohort study of 62 infants ≤120 days of age undergoing CPB. AP activity and Endotoxin Activity Assay (EAA) were measured pre-operatively, during rewarming, and 24 h after cardiac intensive care unit admission. In 22 subjects, EAA was measured in pre-operative and rewarming whole blood samples with/without addition of 1,600 U/L of human liver AP.

Results:
AP activity decreased during CPB (mean decrease 94.8U/L; P < 0.0001). Median EAA was 0.41 pre-operation, rose to 0.52 (P < 0.05) during rewarming, and remained stably elevated at 24 h. Subjects with low pre-operative AP activity had significantly higher pre-operative (0.47 vs. 0.36; P < 0.05) and rewarming (0.59 vs. 0.43; P < 0.01) EAA with a trend toward higher EAA at 24 h (0.52 vs. 0.45; P = 0.12). Subjects with low rewarming AP activity showed similar differences that did not reach statistical significance. Ex vivo addition of human liver AP decreased pre-operative EAA by 29% (P < 0.001) and rewarming EAA by 51% (P < 0.0001).

Conclusion:
Endotoxemia is common in infants undergoing CPB. Native AP activity and endotoxemia are inversely related and ex vivo addition of exogenous AP reduces whole blood EAA. Future research should evaluate AP as a therapy to reduce the harmful effects of endotoxemia following infant CPB.
Health literacy and quality of physician-trauma patient communication: Opportunity for improvement
Authors: Dameworth Jonathan L. , Weinberg Jordan A. , Goslar Pamela W. , Stout Dana J. , Israr Sharjeel , Jacobs Jordan V. , Gillespie Thomas L. , Thompson Terrell M. , Petersen Scott R. 
Published: April 2018

BACKGROUND
Although physician-patient communication and health literacy (HL) have been studied in diverse patient groups, there has been little focus on trauma patients. A quality improvement project was undertaken at our Level I trauma center to improve patient perception of physician-patient communication, with consideration of the effect of HL. We report the first phase of this project, namely the reference level of satisfaction with physician-patient communication as measured by levels of interpersonal care among patients at an urban Level I trauma center.

METHODS
Level I trauma center patients were interviewed during hospitalization (August 2016 to January 2017). Short Assessment of Health Literacy tool was used to stratify subjects by deficient versus adequate HL. Interpersonal Processes of Care survey was administered to assess perception of physician-patient communication. This survey allowed patients to rate physician-patient interaction across six domains: “clarity,” “elicited concerns,” “explained results,” “worked together (on decision making),” “compassion and respect,” and “lack of discrimination by race/ethnicity.” Each is scored on a five-point scale. Frequencies of “top-box” (5/5) scores were compared for significance (p < 0.05) between HL-deficient and HL-adequate patients.

RESULTS
One hundred ninety-nine patients participated. Average age was 42 years, 33% female. Forty-nine (25%) patients had deficient HL. The majority of patients in both groups rated communication below 5/5 across all domains except “compassion and respect” and “lack of discrimination by race/ethnicity.” Health literacy-deficient patients were consistently less likely to give physicians top-box scores, most notably in the “elicited concerns” domain (35% vs. 54%, p = 0.012).

CONCLUSION
Health literacy-deficient patients appear relatively less satisfied with physician communication, particularly with respect to perceiving that their concerns are being heard. Overall, however, the majority of patients in both groups were unlikely to score physician communication in the “top box.” Efforts to improve physician-trauma patient communication are warranted, with attention directed toward meeting the needs of HL-deficient patients.

LEVEL OF EVIDENCE
Prognostic/Epidemiologic, level I.
HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor
Authors: Schiffer Lucas , Azhar Rimsha , Shepherd Lori , Ramos Marcel , Geistlinger Ludwig , Huttenhower Curtis , Dowd Jennifer B , Segata Nicola , Waldron Levi 
Published: April 2018

AbstractPhase 1 of the NIH Human Microbiome Project (HMP) investigated 18 body subsites of 239 healthy American adults, to produce the first comprehensive reference for the composition and variation of the “healthy” human microbiome. Publicly-available data sets from amplicon sequencing of two 16S rRNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.
Magnesium suppresses defects in the formation of 70S ribosomes as well as in sporulation caused by lack of several individual ribosomal proteins
Authors: Akanuma Genki , Yamazaki Kotaro , Yagishi Yuma , Iizuka Yuka , Ishizuka Morio , Kawamura Fujio , Kato-Yamada Yasuyuki 
Published: April 2018

ABSTRACTIndividually, the ribosomal proteins L1, L23, L36 and S6 are not essential for cell proliferation ofB. subtilis, but the absence of any one of these ribosomal proteins causes a defect in the formation of the 70S ribosomes and a reduced growth rate. In mutant strains individually lacking these ribosomal proteins, the cellular Mg2+content was significantly reduced. The deletion of YhdP, an exporter of Mg2+, and overexpression of MgtE, the main importer of Mg2+, increased the cellular Mg2+content and restored the formation of 70S ribosomes in these mutants. The increase in the cellular Mg2+content improved the growth rate of the ΔrplA(L1) and the ΔrplW(L23) mutant but did not restore those of the ΔrpmJ(L36) and the ΔrpsF(S6) mutants. The lack of L1 caused a decrease in the production of Spo0A, the master regulator of sporulation, resulting in a decreased sporulation frequency. However, deletion ofyhdPand overexpression ofmgtEincreased the production of Spo0A and partially restored the sporulation frequency in the ΔrplA(L1) mutant. These results indicate that Mg2+can partly complement the function of several ribosomal proteins, probably by stabilizing the conformation of the ribosome.IMPORTANCEWe previously reported that an increase in the cellular Mg2+content can suppress defects in 70S ribosome formation and growth rate caused by the absence of ribosomal protein L34. In the present study, we demonstrated that even in mutants lacking individual ribosomal proteins other than L34 (L1, L23, L36 and S6), an increase in the cellular Mg2+content could restore the 70S ribosome formation. Moreover, the defect in sporulation caused by the absence of L1 was also suppressed by an increase in the cellular Mg2+content. These findings indicate that at least part of the function of these ribosomal proteins can be complemented by Mg2+, which is essential for all living cells.
Repulsive Guidance Molecule Acts in Axon Branching inCaenorhabditis elegans
Authors: Tsutsui Kaname , Kim Hon-Song , Kubota Yukihiko , Shibata Yukimasa , Tian Chenxi , Liu Jun , Nishiwaki Kiyoji 
Published: April 2018

ABSTRACTRepulsive guidance molecules (RGMs) are evolutionarily conserved proteins implicated in repulsive axon guidance. Here we report the function of theCaenorhabditis elegansortholog DRAG-1 in axon branching. The axons of hermaphrodite-specific neurons (HSNs) branch at the region abutting the vulval muscles and innervate these muscles to control egg laying. Thedrag-1mutants exhibited defects in HSN axon branching in addition to a small body size and egg laying–defective phenotype. DRAG-1 expression in the hypodermal cells was required for the branching of these axons. The C-terminal glycosylphosphatidylinositol anchor of DRAG-1 was important for its function. Genetic analyses suggested that the membrane receptor UNC-40, but neither SMA-1/βH-spectrin nor SMA-5/MAP kinase 7, acts in the same pathway with DRAG-1 in HSN branching. We propose that DRAG-1 expressed in the hypodermis signals via the UNC-40 receptor expressed in HSNs to elicit branching activity of HSN axons.
Autoregulation of theS. mutansSloR metalloregulator is constitutive and driven by an independent promoter
Authors: Monette Patrick , Brach Richard , Cowan Annie , Winters Roger , Weisman Jazz , Seybert Foster , Goguen Kelsey , Chen James , Glasfeld Arthur , Spatafora Grace 
Published: April 2018

AbstractStreptococcus mutans, one of ∼600 bacterial species in the human oral cavity, is among the most acidogenic constituents of the plaque biofilm. Considered to be the primary causative agent of dental caries,S. mutansharbors a 25kDa SloR metalloregulatory protein which controls metal ion transport across the bacterial cell membrane to maintain essential metal ion homeostasis. The expression of SloR derives, in part, from transcriptional readthrough of thesloABCoperon which encodes a Mn2+/Fe2+ABC transport system. Herein, we describe the details of thesloABCpromoter that drives this transcription, as well as a novel independent promoter in an intergenic region (IGR) that contributes to downstreamsloRexpression. RT-PCR studies supportsloRtranscription that is independent ofsloABCexpression, and the results of 5′ RACE revealed asloRtranscription start site in the IGR from which the −10 and −35 promoter regions were predicted. The results of gel mobility shift assays support direct SloR binding to the IGR, albeit with lower affinity than SloR binding to thesloABCRpromoter. Function of thesloRpromoter was validated in qRT-PCR experiments. Interestingly,sloRexpression was not significantly impacted when grown in the presence of high manganese, whereas expression of thesloABCoperon was repressed under these conditions. The results ofin vitrotranscription studies support SloR-mediated transcriptional-activation ofsloRand -repression ofsloABC.Taken together, these findings implicate SloR as a bifunctional regulator that repressessloABCpromoter activity and encouragessloRtranscription from an independent promoter.ImportanceTooth decay is a ubiquitous infectious disease that is especially pervasive in underserved communities worldwide.S. mutans-induced carious lesions cause functional, physical, and/or aesthetic impairment in the vast majority of adults, and in 60-90% of schoolchildren in industrialized countries. Billions of dollars are spent annually on caries treatment, and productivity losses due to absenteeism from the workplace are significant. Research aimed at alleviatingS. mutans-induced tooth decay is important because it can address the socioeconomic disparity that is associated with dental cavities and improve overall general health which is inextricably linked to oral health. Research focused on theS. mutansSloR metalloregulatory protein can guide the development of novel therapeutics and so alleviate the burden of dental cavities.
Microscale tracking of coral disease reveals timeline of infection and heterogeneity of polyp fate
Authors: Gavish Assaf R. , Shapiro Orr H. , Kramarsky-Winter Esti , Vardi Assaf 
Published: April 2018

AbstractCoral disease is often studied at scales ranging from single colonies to the entire reef. This is particularly true for studies following disease progression through time. To gain a mechanistic understanding of key steps underlying infection dynamics, it is necessary to study disease progression, and host-pathogen interactions, at relevant microbial scales. Here we provide a dynamic view of the interaction between the model coral pathogen Vibrio coralliilyticus and its coral host Pocillopora damicornis at unprecedented spatial and temporal scales. This view is achieved using a novel microfluidics-based system specifically designed to allow microscopic study of coral infection in-vivo under controlled environmental conditions. Analysis of exudates continuously collected at the system’s outflow, allows a detailed biochemical and microbial analyses coupled to the microscopic observations of the disease progression. The resulting multilayered dataset provides the most detailed description of a coral infection to-date, revealing distinct pathogenic processes as well as the defensive behavior of the coral host. We provide evidence that infection in this system occurs following ingestion of the pathogen, and may then progress through the gastrovascular system. We further show infection may spread when pathogens colonize lesions in the host tissue. Copious spewing of pathogen-laden mucus from the polyp mouths results in effective expulsion of the pathogen from the gastrovascular system, possibly serving as a first line of defense. A secondary defense mechanism entails the severing of calicoblastic connective tissues resulting in the controlled isolation of diseased polyps, or the survival of individual polyps within infected colonies. Further investigations of coral-pathogen interactions at these scales will help to elucidate the complex interactions underlying coral disease, as we as the versatile adaptive response of the coral ecosystems to fluctuating environments.
Cultivation of 146 Clinical Strains ofNocardiaspecies
Authors: Han Xiang Y. , Holmes Arginea J. , Golshan Mohammad A. 
Published: April 2018

ABSTRACTNocardiaspecies generally grow well on culture media in contrast to limited metabolic activities. Yet there are rare studies that have examined systematically the effect of culture media on the clinical recovery of these Gram-positive branching bacilli, particularly in relation to many recently described or revisedNocardiaspecies. We analyzed 146 clinicalNocardiastrains, of 24 species, recovered at the University of Texas M. D. Anderson Cancer Center from 2002-2018 for their growth on culture media. Among media setups to culture routine bacteria, fungi, and acid-fast bacilli (AFB), the AFB media alone recovered 35 strains as did fungal media with 26 strains and routine media with 10 strains. Seventy five strains were recovered on two and three media setups. On AFB media mostNocardia novastrains (24 of 29) grew, significantly more than all other strains did. Likewise, all four strains ofNocardia mikamiiwere cultivated solely on AFB media. Fungal media yielded all six strains ofNocardia wallaceithat were resistant to tobramycin and/or amikacin; this growth could be explained by the presence of gentamycin in one fungal medium. Specimen source also affected the recovery: moreNocardiastrains grew on every media setup from normally sterile specimens than from nonsterile specimens. These results suggest that diverse culture media support the growth of manyNocardiaspecies. The better recoveries of these organisms from AFB media and fungal media are likely attributable to decontamination of specimens on AFB culture, incorporation of selective antimicrobial agents into the media, and prolonged incubation.
Analysis of the genetic basis of height in large Jewish nuclear families
Authors: Zeevi Danny , Bloom Joshua S. , Sadhu Meru J. , Yehuda Adi Ben , Zangen David , Levy-Lahad Ephra , Kruglyak Leonid 
Published: April 2018

AbstractDespite intensive study, most genetic factors that contribute to variation in human height remain undiscovered. We conducted a family-based linkage study of height in a unique cohort of very large nuclear families from a founder (Jewish) population. This design allowed for increased power to detect linkage, compared to previous family-based studies. We identified loci that together explain an estimated 6% of the variance in height. We showed that these loci are not tagging known common variants associated with height. Rather, we suggest that the observed signals arise from variants with large effects that are rare globally but elevated in frequency in the Jewish population.
Direct inference of base-pairing probabilities with neural networks improves RNA secondary structure prediction with pseudoknots
Authors: Akiyama Manato , Sakakibara Yasubumi , Sato Kengo 
Published: April 2018

AbstractMotivationExisting approaches for predicting RNA secondary structures depend on howto decompose a secondary structure into substructures, so-called the architecture, to define their parameter space. However, the architecture has not been sufficiently investigated especially for pseudoknotted secondary structures.ResultsIn this paper, we propose a novel algorithm to directly infer base-pairing probabilities with neural networks that does not depend on the architecture of RNA secondary structures, followed by performing the maximum expected accuracy (MEA) based decoding algorithms; Nussinov-style decoding for pseudoknot-free structures, and IPknot-style decoding for pseudoknotted structures. To train the neural networks connected to each base-pair, we adopt a max-margin framework, called structured support vector machines (SSVM), as the output layer. Our benchmarks for predicting RNA secondary structures with and without pseudoknots show that our algorithm achieves the best prediction accuracy compared with existing methods.AvailabilityThe source code is available at https://github.com/keio-bioinformatics/neuralfold/.Contactsatoken@bio.keio.ac.jp