bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent progress in the study of transition in the hypersonic boundary layer
Authors: Lee Cunbiao , Chen Shiyi
Published: May 2018

Turbulence is a universal form of fluid motion. It is the key issue in fluid mechanics. Very recently, it has become a bottleneck in some key engineering research of national importance, such as aeronautics, astronautics and navigation. Developed turbulence and the onset of turbulence, i.e. transition, are two interrelated parts of turbulence. The hypersonic boundary-layer transition is a strategic focus in the fluid mechanics community. This article reviews recent developments in the study of the hypersonic boundary-layer transition, research facilities and experimental techniques. The hypersonic quiet wind tunnel is introduced as a necessary device to obtain real flight data in near space. Near-wall measurement techniques, such as temperature-sensitive paint, near-wall particle image velocimetry and Rayleigh-scattering visualization, are shown. The most important issues in the recent development of the transition in the hypersonic boundary layer are addressed. The instability and nonlinear interaction of different instability modes are discussed. The recent contributions from China, especially at Peking University, are also introduced.
Provider Adherence to Pre-exposure Prophylaxis Monitoring Guidelines in a Large Primary Care Network
Authors: Spinelli Matthew A , Scott Hyman M , Vittinghoff Eric , Liu Albert Y , Morehead-Gee Alicia , Gonzalez Rafael , Buchbinder Susan P
Published: May 2018

Insufficient pre-exposure prophylaxis (PrEP) laboratory monitoring could increase HIV resistance and sexually transmitted infections. We examined test-ordering in a primary care network. Providers did not order HIV testing before almost one-quarter of PrEP initiations; panel management was associated with higher testing. Effective monitoring is needed to maximize PrEP’s preventive impact.
Minimally Invasive Bilateral Anterior Cingulotomy via Open Minicraniotomy Using a Novel Multiport Cisternoscope: A Cadaveric Demonstration
Authors: Manjila Sunil , Rosa Benoit , Mencattelli Margherita , Dupont Pierre E
Published: May 2018

BACKGROUND

Bilateral anterior cingulotomy has been used to treat chronic pain, obsessive compulsive disorder, and addictions. Lesioning of the target area is typically performed using bilateral stereotactic electrode placement and target ablation, which involves transparenchymal access through both hemispheres.

OBJECTIVE

To evaluate an endoscopic direct-vision lesioning using a unilateral parasagittal minicraniotomy for minimally invasive bilateral anterior cingulotomy using a novel multiport endoscope through the anterior interhemispheric fissure.

METHODS

A novel multiport magnetic resonance imaging (MRI)-compatible neuroendoscope prototype is used to demonstrate cadaveric cingulate lesioning through a lateral imaging port while simultaneously viewing the pericallosal arteries as landmarks through a tip imaging port. The lateral port enables extended lesioning of the gyrus while rotation of the endoscope about its axis provides access to homologous areas of both hemispheres.

RESULTS

Cadaver testing confirmed the capability to navigate the multiport neuroendoscope between the hemispheres using concurrent imaging from the tip and lateral ports. The lateral port enabled exploration of the gyrus, visualization of lesioning, and subsequent inspection of lesions. Tip-port imaging provided navigational cues and allowed the operator to ensure that the endoscope tip did not contact tissue. The multiport design required instrument rotation in the coronal plane of only 20° to lesion both gyri, while a standard endoscope necessitated a rotation of 54°.

CONCLUSION

Multiport MRI-compatible endoscopy can be effectively used in cisternal endoscopy, whereby a unilateral parasagittal minicraniotomy can be used for endoscopic interhemispheric bilateral anterior cingulotomy.
Interruption and Reduction of Erysiphe necator Chasmothecia Development Utilizing Fungicidal Oil
Authors: Thiessen L. D. , Neill T. M. , Mahaffee W. F.
Published: May 2018

Grape powdery mildew epidemics, caused by Erysiphe necator, are initiated by the release and subsequent germination of ascospores from mature chasmothecia. Interrupting the development of chasmothecia prior to overwintering may reduce or prevent the overwintering of E. necator in vineyards, thereby reducing initial disease incidence observed the following growing season. At the end of the grape growing season in 2014 and 2015, one application of Organic JMS Stylet Oil (Vero Beach, FL) at a rate of 10 ml/liter was applied on four treatment dates using an air-assisted backpack sprayer onto Chardonnay grapevines within a vineyard. Leaves were collected weekly and chasmothecia enumerated from the first observation of chasmothecia primordia development until the onset of rains (approximately 5 weeks). In 2014, all stylet oil treatment plots developed significantly fewer chasmothecia than nontreated control plots in 2014 (P = 0.04), and there were no differences in treatment date observed. No treatment differences were observed in 2015. Because chasmothecia were still produced despite stylet oil treatment, a single post-véraison stylet oil application to interrupt chasmothecia development would not be an economical management option for reduction of grape powdery mildew.
Evaluating Muscle Mass in Survivors of Acute Respiratory Distress Syndrome: A 1-Year Multicenter Longitudinal Study*
Authors: Chan Kitty S. , Mourtzakis Marina , Aronson Friedman Lisa , Dinglas Victor D. , Hough Catherine L. , Ely E. Wesley , Morris Peter E. , Hopkins Ramona O. , Needham Dale M.
Published: May 2018

Objectives:

Rapid muscle wasting occurs during acute respiratory failure, resulting in muscle weakness and functional impairments. This study examines survivors’ body composition in the year after acute respiratory distress syndrome and tests associations of patient characteristics, hospital exposures, and survivors’ strength and physical functioning with whole body percent lean mass.

Design:

Prospective cohort study with 6- and 12-month follow-up.

Setting:

National study enrolling patients from five study centers.

Patients:

Acute respiratory distress syndrome survivors (n = 120).

Interventions:

None.

Measurements and Main Results:

Lean and fat mass from dual energy x-ray absorptiometry. On average, survivors gained whole body total mass (+1.4 kg; 0.1–2.7) and fat mass (+1.2 kg; 0.2–2.2) and maintained lean mass (+0.2 kg; –0.4 to 0.8) between 6 and 12 months. Proportionally, percent fat mass increased and percent lean mass decreased for the whole body, trunk, and legs (p < 0.05). Greater whole body percent lean mass was associated with younger age, male sex, and lower baseline body mass index, but not other patient characteristics or ICU/hospital exposures. Greater percent lean mass was also significantly associated with gait speed and 6-minute walk distance, but not volitional strength or self-reported functional status.

Conclusions:

In the first year after acute respiratory distress syndrome, patients gained fat mass and maintained lean mass. We found no association of whole body percent lean mass with commonly hypothesized hospital risk factors. Direct measurement of body composition and performance-based functional measures may be helpful for understanding functional recovery in ICU survivors.
Asthma action plans in the adult population: Rediscovering an invaluable tool in today's health care domain
Authors: Mayeux Jack , Arekapudi Krysten Lisella , Amiri Azita
Published: May 2018

Background and purpose:

Asthma in adults remains a leading cause of morbidity, mortality, and increased health care costs. Asthma action plans (AAPs) have demonstrated improved health outcomes in this populace; however, AAPs continue to be underused by providers. This article aims to re-emphasize the importance of AAPs for adults and refresh providers on the effectiveness and methods to use this indispensable tool.

Methods:

A literature search of MEDLINE, PubMed, Google Scholar, and CINAHL was performed, and subsequent findings were reported.

Conclusions:

With proper involvement and inclusion of the patient in the creation of an AAP, adult patients can greatly improve their self-management capabilities through its use.

Implications for practice:

By recognizing the importance and success of AAPs for adults, providers can improve their personal practice through increased AAP delivery. Understanding today's available platforms and formats for AAPs will allow providers a widened subject knowledge base and increased adaptation of patient AAP needs for the adult population. Increased provider knowledge can potentially increase AAP use for adults, as well as improve overall patient outcomes.
Secondary prophylaxis of hepatic encephalopathy in cirrhosis of liver: a double-blind randomized controlled trial of l-ornithine l-aspartate versus placebo
Authors: Varakanahalli Shivakumar , Sharma Barjesh C. , Srivastava Siddharth , Sachdeva Sanjeev , Dahale Amol S.
Published: May 2018

Background and aims

Hepatic encephalopathy (HE) is associated with a poor prognosis. There is no study on the prevention of recurrence of encephalopathy withl-ornithinel-aspartate (LOLA).

Patients and methods

We conducted a double-blind randomized controlled trial at a tertiary center. Consecutive patients with cirrhosis who had recovered from HE were randomized to receive LOLA (6 g thrice daily) or similar amount of placebo by computer-based randomization for 6 months. Patients were assessed by psychometric HE scores using five paper–pencil tests, critical flicker frequency test, arterial ammonia, and sickness impact profile scores at inclusion. Primary end point was development of overt HE.

Results

Of 306 patients, 150 patients were enrolled. HE recurred in nine (12.3%) of 73 and in 20 (27.7%) of 72 patients receiving LOLA and placebo, respectively (P=0.02), with hazard ratio of 0.389 (95% confidence interval=0.174–0.870). Mortality was similar in both groups (6.8 vs. 13.8%,P=0.18). At 6 months follow-up, there was a significant change in the psychometric hepatic encephalopathy score (2.53±2.18 vs. −0.01±1.92,P<0.001), ammonia level (−23.58±14.8 vs. 1.41±13.34 μmol/l,P<0.001), CFF (5.85±4.82 vs. 0.58±4.53,P<0.001), and SIP scores (−7.89±5.52 vs. −0.95±4.25,P<0.001) in patients treated with LOLA compared with placebo. On multivariate analysis, only MELD score predicted the recurrence of overt HE, with odds ratio of 2.21 (95% confidence interval: 1.526–3.204,P<0.001).

Conclusion

LOLA is effective in the secondary prophylaxis of HE and is associated with significant improvements in psychometric hepatic encephalopathy score, ammonia level, critical flicker frequency scores, and health-related quality of life.
Hepatitis C virus treatment by direct-acting antivirals in successfully treated hepatocellular carcinoma and possible mutual impact
Authors: Hassany Mohamed , Elsharkawy Aisha , Maged Amr , Mehrez Mai , Asem Noha , Gomaa Ahmed , Mostafa Zeinab , Abbas Bahaa , Soliman Mohamad , Esmat Gamal
Published: May 2018

Background and aims

Treatment of hepatitis C virus (HCV) after successfully treated hepatocellular carcinoma (HCC) becomes possible with the introduction of direct-acting antivirals because of their favorable efficacy, safety, and short period of treatment. Few data are available on the results of treatment using different direct-acting antiviral regimens in successfully treated HCC and a lot of debate about its role in tumor recurrence.

Methods

Sixty-two HCV-related HCC patients were enrolled in the study after successfully treated HCC; the studied population included either Child–Pugh ‘A’ or ‘B7’. The patients were subcategorized to receive one of the following regimens: group 1: sofosbuvir (SOF)+ribavirin (RBV) for 24 weeks, group 2: SOF+simeprevir for 12 weeks, group 3: SOF+daclatasvir for 24 weeks, and group 4: SOF+daclatasvir+RBV for 12 weeks. The overall median follow-up period is 12 months after treatment initiation.

Results

All treatment regimens were tolerable for all patients, with no reported major adverse events during treatment. The overall sustained virologic response rate was 64.5%, with the highest result in group 4 and the lowest result in group 1; 87.5 and 26.7%, respectively. HCC recurrence was observed in 42% of patients; 80.7% of these patients developed recurrence within 6 months of treatment initiation.

Conclusion

Treatment of HCV in successfully treated HCC is feasible, with the best results achieved using multiple direct-acting antivirals and RBV; a high rate of HCC recurrence was observed, especially within the first 6 months of treatment initiation (ClinicalTrials.gov no: NCT02771405).
Development of the End-of-Life Care Nursing Attitude Scale for Japanese Geriatrics
Authors: Okumura-Hiroshige Akemi , Fukahori Hiroki , Yoshioka Sachiko , Kuwata Miyoko , Nishiyama Midori , Takamichi Kaori
Published: May 2018

This study aimed to develop an end-of-life (EOL) care nursing attitude scale for Japanese geriatric nurses (ELNAS-JG). The items of the ELNAS-JG were developed to cover important topics related to EOL care (eg, motivation for providing EOL care, pain and symptom management, and decision-making support care for older adults). Participants were 1663 nurses employed in 32 institutions across Japan. Of these, 1298 participants were analyzed. An exploratory factor analysis of the 26 scale items revealed a 3-factor solution describing the concepts of responsibility, willingness, and confidence: responsibility and willingness were captured in factor 1 (16 items), and confidence was split into factor 2 (6 items) and factor 3 (4 items) to capture individual and collaborative behaviors. The overall Cronbach α coefficient for the 26 items was 0.95, and the intraclass correlation coefficient was 0.83. Overall, the ELNAS-JG was confirmed to have good internal consistency, test-retest reliability, content validity, known-groups validity, and construct validity. It can comprehensively measure nurses' attitudes toward EOL care for older adults in any EOL setting. Furthermore, this scale can be used to evaluate educational programs aimed at improving care quality and encouraging related activities in facilities that provide EOL care.
The Mayo Clinic Experience With the Neurological Complications of the CTLA-4 Inhibitor Ipilimumab
Authors: Ruff Michael W. , Mauermann Michelle L.
Published: May 2018

Neurological complications are an increasingly recognized complication of the use of the immune checkpoint inhibitors in the treatment of solid tumors. Ipilimumab is a monoclonal antibody against cytotoxic T-lymphocyte antigen-4, an immune checkpoint inhibitor that suppresses T-cell effector function. The clinical spectrum of ipilimumab-associated neurological complications and optimum treatment approach is not established. We describe our institution’s experience with ipilimumab and illustrate 2 cases of presumed autoimmune neurological phenomenon resulting from its use.
Targeted Ultrasound-Guided Perineural Hydrodissection of the Sciatic Nerve for the Treatment of Piriformis Syndrome
Authors: Burke Christopher J. , Walter William R. , Adler Ronald S.
Published: May 2018

Piriformis syndrome is a common cause of lumbar, gluteal, and thigh pain, frequently associated with sciatic nerve symptoms. Potential etiologies include muscle injury or chronic muscle stretching associated with gait disturbances. There is a common pathological end pathway involving hypertrophy, spasm, contracture, inflammation, and scarring of the piriformis muscle, leading to impingement of the sciatic nerve. Ultrasound-guided piriformis injections are frequently used in the treatment of these pain syndromes, with most of the published literature describing injection of the muscle. We describe a safe, effective ultrasound-guided injection technique for the treatment of piriformis syndrome using targeted sciatic perineural hydrodissection followed by therapeutic corticosteroid injection.
Common genetic variants contribute to risk of rare severe neurodevelopmental disorders
Authors: Niemi Mari E. K. , Martin Hilary C. , Rice Daniel L. , Gallone Giuseppe , Gordon Scott , Kelemen Martin , McAloney Kerrie , McRae Jeremy , Radford Elizabeth J. , Yu Sui , Gecz Jozef , Martin Nicholas G. , Wright Caroline F. , Fitzpatrick David R. , Firth Helen V. , Hurles Matthew E. , Barrett Jeffrey C.
Published: May 2018

There are thousands of rare human disorders caused by a single deleterious, protein-coding genetic variant 1. However, patients with the same genetic defect can have different clinical presentation 2–4, and some individuals carrying known disease-causing variants can appear unaffected 5. What explains these differences? Here, we show in a cohort of 6,987 children with heterogeneous severe neurodevelopmental disorders expected to be almost entirely monogenic that 7.7% of variance in risk is attributable to inherited common genetic variation. We replicated this genome wide common variant burden by showing that it is over-transmitted from parents to children in an independent sample of 728 trios from the same cohort. Our common variant signal is significantly positively correlated with genetic predisposition to fewer years of schooling, decreased intelligence, and risk of schizophrenia. We found that common variant risk was not significantly different between individuals with and without a known protein-coding diagnostic variant, suggesting that common variant risk is not confined to patients without a monogenic diagnosis. In addition, previously published common variant scores for autism, height, birth weight, and intracranial volume were all correlated with those traits within our cohort, suggesting that phenotypic expression in individuals with monogenic disorders is affected by the same variants as the general population. Our results demonstrate that common genetic variation affects both overall risk and clinical presentation in disorders typically considered to be monogenic.
Improving cross-cultural “mind-reading” with electrical brain stimulation
Authors: Martin A. K. , Su P. , Meinzer M
Published: May 2018

Background: A cross-cultural disadvantage exists when inferring the mental state of others, which may be detrimental for individuals acting in an increasingly globalized world. The dorsomedial prefrontal cortex (dmPFC) is a key hub of the social brain involved in ToM. Therefore, we explored whether facilitation of dmPFC function by focal high-definition tDCS can improve cross-cultural mind-reading.

Method: 52 (26 F/M) Singaporeans performed the Caucasian version of the Reading the Mind in the Eyes Test (RMET) and received HD-tDCS to either the dmPFC or a control site (right temporoparietal junction,rTPJ) in sham-controlled, double-blinded, crossover studies. Contact with Caucasians was determined for the Singaporean cohort as a potential mediator of RMET performance and HD-tDCS response. 52 Caucasians completed the RMET during sham-tDCS and served as a comparison group.

Results: A cross-cultural disadvantage on the RMET was confirmed in the Singaporean cohort and this disadvantage was more pronounced in those participants who had less contact with Caucasians. Importantly, HD-tDCS to the dmPFC improved RMET performance in those with less contact. No effect was identified for rTPJ HD-tDCS or for the age/sex control task demonstrating task and site specificity of the stimulation effects.

Conclusion: Electrical stimulation of the dmPFC selectively improves the rate of cross-cultural ToM inference from facial cues, effectively removing cross-cultural disadvantage that was found in individuals with lower cross-cultural exposure.
Heterogeneous Absorption of Antimicrobial Peptide LL37 inEscherichia coliCells Enhances Population Survivability
Authors: Snoussi Mehdi , Talledo John Paul , Del Rosario Nathan-Alexander , Ha Bae-Yeun , Košmrlj Andrej , Taheri-Araghi Sattar
Published: May 2018

Antimicrobial peptides (AMPs) are broad spectrum antibiotics that selectively target bacteria. Here we investigate the activity of human AMP LL37 againstEscherichia coliby integrating quantitative, population and single-cell level experiments with theoretical modeling. Our data indicate an unexpected, rapid absorption and retention of a large number of LL37 byE. colicells upon the inhibition of their growth, which increases the chance of survival for the rest of population. Cultures with high-enough cell density exhibit two distinct subpopulations: a non-growing population that absorb peptides and a growing population that survive owing to the sequestration of the AMPs by others. A mathematical model based on this binary picture reproduces the rather surprising behaviors ofE. colicultures in the presence of LL37, including the increase of the minimum inhibitory concentration with cell density (even in dilute cultures) and the extensive lag in growth introduced by sub-lethal dosages of LL37.
Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota
Authors: Yan Wei , Zheng Jiangxia , Wen Chaoliang , Ji Congliang , Zhang Dexiang , Chen Yonghua , Sun Congjiao , Yang Ning
Published: May 2018

Background

Despite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.

Results

In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 – 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54 – 0.71 and 0.71 – 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high (ρ = −0.2 – 0.4, P < 0.05) for most genera.

Conclusions

Our results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.
Sound colless-like balance indices for multifurcating trees
Authors: Mir Arnau , Rotger Lucía , Rosselló Francesc
Published: May 2018

The colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. in this paper we propose a family of colless-like balance indices ℭD,f, which depend on a dissimilarity D and a function f: ℕ→ ℝ ⩾0, that generalize the colless index to multifurcating phylogenetic trees. We provide two functions f such that the most balanced phylogenetic trees according to the corresponding indices ℭD,f are exactly the fully symmetric ones. Next, for each one of these two functions f and for three popular dissimilarities D (the variance, the standard deviation, and the mean deviation from the median), we determine the range of values of ℭD,f on the sets of phylogenetic trees with a given number n of leaves. We end the paper by assessing the performance of one of these indices on TreeBASE and using it to show that the trees in this database do not seem to follow either the uniform model for multifurcating trees or the α-γ-model, for any values of α and γ.
Rapid, inexpensive measurement of synthetic bacterial community composition by Sanger sequencing
Authors: Cermak Nathan , Datta Manoshi Sen , Conwill Arolyn
Published: May 2018

Simple synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. For instance, while next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we introduce a new approach for quantifying composition in synthetic bacterial communities based on Sanger sequencing. First, for a given community, we PCR-amplify a universal marker gene (here, the 16S rRNA gene), which yields a mixture of amplicons. Second, we sequence this amplicon mixture in a single Sanger sequencing reaction, which produces a “mixed” electropherogram with contributions from each community member. We also sequence each community member’s marker gene individually to generate “individual” electropherograms. Third, we fit the mixed electropherogram as a linear combination of time-warped individual electropherograms, thereby allowing us to estimate the fractional amplicon abundance of each strain within the community. Importantly, our approach accounts for retention-time variability in electrophoretic signals, which is crucial for accurate compositional estimates. Using synthetic communities of marine bacterial isolates, we show that this approach yields accurate and reproducible abundance estimates for two-, four-, and seven-strain bacterial communities. Furthermore, this approach can provide results within one day and costs ~$5 USD per sample. We envision this approach will enable new insights in microbial ecology by increasing the number of samples that can be analyzed and enabling faster iteration between experiments and theory. We have implemented our method in a free and open-source R package called CASEU (“Compositional Analysis by Sanger Electropherogram Unmixing”), available at https://bitbucket.org/DattaManoshi/caseu.
Retrospective harmonization of multi-site diffusion MRI data acquired with different acquisition parameters
Authors: Cetin Karayumak Suheyla , Bouix Sylvain , Ning Lipeng , Shenton Martha , Kubicki Marek , Rathi Yogesh
Published: May 2018

A joint and integrated analysis of multi-site diffusion MRI (dMRI) datasets can dramatically increase the statistical power of neuroimaging studies and enable comparative studies pertaining to several brain disorders. However, dMRI data sets acquired on multiple scanners cannot be naively pooled for joint analysis due to scanner specific nonlinear effects as well as differences in acquisition parameters. Consequently, for joint analysis, the dMRI data has to be harmonized, which involves removing scanner-specific differences from the raw dMRI signal. In this work, we present a dMRI harmonization method that, when applied to multi-site data, is capable of removing scanner-specific effects, while accounting for minor differences in acquisition parameters such as b-value, spatial resolution and number of gradient directions in the dMRI data (typical for multi-site clinical research scans). We validate our algorithm on dMRI data acquired from two sites: Philadelphia Neurodevelopmental Cohort (PNC) with 800 healthy adolescents (ages 8 to 22 years) and Brigham and Women’s Hospital (BWH) with 70 healthy subjects (ages 14 to 54 years). In particular, we show that gender differences and maturation in different age groups are preserved after harmonization, as measured using effect sizes (small, medium and large), irrespective of the test sample size. Further, because we use matched control subjects from different scanners to estimate scanner-specific effects, we tested how many subjects are needed from each site to achieve best harmonization results. Our results indicate that at-least 16 to 18 well-matched healthy controls from each site are needed to reliably capture scanner related differences. The proposed method can thus be used for retrospective harmonization of raw dMRI data across sites despite differences in acquisition parameters, while preserving inter-subject anatomical variability.
Genetically encoded multimode reporter of adaptor protein 3 (AP-3) traffic in budding yeast
Authors: Plemel Rachael L. , Odorizzi Greg , Merz Alexey J.
Published: May 2018

SYNOPSIS

The AP-3 (adaptor complex 3) mediates traffic from the late Golgi or early endosomes to late endosomal compartments. Here, a synthetic reporter is presented that allows convenient monitoring of AP-3 traffic, and direct screening or selection for mutants with defects in the pathway. The reporter can be assayed by fluorescence microscopy or in liquid or agar plate formats and is adaptable to high-throughput screening.

AP-3 (adaptor complex 3) mediates traffic from the late Golgi or early endosomes to late endosomal compartments. In mammals, mutations in AP-3 cause Hermansky-Pudlak Syndrome type 2, cyclic neutropenias, and a form of epileptic encephalopathy. In budding yeast, AP-3 carries cargo directly from the trans-Golgi to the lysosomal vacuole. Despite the pathway’s importance and its discovery two decades ago, rapid screens and selections for AP-3 mutants have not been available. We now report GNSI, a synthetic, genetically encoded reporter that allows rapid plate-based assessment of AP-3 functional deficiency, using either chromogenic or growth phenotype readouts. This system identifies defects in both the formation and consumption of AP-3 carrier vesicles and is adaptable to high-throughput screening or selection in both plate array and liquid batch culture formats. Episomal and integrating plasmids encoding GNSI have been submitted to the Addgene repository.
Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d
Authors: Zhang Cheng , Konermann Silvana , Brideau Nicholas J. , Lotfy Peter , Novick Scott J. , Strutzenberg Timothy , Griffin Patrick R. , Hsu Patrick D. , Lyumkis Dmitry
Published: May 2018

CRISPR-Cas endonucleases directed against foreign nucleic acids mediate prokaryotic adaptive immunity and have been tailored for broad genetic engineering applications. Type VI-D CRISPR systems contain the smallest known family of single effector Cas enzymes, and their signature Cas13d ribonuclease employs guide RNAs to cleave matching target RNAs. To understand the molecular basis for Cas13d function, we resolved cryo-electron microscopy structures of Cas13d-guide RNA binary complex and Cas13d-guide-target RNA ternary complex to 3.4 and 3.3 Å resolution, respectively. Furthermore, a 6.5 Å reconstruction of apo Cas13d combined with hydrogen-deuterium exchange revealed conformational dynamics that have implications for RNA scanning. These structures, together with biochemical and cellular characterization, explain the compact molecular architecture of Cas13d and provide insights into the structural transitions required for enzyme activation. Our comprehensive analysis of Cas13d in diverse enzymatic states facilitated site-specific truncations for minimal size and delineates a blueprint for improving biomolecular applications of RNA targeting.
Detection of the altered metabolites of Raji cells in the presence of Epstein-Barr virus (EBV) using 1HNMR Spectroscopy
Authors: Dindar Zahra , Hosseini Reza Haj , Vahhabpoor Ruhollah , Zamani Zahra
Published: May 2018

EBV is one of the most common viruses in humans and is directly implicated in carcinogenesis. The present study aimed to detect the altered metabolites of Raji cells in the presence of Epstein-Barr virus (EBV) using 1H NMR by NOESY technique. The cells and EBV were maintained in RPMI 1640 and 1 ml of cells were transfected into falcon tubes containing cells and were incubated at 37°C for 2 hours. Metabolites extracted using water or chloroform/methanol, lyophilized and sent for 1H NMR analysis by NOESY technique. The NMR spectrum comprising of Fourier Transformed information about metabolites in the control and treated were imported into MATLAB (v.7.8.0.347) software and the metabolic cycles were determined using Metabo-Analyst software. The data have demonstrated that infected cells leads to proliferation and subsequent immortalization of cell lines through cellular replication machinery recruitment and changes the metabolic profile and promotes vital metabolites such as the carbohydrates engage in pentose phosphate and glycolactic, biosynthesis of nucleotide and amino acid pathways. The results also indicate that essential amino acids are required for protecting viral structure and the function of viral genes. Therefore, EBV infection of cells leads to the sustained elevation of cell growth and cell immortalization.
The gene regulatory basis of genetic compensation during neural crest induction
Authors: Dooley Christopher M. , Wali Neha , Sealy Ian M. , White Richard J. , Stemple Derek L. , Collins John E. , Busch-Nentwich Elisabeth M.
Published: May 2018

Background

The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors but detailed interactions within the network remain to be resolved.

Results

We have used gene knockout and RNA sequencing strategies to dissect NC differentiation in zebrafish. We establish that initiation of the NC GRN takes place just after genome activation. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that although a single allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, expression of many target genes remains abnormal and sensitive to tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation.

Conclusions

Stepwise genetic ablation of the NC identifies the core gene module required for neural crest induction. This work extends and refines the NC GRN while also uncovering the complex transcriptional basis of genetic compensation via paralogues.
Genomic determinants of speciation and spread of theMycobacterium tuberculosiscomplex
Authors: Chiner-Oms Álvaro , Sánchez-Busó Leonor , Corander Jukka , Gagneux Sebastien , Harris Simon , Young Douglas , González-Candelas Fernando , Comas Iñaki
Published: May 2018

BACKGROUND

Models on how bacterial lineages differentiate increase our understanding on early bacterial speciation events and about the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen.

RESULTS

The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify thephoRgene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the MTBC from its ancestor. Previous evidence showed thatphoRmutations played a central role in the adaptation of the pathogen to different host species. Now we show thatphoRhave been under selection during the early spread of human tuberculosis, during later expansions and in on-going transmission events.

CONCLUSIONS

Our results show that linking pathogen evolution across evolutionary and epidemiological timescales point to past and present virulence determinants.
Genomic prediction using individual-level data and summary statistics from multiple populations
Authors: Vandenplas Jeremie , Calus Mario P.L. , Gorjanc Gregor
Published: May 2018

This study presents a method for genomic prediction that uses individual-level data and summary statistics from multiple populations. Genome-wide markers are nowadays widely used to predict complex traits, and genomic prediction using multi-population data is an appealing approach to achieve higher prediction accuracies. However, sharing of individual-level data across populations is not always possible. We present a method that enables integration of summary statistics from separate analyses with the available individual-level data. The data can either consist of individuals with single or multiple (weighted) phenotype records per individual. We developed a method based on a hypothetical joint analysis model and absorption of population specific information. We show that population specific information is fully captured by estimated allele substitution effects and the accuracy of those estimates, i.e. the summary statistics. The method gives identical result as the joint analysis of all individual-level data when complete summary statistics are available. We provide a series of easy-to-use approximations that can be used when complete summary statistics are not available or impractical to share. Simulations show that approximations enables integration of different sources of information across a wide range of settings yielding accurate predictions. The method can be readily extended to multiple-traits. In summary, the developed method enables integration of genome-wide data in the individual-level or summary statistics form from multiple populations to obtain more accurate estimates of allele substitution effects and genomic predictions.
Estrus-Cycle Regulation of Cortical Inhibition
Authors: Clemens Ann M. , Lenschow Constanze , Beed Prateep , Li Lanxiang , Sammons Rosanna , Naumann Robert K. , Wang Hong , Schmitz Dietmar , Brecht Michael
Published: May 2018

Female mammals experience cyclical changes in sexual receptivity known as the estrus-cycle. Little is known about how estrus affects the cortex although alterations in sensation, cognition and the cyclic occurrence of epilepsy suggest brain-wide processing changes. We performedin vivojuxtacellular and whole-cell recordings in somatosensory cortex of female rats and found that the estrus-cycle potently altered cortical inhibition. Fast-spiking interneurons strongly varied their activity with the estrus-cycle and estradiol in ovariectomized females, while regular-spiking excitatory neurons did not change.In vivowhole-cell recordings revealed a varying excitation-to-inhibition-ratio with estrus.In situhybridization for estrogen receptor β (Esr2) showed co-localization with parvalbumin-positive interneurons in deep cortical layers, mirroring the laminar distribution of our physiological findings.In vivoandin vitroexperiments confirmed that estrogen acts locally to increase fast-spiking interneuron excitability through an estrogen receptor β mechanism. We conclude that sex hormones powerfully modulate cortical inhibition in the female brain.
IdentifyingStreptococcus pneumoniaegenes associated with invasive disease using pangenome-based whole genome sequence typing
Authors: Obolski Uri , Gori Andrea , Lourenço José , Thompson Craig , Thompson Robin , French Neil , Heyderman Robert , Gupta Sunetra
Published: May 2018

Streptococcus pneumoniaeis a normal commensal of the upper respiratory tract but can also invade the bloodstream or CSF (cerebrospinal fluid), causing invasive pneumococcal disease (IPD). In this study, we attempt to identify genes associated with IPD by applying a random forest machine-learning algorithm to whole genome sequence (WGS) data. We find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of these genes, 23 genes have previously shown to be directly relevant to IPD, while the other 18 are uncharacterized.
Grapevine virus L: a Novel Vitivirus in Grapevine
Authors: Debat Humberto , Zavallo Diego , Brisbane Reid Soltero , Vončina Darko , Almeida Rodrigo P.P. , Blouin Arnaud G. , Rwahnih Maher Al , Gomez-Talquenca Sebastian , Asurmendi Sebastian
Published: May 2018

Vitivirus are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the characterization of a novel virus from grapevines, which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Here, we present the characterization of a novel virus from grapevines. Phylogenetic analyses based on the predicted RP and CP protein unequivocally places the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.9%-97.9% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.
A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation
Authors: Baumdick Martin , Gelléri Márton , Uttamapinant Chayasith , Beránek Václav , Chin Jason W , Bastiaens Philippe IH
Published: May 2018

Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight in EGFR activation mechanisms in living cells, we developed a Förster Resonance Energy Transfer (FRET) basedconformationalEGFRindicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant revealed that Y845phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C–terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose.
Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression
Authors: Lun Xiao-Kang , Szklarczyk Damian , Gábor Attila , Dobberstein Nadine , Zanotelli Vito RT , Saez-Rodriguez Julio , von Mering Christian , Bodenmiller Bernd
Published: May 2018

Kinase and phosphatase overexpression drives tumorigenesis and drug resistance in many cancer types. Signaling networks reprogrammed by protein overexpression remain largely uncharacterized, hindering discovery of paths to therapeutic intervention. We previously developed a single cell proteomics approach based on mass cytometry that enables quantitative assessment of overexpression effects on the signaling network. Here we applied this approach in a human kinome- and phosphatome-wide study to assess how 649 individually overexpressed proteins modulate the cancer-related signaling network in HEK293T cells. Based on these data we expanded the functional classification of human kinases and phosphatases and detected 208 novel signaling relationships. In the signaling dynamics analysis, we showed that increased ERK-specific phosphatases sustained proliferative signaling, and using a novel combinatorial overexpression approach, we confirmed this phosphatase-driven mechanism of cancer progression. Finally, we identified 54 proteins that caused ligand-independent ERK activation with potential as biomarkers for drug resistance in cells carrying BRAF mutations.
Stability-normalised walking speed: a new approach for human gait perturbation research
Authors: McCrum Christopher , Willems Paul , Karamanidis Kiros , Meijer Kenneth
Published: May 2018

In gait stability research, neither self-selected walking speeds, nor the same prescribed walking speed for all participants, guarantee equivalent gait stability among participants. Furthermore, these options may differentially affect the response to different gait perturbations, which is problematic when comparing groups with different capacities. We present a method for decreasing inter-individual differences in gait stability by adjusting walking speed to equivalent margins of stability (MoS). Eighteen healthy adults walked on a split-belt treadmill for two-minute bouts at 0.4m/s up to 1.8m/s in 0.2m/s intervals. The stability-normalised walking speed (MoS=0.05m) was calculated using the mean MoS at touchdown of the final 10 steps of each speed. Participants then walked for three minutes at this speed and were subsequently exposed to a treadmill belt acceleration perturbation. A further 12 healthy adults were exposed to the same perturbation while walking at 1.3m/s: the average of the previous group. Large ranges in MoS were observed during the prescribed speeds (6-10cm across speeds) and walking speed significantly (P<0.001) affected MoS. The stability-normalised walking speeds resulted in MoS equal or very close to the desired 0.05m and reduced between-participant variability in MoS. The second group of participants walking at 1.3m/s had greater inter-individual variation in MoS during both unperturbed and perturbed walking compared to 12 sex, height and leg length-matched participants from the stability-normalised walking speed group. The current method decreases inter-individual differences in gait stability which may be beneficial for gait perturbation and stability research, in particular for studies on populations with different locomotor capacities.
Distinct temporal requirements for Sonic hedgehog signaling in development of the tuberal hypothalamus
Authors: Corman Tanya S. , Zevallos Solsire E. , Epstein Douglas J.
Published: May 2018

Sonic hedgehog (Shh) plays well characterized roles in the development of several regions of the brain and spinal cord, but its functions in the hypothalamus have been more difficult to elucidate due to the complex neuroanatomy of this brain area. Here, we utilize fate-mapping and conditional deletion models in mice to define requirements for dynamic Shh activity at distinct stages of tuberal hypothalamic development, a brain region with important homeostatic functions. At early time points, Shh signaling regulates dorsoventral patterning, neurogenesis, and the size of the ventral midline. Fate mapping experiments demonstrate that Shh expressing and responsive progenitors contribute to distinct neuronal subtypes, accounting for some of the cellular heterogeneity in tuberal hypothalamic nuclei. Conditional deletion of the Hedgehog transducer Smoothened (Smo), after dorsoventral patterning has been established, reveals that Shh signaling is necessary to maintain proliferation and progenitor identity during peak periods of hypothalamic neurogenesis. We also find that mosaic disruption ofSmocauses a non-cell autonomous gain in Shh signaling activity in neighboring wild type cells, suggesting a mechanism for the pathogenesis of hypothalamic hamartomas, a benign tumor that forms during hypothalamic development.

SUMMARY STATEMENT

Requirements for dynamic Sonic hedgehog activity at distinct stages of tuberal hypothalamic development are defined using fate-mapping and conditional deletion models in mice.