bluuebunny/crossref_metadata_2025 huggingface dataset:
Handwashing with soap after potential faecal contact: global, regional and country estimates
Authors: Wolf Jennyfer , Johnston Richard , Freeman Matthew C , Ram Pavani K , Slaymaker Tom , Laurenz Eric , Prüss-Ustün Annette
Published: November 2018

Background

Limited data have been available on the global practice of handwashing with soap (HWWS). To better appreciate global HWWS frequency, which plays a role in disease transmission, our objectives were to: (i) quantify the presence of designated handwashing facilities; (ii) assess the association between handwashing facility presence and observed HWWS; and (iii) derive country, regional and global HWWS estimates after potential faecal contact.

Methods

First, using data from national surveys, we applied multilevel linear modelling to estimate national handwashing facility presence. Second, using multilevel Poisson modelling on datasets including both handwashing facility presence and observed HWWS after potential faecal contact, we estimated HWWS prevalence conditional on handwashing facility presence by region. For high-income countries, we used meta-analysis to pool handwashing prevalence of studies identified through a systematic review. Third, from the modelled handwashing facility presence and estimated HWWS prevalence conditional on the presence of a handwashing facility, we estimated handwashing practice at country, regional and global levels.

Results

First, approximately one in four persons did not have a designated handwashing facility in 2015, based on 115 data points for 77 countries. Second the prevalence ratio between HWWS when a designated facility was present compared with when it was absent was 1.99 (1.66, 2.39) P <0.001 for low- and middle-income countries, based on nine datasets. Third, we estimate that in 2015, 26.2% (23.1%, 29.6%) of potential faecal contacts were followed by HWWS.

Conclusions

Many people lack a designated handwashing facility, but even among those with access, HWWS is poorly practised. People with access to designated handwashing facilities are about twice as likely to wash their hands with soap after potential faecal contact as people who lack a facility. Estimates are based on limited data.
CE: Original Research: Advance Care Planning: An Exploration of the Beliefs, Self-Efficacy, Education, and Practices of RNs and LPNs
Authors: Ludwick Ruth , Baughman Kristin R. , Jarjoura David , Kropp Denise J.
Published: November 2018

Objective: This study compared the advance care planning (ACP)–related beliefs, sense of self-efficacy, education, and practices of RNs and LPNs.

Methods: Data were extrapolated from a larger multisite study that was conducted across seven counties in one midwestern state. The sample consisted of RNs and LPNs working in 29 urban skilled nursing facilities in zip code areas with greater than 10% African American residents. The survey tool, a self-administered written questionnaire, gathered data on participants’ demographics and ACP-related beliefs, sense of self-efficacy, education, and practices. The two main outcome variables were the percentage of residents with whom a nurse discussed ACP and the timing of the most recent such discussion.

Results: A total of 136 RNs and 178 LPNs completed the survey. Multivariate mixed-model analysis of the two main outcome variables showed that negative beliefs were not significantly associated with the percentage of residents with whom nurses discussed ACP but were significantly associated with the timing of the most recent ACP discussion. Having higher levels of ACP-related self-efficacy and education were significantly and positively associated with both outcome variables. RNs and LPNs did not differ significantly in their ACP-related beliefs, but RNs reported significantly higher levels of self-efficacy and education than LPNs did.

Conclusions: There has been a paucity of research comparing RNs and LPNs regarding their ACP practices in skilled nursing facilities. Better education and policies that empower nurses to take a more active role are critical to increasing conversations about ACP. Further research exploring how the complementary roles of RNs and LPNs can be used to improve ACP processes and inform ACP policies is needed.
Utility of Urine Drug Testing in Outpatient Addiction Evaluations
Authors: Kolla Bhanu Prakash , Callizo Guillermo Leoz , Schneekloth Terry D.
Published: November 2018

Objective:

Data examining usefulness of urine drug testing in addiction settings for accurately establishing diagnoses and informing treatment is limited. In this retrospective-cohort study we examined the utility of performing urine drug testing in patients presenting for an outpatient addiction assessment.

Methods:

Urine drug testing and patient-reported substance use history were obtained from the medical record of patients who presented for an outpatient addiction evaluation. Patients who denied use of a substance within the window of detection but tested positive were considered to have misrepresented their use. Differences between patients accurately representing versus misrepresenting their use were evaluated. Sensitivity/specificity of drug tests were calculated from self-report and changes to treatment recommendations and diagnoses assessed.

Results:

One hundred and seventy-four patients (mean age = 43.35 ± 15.68 years) were included and the sample was majority male (67%). Ninety-four (54%) patients reported use of a substance within the window of detection. Of 80 patients denying recent use, 14 tested positive (8%). There were no differences in sex (P = 0.78) or age (P = 0.12); referral sources differed significantly between correct and incorrect responders (P = 0.01). Specificity varied between 96% and 99%, while sensitivity had a wider range (17%–87%). Treatment recommendations and diagnoses were altered after review of drug testing results in 1 patient (0.5%). However, in the remainder, all patients were already diagnosed with a severe substance use disorder and had received recommendations to initiate residential/outpatient substance use treatment.

Conclusions:

Among patients completing urine drug testing during outpatient substance use disorder evaluation positive screens alerted providers to undisclosed persistent substance use and potential withdrawal in 8% of the cohort and resulted in a change in diagnoses and/or treatment in 1 patient.
Trends and Related Factors of Cannabis-Associated Emergency Department Visits in the United States: 2006–2014
Authors: Shen Jay J. , Shan Guogen , Kim Pearl C. , Yoo Ji Won , Dodge-Francis Carolee , Lee Yong-Jae
Published: November 2018

Objectives:

To examine national trends and contributing factors of cannabis-associated emergency department visits in the United States.

Methods:

This pooled serial cross-sectional study used a hierarchical multivariable analysis on emergency department visit adjusting for year, patient and hospital characteristics. We analyzed 2006 to 2014 National Emergency Department Sample data that identified cannabis-associated emergency department visits among patients aged 12 years or older (n = 265,128).

Results:

Cannabis-associated emergency department visits per 100,000 emergency department discharges increased monotonically (annually by 7%). As compared with privately insured patients, Medicare, and Medicaid, uninsured patients were over 40% more likely to visit emergency department. The age group 12 to 17 had the highest risk of emergency department visits and the risk monotonically declined as the age increased. Hospitals in the South region showed the highest cannabis-associated emergency department utilization, yet trends of cannabis-associated emergency department visits increased in the West region from 15.4% to 26% over time.

Conclusions:

Cannabis-associated emergency department visits increase monotonically over time. Although vulnerable persons were identified, additional policy or regional factors should explore risks of emergency department visits associated with cannabis use.
Evaluation of a New Algorithm to Optimize Audibility in Cochlear Implant Recipients
Authors: Holden Laura K. , Firszt Jill B. , Reeder Ruth M. , Dwyer Noël Y. , Stein Amy L. , Litvak Leo M.
Published: November 2018

Objectives:

A positive relation between audibility and speech understanding has been established for cochlear implant (CI) recipients. Sound field thresholds of 20 dB HL across the frequency range provide CI users the opportunity to understand soft and very soft speech. However, programming the sound processor to attain good audibility can be time-consuming and difficult for some patients. To address these issues, Advanced Bionics (AB) developed the SoftVoice algorithm designed to remove system noise and thereby improve audibility of soft speech. The present study aimed to evaluate the efficacy of SoftVoice in optimizing AB CI recipients’ soft-speech perception.

Design:

Two studies were conducted. Study 1 had two phases, 1A and 1B. Sixteen adult, AB CI recipients participated in Study 1A. Acute testing was performed in the unilateral CI condition using a Harmony processor programmed with participants’ everyday-use program (Everyday) and that same program but with SoftVoice implemented. Speech recognition measures were administered at several presentation levels in quiet (35 to 60 dB SPL) and in noise (60 dB SPL). In Study 1B, 10 of the participants compared Everyday and SoftVoice at home to obtain feedback regarding the use of SoftVoice in various environments. During Study 2, soft-speech perception was acutely measured with Everyday and SoftVoice for 10 participants using the Naida CI Q70 processor. Results with the Harmony (Study 1A) and Naida processors were compared. Additionally, Study 2 evaluated programming options for setting electrode threshold levels (T-levels or Ts) to improve the usability of SoftVoice in daily life.

Results:

Study 1A showed significantly higher scores with SoftVoice than Everyday at soft presentation levels (35, 40, 45, and 50 dB SPL) and no significant differences between programs at a conversational level (60 dB SPL) in quiet or in noise. After take-home experience with SoftVoice and Everyday (Study 1B), 5 of 10 participants reported preferring SoftVoice over Everyday; however, 6 reported bothersome environmental sound when listening with SoftVoice at home. Results of Study 2 indicated similar soft-speech perception between Harmony and Naida processors. Additionally, implementing SoftVoice with Ts at the manufacturer’s default setting of 10% of Ms reduced reports of bothersome environmental sound during take-home experience; however, soft-speech perception was best with SoftVoice when Ts were behaviorally set above 10% of Ms.

Conclusions:

Results indicate that SoftVoice may be a potential tool for optimizing AB users’ audibility and, in turn, soft-speech perception. To achieve optimal performance at soft levels and comfortable use in daily environments, setting Ts must be considered with SoftVoice. Future research should examine program parameters that may benefit soft-speech perception when used in combination with SoftVoice (e.g., increased input dynamic range).
Anatomical Considerations to Optimize Sensory Recovery in Breast Neurotization with Allograft
Authors: Ducic Ivica , Yoon Joshua , Momeni Arash , Ahcan Uros
Published: November 2018

Background:

Breast numbness is a recognized problem following mastectomy and subsequent reconstruction. Contemporary literature acknowledges the positive role of breast neurotization, but it is characterized by a variety of technical approaches and substantial heterogeneity with respect to the degree of recovered sensibility that remains suboptimal in comparison with other sensory nerve reconstructions. This study’s purpose was to provide an anatomical basis for observed inconsistencies and therein provide a principle that can be used to develop a technical approach that will optimize sensory recovery.

Methods:

Anatomical dissections on 6 fresh cadavers, that is, 12 hemi-abdominal flaps and 12 hemi-chest dissections, were performed. The technical aspects of harvesting the abdominal flap with a nerve target, that is, inclusion of a sensory nerve branch only, recipient nerves in the chest, and the applications of allograft for acquired nerve gap reconstruction were investigated.

Results:

Abdominal flaps that include sensory-only intercostal nerve 10–12 segments and identification of recipient chest wall intercostal nerves 2–4 could be consistently performed. The dissection and extraction of the donor sensory nerve target allowed preservation of the motor rectus innervation. The acquired nerve gap was easily bridged by an interposing allograft, allowing free arch of rotation for flap inset, suitable for either single or dual neurotization.

Conclusions:

We provide a likely anatomical explanation for suboptimal sensory recovery after deep inferior epigastric perforator (DIEP) flap breast neurotization, as mixed intercostal autograft is prohibitive to maximal sensory recovery. Breast neurotization with allograft that bridges sensory donor intercostal nerves to sensory recipient intercostal nerves should anatomically optimize restoration of breast sensibility.
Localized Provoked Vulvodynia: Association With Nerve Growth Factor and Transient Receptor Potential Vanilloid Type 1 Genes Polymorphisms
Authors: Kalfon Limor , Azran Audrey , Farajun Yaniv , Golan-Hamu Oshrat , Toben Aylah , Abramov Liora , Yeshaya Arie , Yakir Orly , Zarfati Doron , Falik Zaccai Tzipora C. , Bornstein Jacob
Published: November 2018

Objective

The aim of the study was to study the associations between localized provoked vulvodynia (LPV) and several single-nucleotide polymorphisms (SNPs) in the transient receptor potential vanilloid type 1 (TRPV1), nerve growth factor (NGF), and the heparanase (HPSE) genes.

Materials and Methods

Prevalence of SNPs among 65 women with moderate or severe primary LPV (initial symptoms occur with first provoking physical contact) and 126 healthy, ethnically matched controls was analyzed in an observational case-control study. Each participant answered a questionnaire addressing familial LPV occurrence and comorbid pain conditions.

Results

Familial occurrences of LPV, temporomandibular joint (TMJ) symptoms, recurrent vaginitis, and irritable bowel syndrome were significantly higher among LPV women than healthy controls. Genotyping analyses revealed a novel, statistically significant high prevalence of polymorphism c.945G>C (rs222747) ofTRPV1and a SNP in the promoter region ofNGF(rs11102930) in LPV women compared with controls. A logistic regression model for rs222747 and rs11102930 frequent alleles indicates significant LPV association within the entire study group and Ashkenazi Jewish women, respectively. Comparison of pain conditions with frequent alleles showed the rs222747 “CC” genotype ofTRPV1associated with women with TMJ, recurrent vaginitis, and LPV.

Conclusions

Our results suggest novel genetic susceptibility to primary LPV associated with specific alleles in genesTRPV1andNGFand propose the rs222747 “C” allele ofTRPV1as a common genetic predisposition for other pain syndromes.
The Impact of Patient and Family Advisors on Critical Care Nurses’ Empathy
Authors: Cosper Pam , Kaplow Roberta , Moss Jacqueline
Published: November 2018

Objective

The objective of this study was to determine if patient and family advisors’ (PFAs) collaboration in an educational program could increase the empathy levels of intensive care unit (ICU) nurses.

Background

Data suggest that nurse empathy is on the decline. Ensuring that nurses consistently empathize with patients and families helps create positive patient experiences.

Methods

Thirty nurses participated in a PFA-designed educational intervention using simulation-based role playing. The Toronto Empathy Questionnaire (TEQ) was used to measure empathy before and after the intervention.

Results

The TEQ empathy scores increased significantly after nurses completed the PFA-designed educational program. Younger nurses (<30 years) improved on average 3.03 ± 3.6 points compared with older nurses (>30 years), who improved, on average, only 0.43 ± 2.06 points (t
24.4 = 2.46, P = .021). For the changes in TEQ scores from preintervention to postintervention, age was significantly associated with improvements in TEQ scores.

Conclusions

Patient and family advisors can positively impact empathy among ICU nurses.
Epidemiologic Assessment of Microtia in Over 23 Million Consecutive United States Births
Authors: Cabrejo Raysa , Persing John , Alperovich Michael
Published: November 2018

Purpose:

Conflicting data exist regarding the incidence, demographics, and abnormalities associated with microtia. Using a large national cohort database, a comprehensive evaluation of microtia in the United States was performed.

Methods:

The Kids’ Inpatient Database was reviewed over a 15-year consecutive period. Information regarding patient demographics, comorbidities, postoperative complications, and hospital setting was collected. Statistical tests were analyzed using independent t tests and χ
2 analysis.

Results:

A total of 23,479,792 births over 15 consecutive years from 1997 to 2012 were included in the study. Microtia was identified in 1563 births. Incidence of microtia was higher in males (P<0.01) and patients of Asian or Hispanic race (P<0.01). Patients with microtia had significantly more congenital anomalies relative to the rest of the population (P<0.01). Specifically, cardiac and genitourinary anomalies were 51 and 19 times, respectively, more likely in microtia patients. Risk of associated congenital anomalies with microtia was highest in female and Black patients. 12.6% of all microtia patients had an associated craniofacial syndrome with a comparable postsurgical course to the nonsyndromic population.

Conclusion:

This study represents the largest national, longitudinal study of microtia allowing for demographic, socioeconomic, and comorbidity commentary. By quantifying relative risk of associated congenital anomalies, it can help inform the type and utility of screening modalities when evaluating microtia patients.
Posterior Distraction First or Fronto-Orbital Advancement First for Severe Syndromic Craniosynostosis
Authors: Iida Chie , Sakamoto Yoshiaki , Miwa Tomoru , Yoshida Kazunari , Kishi Kazuo
Published: November 2018

Purpose:

Posterior calvarial vault expansion using distraction osteogenesis is performed for syndromic craniosynostosis as the first choice. This procedure allows far greater intracranial volume than fronto-orbital advancement (FOA). This study aimed to determine the most suitable timing of posterior distraction or FOA to sufficiently increase the intracranial volume and remodel the skull shape.

Patients and Methods:

From 2014 to 2017, the authors performed posterior distraction in 13 patients with syndromic craniosynostosis. Data on premature suture fusion, age at first visit, age at surgery, skull thickness, and complications were collected.

Results:

Five patients underwent posterior distraction at approximately 12 months of age and had no complications, including cerebrospinal fluid leakage or gull wing deformity. However, during the waiting period for the operation, the skull deformity continues to extend upward (turribrachycephaly). To prevent progress of the skull deformity, the authors performed the operation at approximately 6 months of age in 7 patients. However, in 3 of 7 patients whose lambdoid sutures were opening, gull wing deformity occurred. From these results, in a patient with severe Beare–Stevenson syndrome, the authors performed FOA first at 5 months of age, followed by posterior distraction at 12 months of age, and achieved favorable results.

Conclusions:

Treatment patterns are patient specific and should be tailored to premature suture fusion, specific skull deformity, and required intracranial volume of each patient.
A 10-Year Case Series of Surgically Managed Periurethral Masses at a Single Tertiary Care Institution
Authors: Wyman Allison M. , McDowell Megan , Prieto Isabel , Jackson Elisha , Bassaly Renee , Ordorica Raul , Greene Kristie A.
Published: November 2018

Objective

This study aimed to present the evaluation, diagnoses, and surgical management of symptomatic periurethral masses of women at an academic institution.

Methods

This study is an institutional review board–approved retrospective case series of women who presented with a symptomatic periurethral mass and scheduled for surgery within the Department of Urology and Female Pelvic Medicine and Reconstructive Surgery over a 10-year period (October 2003–July 2014).

Results

Fifty-nine women (mean age, 46 years; range, 22–73 years) were evaluated during the study period. Final pathology revealed 38 (64%) urethral diverticula and 21 (36%) from other benign etiologies. Of the 38 urethral diverticula, 2 (5%) were associated with adenocarcinoma and 4 (11%) with previous bulking agents. Of the 21 nondiverticula, there were 7 (12%) Skene duct cysts/abscesses, 3 (5%) Gartner duct cysts, 2 (3%) vaginal wall inclusion cysts, 2 (3%) bulking agents, 2 (3%) urethral polyps, and one (2%) of each of the following: leiomyoma, angiomyofibroblastoma, redundant vaginal mucosa epithelium, suture abscess, and encapsulated mesh remnant. Fifty-seven women underwent surgical excision (97%), and 2 elected observation. Most (78%) reported resolution of symptoms after excision. Of the patients surgically managed, 7% had postoperative stress urinary incontinence and 12% had persistent lower urinary tract symptoms. Of the 38 women with urethral diverticula, 17% had recurrence and were more likely to have multiple diverticula (44% vs 8%, P = 0.03).

Conclusion

Although urethral diverticulum was the most common cause of a periurethral mass, final pathology revealed a variety of benign diagnoses in more than one-third of cases, demonstrating the importance of a thorough investigation for accurate diagnosis.
Identification of a chimeric emm gene and novel emm pattern in currently circulating strains of emm4 Group A Streptococcus
Authors: DebRoy Sruti , Li Xiqi , Kalia Awdhesh , Galloway-Pena Jessica , Shah Brittany J. , Fowler Vance G. , Flores Anthony R. , Shelburne Samuel A.
Published: November 2018

Group A Streptococcus (GAS) is classified on the basis of the sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm–enn fusion event in 51 out of 52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm–enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013–2017). The novel emm–enn gene fusion and new emm pattern has potential vaccine implications.
Dynamic modelling of hepatitis C transmission among people who inject drugs: A tool to support WHO elimination targets
Authors: Stocks Theresa , Martin Leah J. , Kühlmann-Berenzon Sharon , Britton Tom
Published: November 2018

To reach the WHO goal of hepatitis C elimination, it is essential to identify the number of people unaware of their hepatitis C virus (HCV) infection and to investigate the effect of interventions on the disease transmission dynamics. In many middle- and high-income countries, one of the primary routes of HCV transmission is via contaminated needles shared by people who inject drugs (PWIDs). However, substantial underreporting combined with high uncertainty regarding the size of this difficult to reach population, makes it challenging to estimate the core indicators recommended by the WHO. To help enable countries to monitor their progress towards the elimination goal, we present a novel multi-layered dynamic transmission model for HCV transmission within a PWID population. The model explicitly accounts for disease stage (acute and chronic), injection drug use status (active and former PWIDs), status of diagnosis (diagnosed and undiagnosed) and country of disease acquisition (domestic or abroad). First, based on this model, and using routine surveillance data, we estimate the number of undiagnosed PWIDs, the true incidence, the average time until diagnosis, the reproduction numbers and associated uncertainties. Second, we examine the impact of two interventions on disease dynamics: 1) direct-acting antiviral drug treatment, and 2) needle exchange programs. To make the model accessible to relevant users and to support communication of our results to public health decision makers, the model and its output are made available through a Shiny app. As a proof of concept, we illustrate our results for a specific data set; however, through the app our model can be easily adapted to other high-income countries with similar transmission patterns among PWIDs where the disease is endemic.
Efficient GFP-labeling and analysis of spermatogenic cells using the IRG transgene and flow cytometry
Authors: Zagore Leah L. , Akesson Cydni C. , Licatalosi Donny D.
Published: November 2018

Spermatogenesis is a highly ordered developmental program that produces haploid male germ cells. The study of male germ cell development in the mouse has provided unique perspectives into the molecular mechanisms that control cell development and differentiation in mammals, including tissue-specific gene regulatory programs. An intrinsic challenge in spermatogenesis research is the heterogeneity of germ and somatic cell types present in the testis. Techniques to separate and isolate distinct mouse spermatogenic cell types have great potential to shed light on molecular mechanisms controlling mammalian cell development, while also providing new insights into cellular events important for human reproductive health. Here, we detail a versatile strategy that combines Cre-lox technology to fluorescently label germ cells, with flow cytometry to discriminate and isolate germ cells in different stages of development for cellular and molecular analyses.
A Two-Player Iterated Survival Game
Authors: Wakeley John , Nowak Martin
Published: November 2018

We describe an iterated game between two players, in which the payoff is to survive a number of steps. Expected payoffs are probabilities of survival. A key feature of the game is that individuals have to survive on their own if their partner dies. We consider individuals with hardwired, unconditional behaviors or strategies. When both players are present, each step is a symmetric two-player game. The overall survival of the two individuals forms a Markov chain. As the number of iterations tends to infinity, all probabilities of survival decrease to zero. We obtain general, analytical results for n-step payoffs and use these to describe how the game changes as n increases. In order to predict changes in the frequency of a cooperative strategy over time, we embed the survival game in three different models of a large, well-mixed population. Two of these models are deterministic and one is stochastic. Offspring receive their parent’s type without modification and fitnesses are determined by the game. Increasing the number of iterations changes the prospects for cooperation. All models become neutral in the limit (n → ∞). Further, if pairs of cooperative individuals survive together with high probability, specifically higher than for any other pair and for either type when it is alone, then cooperation becomes favored if the number of iterations is large enough. This holds regardless of the structure of pairwise interactions in a single step. Even if the single-step interaction is a Prisoner’s Dilemma, the cooperative type becomes favored. Enhanced survival is crucial in these iterated evolutionary games: if players in pairs start the game with a fitness deficit relative to lone individuals, the prospects for cooperation can become even worse than in the case of a single-step game.
Unitization modulates recognition of within-domain and cross-domain associations: Evidence from event related potentials
Authors: Li Bingcan , Han Meng , Guo Chunyan , Tibon Roni
Published: November 2018

Although it is often assumed that memory of episodic associations requires recollection, it has been suggested that when stimuli are experienced as a unit, familiarity processes might contribute to their subsequent associative recognition. We investigated the effects of associative relations and perceptual domain during episodic encoding on retrieval of associative information. During study, participants encoded compound and non-compound words-pairs, presented either to the same sensory modality (visual presentation) or to different sensory modalities (audio-visual presentation). At test, they discriminated between old, rearranged, and new pairs while event related potentials (ERPs) were recorded. In an early ERP component, generally associated with familiarity processes, differences related to associative memory only emerged for compounds, regardless their encoding modality. In contrast, in a later ERP component associated with recollection, differences related to associative memory emerged in all encoding conditions. These findings may indicate that episodic retrieval of compound words can be supported by familiarity-related processes, regardless of whether both words were presented to the same or different sensory modalities.
Bile acid metabolites control Th17 and Treg cell differentiation
Authors: Hang Saiyu , Paik Donggi , Devlin A. Sloan , Jamma Trinath , Lu Jingping , Ha Soyoung , Nelson Brandon N. , Kelly Samantha P. , Wu Lin , Zheng Ye , Rastinejad Fraydoon , Krout Michael R. , Fischbach Michael A. , Littman Dan R. , Huh Jun R.
Published: November 2018

Bile acids are abundantly present in the mammalian gut, where they undergo bacteria-mediated transformation, generating a large pool of bioactive molecules. While they have been shown to affect host metabolism, cancer progression and innate immunity, it is unknown whether bile acids affect the function of adaptive immune cells such as T cells expressing IL-17a (Th17 cells) and regulatory T cells (Tregs) that mediate inflammatory and anti-inflammatory responses, respectively. By screening a small-molecule library primarily composed of bile acid metabolites, we identified two distinct derivatives of lithocholic acid (LCA), 3-oxoLCA and isoalloLCA, as specific regulators of Th17 and Treg cells. While 3-oxoLCA inhibited Th17 cell differentiation by directly binding to its key transcription factor RORγt (retinoid-related orphan receptor γ t), isoalloLCA enhanced differentiation of Tregs through mitochondrial-dependent metabolic changes, leading to an increased expression of Foxp3. IsoalloLCA-dependent Treg enhancement required an intronic Foxp3 enhancer, the conserved noncoding sequence 3 (CNS3), which acts as an epigenetic switch that confers a poised state to the Foxp3 promoter. Lastly, oral administration of 3-oxoLCA and isoalloLCA to mice led to reduced Th17 and increased Treg cell differentiation in the intestinal lamina propria. Altogether, our data suggest novel mechanisms by which bile acid metabolites control host immune responses by directly modulating the Th17 and Treg balance.
Desiccation Does Not Drastically Increase the Accessibility of Foreign DNA to the Nuclear Genomes: Evidence from the Frequency of Endosymbiotic DNA Transfer
Authors: Li Xi-Xi , Fang Cheng , Zhao Jun-Peng , Zhou Xiao-Yu , Ni Zhihua , Niu Deng-Ke
Published: November 2018

Horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes. However, in eukaryotes, it is still in hot debate. Some bdelloid rotifers that are resistant to extreme desiccation and radiation were reported to have a very high level of HGTs. However, a similar report in another resistant invertebrate, tardigrades, has been mired in controversy. The DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open the gateway of nuclear genome for foreign DNA integration and thus facilitate the HGT process. If so, the rate of endosymbiotic DNA transfer should also be enhanced. We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in three groups of eukaryotes that are extremely resistant to desiccation, bdelloid rotifers, A. vaga and A. ricciae, tardigrades, H. dujardini and R. varieornatus, and the resurrection plants, D. hygrometricum and S. tamariscina. Excessive NUMTs or NUPTs have not been detected. Furthermore, we compared nine groups of desiccation-tolerant organisms with their desiccation-sensitive relatives but did not find significant difference in the NUMT/NUPT contents. Desiccation could induce DSBs, but it unlikely dramatically increase the frequency of foreign sequence integration in most eukaryotes. Only in the nuclear genomes enriched in repetitive sequences, the DSBs are predominantly repaired by non-homologous end joining (NHEJ) and desiccation-induced DSBs is possible to enhance the integration of foreign sequences into nuclear genome for some degree.
GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data
Authors: Yang Xingyu , Tipton Christopher M. , Woodruff Matthew C. , Zhou Enlu , Lee F. Eun-Hyung , Sanz Inãki , Qiu Peng
Published: November 2018

B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. GLaMST constructs the minimum-spanning-tree (MST) to approximate the landscape of how observed BCR sequences are related, uses the MST to guide the interpolation of the closest unobserved sequence, updates the MST for the interpolation of additional unobserved sequences, and iterates until a full lineage tree is completed, where all observed sequences are connected by interpolated unobserved sequences and single base operations of mutations, insertions and deletions. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure.
A missense mutation of Ip3r1 in Dp2 mice leads to short-term mydriasis and unfolded protein response in the iris constrictor muscles
Authors: Chen Bing , Qi Chongyang , Chen Li , Dai Mengjun , Miao Yayou , Chen Rui , Wei Wane , Yang Shun , Wang Hongling , Duan Xiaoge , Gong Minwei , Yi Wang , Xue Zhengfeng
Published: November 2018

Ip3r1 encodes an inositol 1,4,5-triphosphate-responsive calcium channel. Mutations in the Ip3r1 gene in humans may cause Gillespie syndrome (GS) typically presents as fixed dilated pupils in affected infants, which was referred to as iris hypoplasia. However, there is no report of mice with Ip3r1 heterozygous mutations showing dilated pupils. Here, we report a new Ip3r1 allele (dilated pupil 2; Dp2) with short-term dilated pupil phenotype derived from an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. This allele carries a G5927A transition mutation, which is predicted to result in a C1976Y amino acid change in the open reading frame. Histology and pharmacological tests show that the dilated pupil phenotype is a mydriasis caused by the functional defect in the iris constrictor muscles in Dp2. The dilated pupil phenotype in Dp2 was referred to as mydriasis and excluding iris hypoplasia. IHC analysis revealed increased expression of BIP protein, the master regulator of unfolded protein response (UPR) signaling, in Dp2 mice that did not recover. Apart from the dilated pupil phenotype (mydriasis), there are no other abnormal phenotypes including Ip3r1-related ataxia that may be found. This study is the first report of an Ip3r1 mutation being associated with the mydriasis phenotype. Dp2 mice represent a valuable self-healing model that may be used to study the therapeutic approach for Ip3r1-related diseases or diseases caused by similar pathomechanisms.
No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5’-OH ends phosphorylated by Trl1
Authors: Navickas Albertas , Chamois Sébastien , Saint-Fort Rénette , Henri Julien , Torchet Claire , Benard Lionel
Published: November 2018

The No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stacks of stalled ribosomes. Although an endoribonuclease has been proposed to initiate cleavages upstream of the stall sequence, the production of two RNA fragments resulting from a unique cleavage has never been demonstrated. We have used mRNAs expressing a 3’-ribozyme to produce truncated transcriptsin vivoto mimic naturally occurring truncated mRNAs known to trigger NGD. This technique allows us to analyse endonucleolytic cleavage events at single-nucleotide resolution starting at the third collided ribosome, which we show to be Hel2-dependent. These cleavages map precisely in the mRNA exit tunnel of the ribosome, 8 nucleotides upstream of the first P-site residue and release 5’-hydroxylated RNA fragments requiring 5’-phosphorylation prior to digestion by the exoribonuclease Xrn1, or alternatively by Dxo1. Finally, we identify the RNA kinase Trl1, alias Rlg1, as an essential player in the degradation of NGD RNAs.
GenGraph: a python module for the simple generation and manipulation of genome graphs
Authors: Ambler Jon Mitchell , Mulaudzi Shandukani , Mulder Nicola
Published: November 2018

Background

As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph based representation of collections of genomes as a single genome graph. Though there are currently a handful of tools that can create genome graphs and have demonstrated the advantages of this new paradigm, there still exists a need for flexible tools that can be used by researchers to overcome challenges in genomics studies.

Results

We present the GenGraph toolkit, a tool that uses existing multiple sequence alignment tools to create genome graphs. It is written in Python, one of the most popular coding languages for the biological sciences, and creates the genome graphs as Python NetworkX graph objects. The conceptual model is highly intuitive, and as much as possible represents the biological relationship between the genomes. This design means that users will quickly be able to start creating genome graphs and using them in their own projects.

We outline the methods used in the generation of the graphs, and give some examples of how the created graphs may be used. GenGraph utilises existing file formats and methods in the generation of these graphs, allowing graphs to be visualised and imported with widely used applications, including Cytoscape, R, and Java Script.

Conclusion

GenGraph provides a set of tools for generating graph based representations of sets of sequences with a simple conceptual model in a widely used coding language. It is publicly available on Github (https://github.com/jambler24/GenGraph).
Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates
Authors: Riba Andrea , Nanni Noemi Di , Mittal Nitish , Arhné Erik , Schmidt Alexander , Zavolan Mihaela
Published: November 2018

Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output than other transcripts with equally high ribosome densities.

Significance Statement

Although sequencing of ribosome footprints has uncovered new aspects of mRNA translation, the determinants of ribosome flux remain incompletely understood. Combining ribosome footprint data with measurements of protein synthesis rates, we here inferred translation initiation and elongation rates for over a thousand ORFs in yeast strains with varying translation capacity. We found that the translation elongation rate varies up to ~20-fold among yeast transcripts, and is significantly correlated with the rate of translation initiation. Furthermore, the amino acid composition of synthesized proteins impacts the rate of translation elongation to the same extent as measures of codon and tRNA adaptation. Transcripts encoding ribosomal proteins are translated especially slow, having markedly lower protein output than other transcripts with equally high ribosome densities.
Improved spatial ecological sampling using open data and standardization: an example from malaria mosquito surveillance
Authors: Sedda Luigi , Lucas Eric R. , Djogbénou Luc S. , Edi Ako V.C. , Egyir-Yawson Alexander , Kabula Bilali I. , Midega Janet , Ochomo Eric , Weetman David , Donnelly Martin J.
Published: November 2018

Vector-borne disease control relies on efficient vector surveillance, mostly carried out using traps whose number and locations are often determined by expert opinion rather than a rigorous quantitative sampling design. In this work we first propose a framework for ecological sampling design which in its preliminary stages can take into account environmental conditions obtained from open data (i.e. remote sensing and meteorological stations). These environmental data are used to delimit the area into ecologically homogenous strata. By employing a model-based sampling design, the traps are deployed among the strata using a mixture of random and grid locations which allows balancing predictions and fitting accuracies. Sample sizes and the effect of ecological strata on sample sizes are estimated from previous sampling campaigns. Notably, we found that a configuration of 30 locations with 4 households each (120 traps) will have a similar accuracy in the estimates of mosquito abundance as 300 random samples. In addition, we show that random sampling independently from ecological strata, produces biased estimates of the mosquito abundance. Finally, we propose standardizing reporting of sampling designs to allow transparency and repetition / re-use in subsequent sampling campaigns.
TriPepSVM -de novoprediction of RNA-binding proteins based on short amino acid motifs
Authors: Bressin Annkatrin , Schulte-Sasse Roman , Figini Davide , Urdaneta Erika C , Beckmann Benedikt M , Marsico Annalisa
Published: November 2018

In recent years hundreds of novel RNA-binding proteins (RBPs) have been identified leading to the discovery of novel RNA-binding domains (RBDs). Furthermore, unstructured or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids. However, these advances in understanding RBPs are limited mainly to eukaryotic species and we only have limited tools to faithfully predict RNA-binders from bacteria. Here, we describe a support vector machine (SVM)-based method, called TriPepSVM, for the classification of RNA-binding proteins and non-RBPs. TriPepSVM applies string kernels to directly handle protein sequences using tri-peptide frequencies. Testing the method in human and bacteria, we find that several RBP-enriched tripeptides occur more often in structurally disordered regions of RBPs. TriPepSVM outperforms existing applications, which consider classical structural features of RNA-binding or homology, in the task of RBP prediction in both human and bacteria. Finally, we predict 66 novel RBPs inSalmonellaTyphimurium and validate the bacterial proteins ClpX, DnaJ and UbiG to associate with RNA in vivo.
Ancestry-agnostic estimation of DNA sample contamination from sequence reads
Authors: Zhang Fan , Flickinger Matthew ,   InPSYght Psychiatric Genetics Consortium
Published: November 2018

Detecting and estimating DNA sample contamination are important steps to ensure high quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process samples from multiple studies across diverse populations. On the other hand, incorrectly specified allele frequencies may result in substantial bias in estimated contamination rates. For example, we observed that existing methods often fail to identify 10% contaminated samples at a typical 3% contamination exclusion threshold when genetic ancestry is misspecified. Such an incomplete screening of contaminated samples substantially inflates the estimated rate of genotyping errors even in deeply sequenced genomes and exomes.

We propose a robust statistical method that accurately estimates DNA contamination and is agnostic to genetic ancestry of the intended or contaminating sample. Our method integrates the estimation of genetic ancestry and DNA contamination in a unified likelihood framework by leveraging individual-specific allele-frequencies projected from reference genotypes onto principal component coordinates. We demonstrate this method robustly and accurately estimates contamination rates across different populations and contamination rates. We further demonstrate that in the presence contamination, quantitative estimates of genetic ancestry (e.g. principal component coordinates) can be substantially biased if contamination is ignored, and that our proposed method corrects for this bias. Our method is publicly available at http://github.com/Griffan/verifyBamID