bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Corneal Collagen Cross-Linking Protocols Measured With Scheimpflug Tomography
Authors: Shajari Mehdi , Sowwa Gabriela , Steinwender Gernot , Hofmann Christian , Pahlitzsch Marie-Luise , Petermann Kerstin , Kohnen Thomas
Published: May 2018

Purpose:

To evaluate the effectiveness of corneal collagen cross-linking with Dresden and accelerated protocols to treat keratoconus by Scheimpflug tomography.

Methods:

Fifty-eight eyes with manifest keratoconus were measured preoperatively at least twice with the Pentacam. The difference of relevant variables for keratoconus progression (eg, D value, thinnest pachymetry, Kmax) was established. After evident progression, patients underwent corneal cross-linking (29 eyes with the Dresden protocol and 29 eyes with the accelerated protocol). Postoperatively, variables used for defining manifest progression were compared again by measuring the difference between 2 measurements.

Results:

Preoperatively, the mean D value was 9.6 ± 4.8 for the Dresden cohort and 8.3 ± 5.1 for the accelerated cohort. There was no significant difference between both cohorts in terms of the mean preoperative difference in the D value (0.59 ± 1.7 for the Dresden cohort vs. 0.4 ± 1.49, P = 1). Postoperatively, however, a significant difference (P < 0.01 for the accelerated corhort) was found (Dresden: −0.47 ± 0.88 vs. accelerated: 0.04 ± 0.67). Regression analysis showed that keratoconus progression was significant in both study groups preoperatively (with a significant reduction of corneal thickness and increase in the D value). Postoperative data show an improvement in all observed keratoconus indices in both study groups and stagnation in progression for the accelerated cohort, P = 0.774, for the D value and a regression in manifestation for the Dresden cohort (decrease in the D value, P < 0.01).

Conclusions:

Before operative intervention, Scheimpflug imaging showed signs of a progressive disease in all eyes. Both conventional Dresden protocol and accelerated pulsed corneal collagen cross-linking techniques effectively stopped this progression.
Effect of Posterior Corneal Vesicles on Corneal Endothelial Cell Density and Anisometropic Amblyopia
Authors: Noguchi Atsushi , Okumura Naoki , Sotozono Chie , Kinoshita Shigeru
Published: May 2018

Purpose:

To evaluate the effect of corneal vesicles in patients with posterior corneal vesicles (PCV) on corneal endothelial cell (CEC) density and the acquisition of amblyopia.

Methods:

In this retrospective study of patients with PCV (18 eyes of 14 patients), CEC density was examined by noncontact specular microscopy during each follow-up examination. Best-corrected visual acuity and the objective refractive error were also examined.

Results:

Of the 14 total patients, 10 were diagnosed with PCV and 4 were diagnosed with bilateral suspected PCV or posterior polymorphous corneal dystrophy (PPCD), and in all patients, no ocular abnormality other than corneal vesicles was observed. In patients with PCV and patients with bilateral suspected PCV or PPCD, mean CEC density was 1131 ± 338 and 1095 ± 492 cells/mm2, respectively. In both PCV group and the bilateral suspected PCV or PPCD-group patients who were followed for 164.2 ± 25.4 months (range: 123–186 months), CEC density tended not to decrease. In patients with PCV, the mean best-corrected visual acuity of the unaffected eyes was significantly higher than that of the affected eyes with corneal vesicles (−0.10 ± 0.06 and 0.05 ± 0.13, respectively, P = 0.012). Four of 9 affected eyes (1 eye was excluded because of retinal atrophy) exhibited amblyopia, and all 4 eyes had astigmatism higher than 2 diopters.

Conclusions:

Although CEC density of patients with PCV in this study was found to be stable over a long-term follow-up period, strict attention should be given to the possibility of amblyopia in eyes with PCV.
Liposomal Amphotericin B–Associated Cardiac Arrest
Authors: Autry Marcus Tad , Harrison Kiya , White Bryan , Miller Jamie
Published: May 2018

Liposomal amphotericin B (L-AmB) was developed with the intent to minimize the adverse effects associated with amphotericin B deoxycholate, especially nephrotoxicity. Although there has been a substantial decrease in adverse effects with L-AmB compared with its predecessor, there is a small body of evidence suggesting its association with cardiovascular adverse events. We report a case of L-AmB-associated cardiac arrest in a patient with preexisting cardiac-related disease states. In addition, we review currently available literature regarding cardiac-related adverse events associated with L-AmB. When the Naranjo Adverse Drug Reaction Probability Scale was applied to this case, the probability of association was determined as possible. This case adds to a small but important body of literature regarding L-AmB–associated cardiotoxicity. Moreover, a review of the available literature indicates that providers should be aware of the potential for cardiac adverse events with L-AmB.
Mechanical Circulatory Support of the Right Ventricle for Adult and Pediatric Patients With Heart Failure
Authors: Chopski Steven G. , Murad Nohra M. , Fox Carson S. , Stevens Randy M. , Throckmorton Amy L.
Published: May 2018

The clinical implementation of mechanical circulatory assistance for a significantly dysfunctional or failing left ventricle as a bridge-to-transplant or bridge-to-recovery is on the rise. Thousands of patients with left-sided heart failure are readily benefitting from these life-saving technologies, and left ventricular failure often leads to severe right ventricular dysfunction or failure. Right ventricular failure (RVF) has a high rate of mortality caused by the risk of multisystem organ failure and prolonged hospitalization for patients after treatment. The use of a blood pump to support the left ventricle also typically results in an increase in right ventricular preload and may impair right ventricular contractility during left ventricular unloading. Patients with RVF might also suffer from severe pulmonary dysfunction, cardiac defects, congenital heart disease states, or a heterogeneity of cardiophysiologic challenges because of symptomatic congestive heart failure. Thus, the uniqueness and complexity of RVF is emerging as a new domain of significant clinical interest that motivates the development of right ventricular assist devices. In this review, we present the current state-of-the-art for clinically used blood pumps to support adults and pediatric patients with right ventricular dysfunction or failure concomitant with left ventricular failure. New innovative devices specifically for RVF are also highlighted. There continues to be a compelling need for novel treatment options to support patients with significant right heart dysfunction or failure.
Cannula Tip With Integrated Volume Sensor for Rotary Blood Pump Control: Early-Stage Development
Authors: Cysyk Joshua , Newswanger Ray , Popjes Eric , Pae Walter , Jhun Choon-Sik , Izer Jenelle , Weiss William , Rosenberg Gerson
Published: May 2018

The lack of direct measurement of left ventricular unloading is a significant impediment to the development of an automatic speed control system for continuous-flow left ventricular assist devices (cf-LVADs). We have developed an inlet cannula tip for cf-LVADs with integrated electrodes for volume sensing based on conductance. Four platinum-iridium ring electrodes were installed into grooves on a cannula body constructed from polyetheretherketone (PEEK). A sinusoidal current excitation waveform (250 μA pk-pk, 50 kHz) was applied across one pair of electrodes, and the conductance-dependent voltage was sensed across the second pair of electrodes. The conductance catheter was tested in an acute ovine model (n = 3) in conjunction with the HeartMate II rotary blood pump to provide circulatory support and unload the ventricle. Echocardiography was used to measure ventricular size during pump support for verification for the conductance measurements. The conductance measurements correlated linearly with the echocardiography dimension measurements more than the full range of pump support from minimum support to suction. This cannula tip will enable the development of automatic control systems to optimize pump support based on a real-time measurement of ventricular size.
Updates on adolescent dating and sexual violence prevention and intervention
Authors: Miller Elizabeth , Jones Kelley A. , McCauley Heather L.
Published: May 2018

Purpose of review

Dating and sexual violence victimization are not uncommon in early adolescence and increase in prevalence throughout adolescence into young adulthood with profound health and social consequences. Greater attention to what works in prevention is needed to inform current policies and practices.

Recent findings

Adolescent dating violence (ADV) and sexual violence victimization, including cyber dating abuse, are highly prevalent among adolescents. Studies have found sex category differences, with adolescent girls reporting more victimization than boys, particularly sexual violence. Sexual and gender minority youth also experience a higher prevalence of violence victimization than their heterosexual counterparts. Studies on risk factors include examinations of childhood adversities, exposure to sexually explicit material and substance use as well as the role of gender inequitable attitudes on violence perpetration. Recent prevention research includes examining the impact of bystander interventions and transforming gender norms.

Recent ADV/ sexual violence research highlights both prevalence and modifiable risk and protective factors that may help reduce such violence. Practitioners caring for youth should consider ADV/ sexual violence when seeing patients (including those struggling with substance use and other behaviours that contribute to poor health) and not simply rely on screening tools to identify those suffering from ADV/ sexual violence.
PD-L1 Immunohistochemistry Assay Concordance in Urothelial Carcinoma of the Bladder and Hypopharyngeal Squamous Cell Carcinoma
Authors: Hodgson Anjelica , Slodkowska Elzbieta , Jungbluth Achim , Liu Stanley K. , Vesprini Danny , Enepekides Danny , Higgins Kevin , Katabi Nora , Xu Bin , Downes Michelle R.
Published: May 2018

Programmed death ligand-1 (PD-L1) immunohistochemistry is used to guide treatment decisions regarding the use of checkpoint immunotherapy in the management of urothelial carcinoma of the bladder and hypopharyngeal (HP) squamous cell carcinoma. With increasing PD-L1 testing options, a need has arisen to assess the analytical comparability of diagnostic assays in order to develop a more sustainable testing strategy. Using tissue microarrays, PD-L1 expression in tumor cells (TCs) and immune cells (ICs) was manually scored in 197 cases and 27 cases of bladder and HP cancer, respectively. Three commercial kits (Ventana SP263, Ventana SP142, Dako 22C3) and 1 platform-independent test (Cell Signalling Technologies E1L3N) were utilized. Across the 3 commercially available clones, 14% and 74% of urothelial carcinomas were positive and negative, respectively, whereas 7% and 78% of HP carcinomas were positive and negative, respectively. Twelve percent of bladder and 15% HP cases showed discrepant PD-L1 classification results. Regardless of the scoring algorithm used, E1L3N provided comparable PD-L1 staining results. Fleiss’ kappa and intraclass correlation coefficient (ICC) analyses demonstrated substantial agreement among all antibody clones (k=0.639 to 0.791) and excellent reliability among SP263, 22C3, and E1L3N antibodies (ICC, 0.929 to 0.949) in TC staining. Compared with the other 3 clones, SP142 TC staining was lower with only moderate correlation (ICC, 0.500 to 0.619). Generally, the reliability of immune cell staining was lower compared with TC staining (ICC, 0.519 to 0.866). Our results demonstrate good analytic comparability of all 4 antibodies. The results are encouraging and support growing optimism in the pathology and oncology communities concerning strategies in PD-L1 assay use.
Prospective, Randomized, Controlled Comparison of Bupivacaine versus Liposomal Bupivacaine for Pain Management after Unilateral Delayed Deep Inferior Epigastric Perforator Free Flap Reconstruction
Authors: Gatherwright James , Knackstedt Rebecca W. , Ghaznavi Amir M. , Bernard Steven , Schwarz Graham , Moreira Andrea , Gurunluoglu Raffi , Djohan Risal
Published: May 2018

Effective postsurgical analgesia is a critical aspect of patient recovery. The goal of this prospective, randomized, controlled, blinded study was to examine the effect that liposomal bupivacaine delivered by means of a transversus abdominis plane block has on pain control in women undergoing unilateral deep inferior epigastric perforator flap reconstruction. Institutional review board approval was granted for this prospective study. Patients were eligible if they were undergoing unilateral, delayed deep inferior epigastric perforator flap reconstruction. Patients were randomized to one of three groups: liposomal bupivacaine transversus abdominis plane block, or bupivacaine pain pump. Charts were reviewed for demographics, length of stay, and postoperative narcotic use. There were eight patients in the liposomal bupivacaine and bupivacaine transversus abdominis plane block groups and five patients in the pain pump group. A retrospective cohort of six patients who did not receive any intervention was included. Patients who received a liposomal bupivacaine transversus abdominis plane block used statistically significantly less intravenous and total postoperative narcotics in milligrams and milligrams per kilogram per day compared with all other cohorts. They were able to get out of bed at an earlier time point. Overall hospital costs were similar among the groups. This is the first study to investigate liposomal bupivacaine delivered as a transversus abdominis plane block in a prospective, randomized, blinded study in women undergoing unilateral, delayed, abdominally based autologous breast reconstruction. The authors were able to demonstrate a significant reduction in intravenous and total narcotic use when a liposomal bupivacaine transversus abdominis plane block was used. Future studies are needed to prospectively investigate the effect that liposomal bupivacaine would have on immediate and bilateral reconstructions.
SLC22A5 Mutations in a Patient With Systemic Primary Carnitine Deficiency and Cleft Palate-Successful Perioperative Management
Authors: Hu Ching-Wei , Hu Ching-Hsuan , Wu-Chou Yah-Huei , Lo Lun-Jou
Published: May 2018

Background:

Primary systemic carnitine deficiency (SCD) is an autosomal-recessive disorder caused by SLC22A5 gene mutation resulting in defective cellular carnitine transporter organic cation transporter 2. Defective carnitine transporter causes renal carnitine wasting and low serum carnitine. Carnitine is an essential cofactor for the transportation of long-chain fatty acids into the mitochondria. Lacking of carnitine may cause metabolic decompensation and sudden death when the patient is exposed to prolonged fasting before an operation.

Methods:

An asymptomatic 9-month-old boy with SCD diagnosed by local hospital was referred to the authors’ hospital for incomplete cleft palate plastic surgery. Due to potential metabolic decompensation from prolonged fasting before the surgery, the patient underwent proper perioperative management.

Results:

The operation was successful and subsequent clinical course was fine. The patient was discharged on postoperative day 3.

Conclusion:

With proper perioperative management, patients with SCD and cleft palate can survive from prolonged fasting time before and during operation without metabolic decompensation manifestations. Early recognition of SCD and perioperative management can be lifesaving in preoperative infants with SCD.
Spatial gene-by-environment mapping for schizophrenia reveals locale of upbringing effects beyond urban-rural differences
Authors: Fan Chun Chieh , McGrath John J. , Appadurai Vivek , Buil Alfonso , Gandal Michael J. , Schork Andrew J. , Mortensen Preben Bo , Agerbo Esben , Geschwind Sandy A. , Geschwind Daniel , Werge Thomas , Thompson Wesley K. , Pedersen Carsten Bøcker
Published: May 2018

Identification of mechanisms underlying the incidence of psychiatric disorders has been hampered by the difficulty in discovering highly-predictive environmental risk factors. For example, prior efforts have failed to establish environmental effects predicting geospatial clustering of schizophrenia incidence beyond urban-rural differences. Here, we employ a novel statistical framework for decomposing the geospatial risk for schizophrenia based on locale of upbringing (place of residence, ages 0-7 years) and its synergistic effects with genetic liabilities (polygenic risk for schizophrenia). We use this statistical framework to analyze unprecedented geolocation and genotyping data in a case-cohort study of n=24,028 subjects, drawn from the 1.47 million Danish persons born between 1981 and 2005. Using this framework we estimate the effects of upbringing locale (E) and gene-by-locale interactions (GxE). After controlling for potential confounding variables, upbringing at high-risk locales increases the risk for schizophrenia on average by 122%, while GxE modulates genetic risk for schizophrenia on average by 78%. Within the boundaries of Copenhagen (the largest and most densely populated city of Denmark) specific locales vary substantially in their E and GxE effects, with hazard ratios ranging from 0.26 to 9.26 for E and from 0.20 to 5.95 for GxE. This study provides insight into the degree of geospatial clustering of schizophrenia risk, and our novel analytic procedure provides a framework for decomposing variation in geospatial risk into G, E, and GxE components.
Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species
Authors: Foissac Sylvain , Djebali Sarah , Munyard Kylie , Vialaneix Nathalie , Rau Andrea , Muret Kevin , Esquerré Diane , Zytnicki Matthias , Derrien Thomas , Bardou Philippe , Blanc Fany , Cabau Cèdric , Crisci Elisa , Dhorne-Pollet Sophie , Drouet Françoise , Faraut Thomas , Gonzalez Ignacio , Goubil Adeline , Lacroix-Lamandé Sonia , Laurent Fabrice , Marthey Sylvain , Marti-Marimon Maria , Momal-Leisenring Raphaelle , Mompart Florence , Quéré Pascale , Robelin David , Cristobal Magali San , Tosser-Klopp Gwenola , Vincent-Naulleau Silvia , Fabre Stéphane , der Laan Marie-Hélène Pinard-Van , Klopp Christophe , Tixier-Boichard Michelè , Acloque Hervé , Lagarrigue Sandrine , Giuffra Elisabetta
Published: May 2018

Background

Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).

Results

RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.

Conclusions

We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
Estimating the sensorimotor components of cybersickness
Authors: Weech Séamas , Parokaran Varghese Jessy , Barnett-Cowan Michael
Published: May 2018

The user base of the virtual reality (VR) medium is growing, and many of these users will experience cybersickness. Accounting for the vast inter-individual variability in cybersickness forms a pivotal step in solving the issue. Most studies of cybersickness focus on a single factor (e.g., balance, sex, vection), while other contributors are overlooked. Here, we characterize the complex relationship between cybersickness and several indices of sensorimotor processing. In a single session, we conducted a battery of tests of balance control, vection responses, and vestibular sensitivity to self-motion. A principal components regression model, primarily composed of balance control measures during vection, significantly predicted 37% of the variability in cybersickness measures. We observed strong, inverse associations between measures of sway and cybersickness. The results reiterate that the relationship between balance control and cybersickness is anything but straightforward. We discuss other factors that may account for the remaining variance in cybersickness.
Phylogenetic, population genetic, and morphological analyses reveal evidence for one species of Eastern Indigo Snake (Drymarchon couperi)
Authors: Folt Brian , Bauder Javan , Spear Stephen , Stevenson Dirk , Hoffman Michelle , Oaks Jamie R. , Jenkins Christopher , Steen David A. , Guyer Craig
Published: May 2018

Accurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized thatDrymarchon couperiis two species. Here, we use diverse approaches to test the two-species hypothesis forD. couperi. Our analyses reveal that (1) phylogenetic reconstruction in previous studies was based entirely on variance of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant population admixture and nuclear gene flow between mitochondrial lineages, and (3) morphological analyses recover a single diagnosable species. Our results are inconsistent with the two-species hypothesis, thus we reject it and formally placeDrymarchon kolpobasileusinto synonymy withD. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.
Advanced Graph Traversal used in Protein Interactions Network and Systems Biology
Authors: Rameshwari Rashmi , Chapadgaonkar Shilpa S , Prasad T. V.
Published: May 2018

A methodological framework of graph traversal in Systems Biology is presented here. At present there is need to investigate system rather individual component. The proposed analysis generalizes the various idea of network representations of protein interactions. This approach highlights various methods used in construction of protein interaction graph or network using suitable algorithm. The network nodes represent protein residues. Two nodes are connected if two residues are functionally correlated during the protein interaction event. The analysis of the resulting network enables the importance of each protein for its interactions. Furthermore, the determination of the pattern of edge between residues yields insights into the function prediction of an interaction. This is of special interest to investigate intrinsically disordered proteins, since it is difficult to determine structural (three-dimensional) architecture of each proteins in protein interactions network. In present work various approaches for protein interactions network construction, models and methods along with graph theories has been discussed which can be used to reveal hidden properties and features of a network. Further effective algorithm for visualization of protein interactions is suggested. As construction of Biological network is dependent on various properties of graph. A holistic approach such as Systems Biology approach can better solve the problem. This network profiling combined with knowledge extraction will help biologist to explore hidden information in genome as well as in proteome..
Superoanterior Fasciculus (SAF): Novel fiber tract revealed by diffusion MRI fiber tractography
Authors: David Szabolcs , Heemskerk Anneriet M. , Corrivetti Francesco , de Schotten Michel Thiebaut , Sarubbo Silvio , Petit Laurent , Viergever Max A. , Jones Derek K. , Mandonnet Emmanuel , Axer Hubertus , Evans John , Paus Tomáš , Leemans Alexander
Published: May 2018

Substantial progress in acquisition, processing, and analysis boosted the reliability of diffusion-weighted MRI and increased the accuracy of mapping white matter pathways with fiber tractography. Since the introduction of ‘region of interest’ (ROI) based virtual dissection by Conturo et al. in 1999, researchers have used tractography to identify white matter pathways, which faithfully represented previously known structures revealed by dyeing studies or post-mortem descriptions. The reconstructed streamlines are subjects of bundle-specific in vivo investigations to show differences between groups (e.g., comparing fractional anisotropy (FA) between patients and healthy controls) or to describe the relation between diffusion scalars and metrics of interest (e.g.: normal aging or changes due to learning). By applying a reverse strategy in using diffusion-weighted MRI tractography first, then supporting the findings with other techniques, we have identified a bilateral tract in the frontal cortex - the superoanterior fasciculus (SAF). The tract resembles the anterior shape of the cingulum bundle, but is located more frontally. To erase the chance that our findings are confounded by acquisition, processing or modeling artifacts, we analyzed a total of 421 subjects from four cohorts with different acquisition schemes and diverse processing pipelines. The findings were also completed with other non-MRI techniques, such as polarized light microscopy and dissection. Tractography results demonstrate a long pathway and are consistent among cohorts, while dissection indicates a series of U-shaped fibers connecting adjacent gyri. In conclusion, we hypothesize that these consecutive U-shaped fibers emerge to form a pathway, thereby resulting in a multicomponent bundle.
Somatosensory Perceptual Training Enhances Motor Learning by Observing
Authors: McGregor Heather R. , Cashaback Joshua G.A. , Gribble Paul L.
Published: May 2018

Neuroimaging and neurophysiological studies in humans have demonstrated that action observation activates brain regions involved in sensory-motor control. A growing body of work has shown that action observation can also facilitate motor learning; observing a tutor undergoing motor learning results in functional plasticity within the motor system and gains in subsequent motor performance. However, the effects of observing motor learning extend beyond the motor domain. Converging evidence suggests that learning also results in somatosensory functional plasticity and somatosensory perceptual changes. This work has raised the possibility that the somatosensory system is also involved in motor learning that results from observation. Here we tested this hypothesis using a somatosensory perceptual training paradigm. If the somatosensory system is indeed involved in motor learning by observing, then improving subjects' somatosensory function before observation should enhance subsequent observation-related gains in motor performance. Subjects performed a proprioceptive discrimination task in which a robotic manipulandum moved the subject’s passive upper limb and he or she made judgments about the position of the hand. Subjects in a Trained Learning group received trial-by-trial feedback to improve their proprioceptive acuity. Subjects in an Untrained Learning group performed the same task without feedback. All subjects then observed a learning video showing a tutor adapting her reaches to a left force field (FF). We found that subjects in the Trained Learning group, who had superior proprioceptive acuity prior to observation, benefited more from observing learning compared to subjects in the Untrained Learning group. Improving somatosensory function can therefore enhance subsequent observation-related gains in motor learning. This study provides further evidence in favor of the involvement of the somatosensory system in motor learning by observing.

Abbreviations

FF

:Force field

PD

:Maximum perpendicular deviation

IQR

:interquartile range

The authors report no financial interests or conflicts of interests.
A preliminary study of the calcification reason of pit mud in Chinese Strong-flavour liquor
Authors: Chen Bin , Wang Deliang , Yan Yinzhuo
Published: May 2018

Pit mud play a key role in the brewing process of Chinese Strong-flavour liquor. In this study, the organic acids and metal ions was determinated by Ion Chromatograph and Inductively Coupled Plasma Mass Spectrometry, respectively. The diversities and structures in pit mud were analyzed by using high-throughput sequencing based on Illumina Miseq platform. The results showed that the lactic acid in calcified pit mud was about 10 times higher than quality pit mud, and the calcium ions was about 20 times higher than quality pit mud. It could found a strange phenomenon, the calcified pit mud had more pyruvic acid and quality pit mud basically does not had this kind of material. The data analysis shown that the pit mud were detected prokaryotes 908 strains and the eukaryotes 226 strains. It was found that the Lactobacillus and Prevotella in calcified pit mud (the total of both increase 11 times) had a higher percentage. It can be guess that the lactic acid and metal ions would form lactic acid salt compounds and those compounds could affect the growth and reproduction of microbes in pit mud. This study provided a good comparison of physical and chemical properties between the calcified pit mud and the quality pit mud, which was significant for the maintenance of pit mud and the quality of liquor. Because of the first study for pit mud by using high-throughput sequencing, it could provide theoretical basis for improving microbes in pit mud.
Arterial smooth muscle cell PKD2 (TRPP1) channels control systemic blood pressure
Authors: Bulley Simon , Fernandez-Pena Carlos , Hasan Raquibul , Leo M. Dennis , Muralidharan Padmapriya , Mackay Charles E. , Evanson Kirk W. , Burris Sarah K. , Wang Qian , Kuruvilla Korah P. , Jaggar Jonathan H.
Published: May 2018

Systemic blood pressure is determined, in part, by arterial smooth muscle cells (myocytes). Several Transient Receptor Potential (TRP) channels are proposed to be expressed in arterial myocytes, but it is unclear if these proteins control physiological blood pressure and contribute to hypertensionin vivo. We generated the first inducible, smooth muscle-specific knockout for a TRP channel, namely for PKD2 (TRPP1), to investigate arterial myocyte and blood pressure regulation by this protein. Using this model, we show that intravascular pressure and α1-receptors activate PKD2 channels in arterial myocytes of different systemic organs. PKD2 channel activation in arterial myocytes leads to an inward Na+ current, membrane depolarization and vasoconstriction. Inducible, smooth muscle cell-specific PKD2 knockout lowers both physiological blood pressure and hypertension and prevents pathological arterial remodeling during hypertension. In summary, we show for the first time that arterial myocyte PKD2 channels control systemic blood pressure and targeting reduces high blood pressure.
The molecular pathogenesis of superoxide dismutase 1-linked ALS is promoted by low oxygen tension
Authors: Keskin Isil , Forsgren Elin , Lehmann Manuela , Andersen Peter M. , Brännström Thomas , Lange Dale J. , Synofzik Matthis , Nordström Ulrika , Zetterström Per , Marklund Stefan L. , Gilthorpe Jonathan D.
Published: May 2018

Mutations that destabilize superoxide dismutase 1 (SOD1) are a cause of amyotrophic lateral sclerosis (ALS). SOD1, which is located in the reducing cytosol, contains an oxidized disulfide bond required for stability. We show that the bond is an Achilles heel of the protein because it is sensitive to the oxygen tension. Culture of ALS patient-derived fibroblasts, astrocytes and induced pluripotent stem cell-derived mixed motor neuron and astrocyte cultures (MNACs) under lowered oxygen tensions caused reductive bond cleavage and misfolding. The effects were greatest in cells expressing mutant SOD1s, but also occurred in wild type SOD1 in cultures derived from patients carrying ALS-linked mutations inC9orf72, FUSandTBK1, as well as from controls. MNACs showed a greater response than the other cell types, including enhanced SOD1 aggregation, in line with the vulnerability of the motor system. Our results show that oxygen tension is a principal determinant of SOD1 stability and shed light on how risk factors for ALS, such as aging and other conditions causing reduced vascular perfusion, could lead to disease initiation and progression.

Subject categoriesNeuroscience; Molecular Biology of Disease
Floating search methodology for combining classification models for site recognition in DNA sequences
Authors: Pérez-Rodríguez Javier , de Haro-García Aida , García-Pedrajas Nicolás
Published: May 2018

Recognition of the functional sites of genes, such as translation initiation sites, donor and acceptor splice sites and stop codons, is a relevant part of many current problems in bioinformatics. Recognition of the functional sites of genes is also a fundamental step in gene structure predictions in the most powerful programs. The best approaches to this type of recognition use sophisticated classifiers, such as support vector machines. However, with the rapid accumulation of sequence data, methods for combining many sources of evidence are necessary as it is unlikely that a single classifier can solve this type of problem with the best possible performance.

A major issue is that the number of possible models to combine is large and the use of all of these models is impractical. In this paper, we present a framework that is based on floating search for combining as many classifiers as needed for the recognition of any functional sites of a gene. The methodology can be used for the recognition of translation initiation sites, donor and acceptor splice sites and stop codons. Furthermore, we can combine any number of classifiers that are trained on any species. The method is also scalable to large datasets, as is shown in experiments in which the whole human genome is used. The method is also applicable to other recognition tasks.

We present experiments on the recognition of these four functional sites in the human genome, which is used as the target genome, and use another 20 species as sources of evidence. The proposed methodology shows significant improvement over state-of-the-art methods for use in a thorough evaluation process. The proposed method is also able to improve heuristic selection of species to be used as sources of evidence as the search finds the most useful datasets.

Author summary

In this paper we present a methodology for combining many sources of information to recognize some of the most important functional sites in a genomic sequence. The functional sites of the sequences, such as, translation start sites, translation initiation sites, acceptor and donor splice sites and stop codons, play a very relevant role in many Bioinformatics tasks. Their accurate recognition is an important task by itself and also as part of gene structure prediction programs.

Our approach uses a methodology usually termed in Computer Science as “floating search”. This is a powerful heuristics applicable when the cost of evaluating each possible solution is high. The methodology is applied to the recognition of four different functional sites in the human genome using as additional sources of evidence the annotated genomes of other twenty different species.

The results show an advantage of the proposed method and also challenge the standard assumption of using only genomes not very close and not very far from the human to improve the recognition of functional sites in the human genome.
The interplay between small RNA pathways shapes chromatin landscapes inC. elegans
Authors: Gushchanskaia Ekaterina , Esse Ruben , Ma Qicheng , Lau Nelson , Grishok Alla
Published: May 2018

The nematodeC. eleganscontains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both “silencing” siRNAs bound by Worm-specific Argonautes (WAGO) and “activating” siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in thedrh-3(ne4253)mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in thecsr-1partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in bothdrh-3andcsr-1partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in thedrh-3(ne4253)mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.
3D protein structure from genetic epistasis experiments
Authors: Rollins Nathan J. , Brock Kelly P. , Poelwijk Frank J. , Stiffler Michael A. , Gauthier Nicholas P. , Sander Chris , Marks Debora S.
Published: May 2018

High-throughput experimental techniques have made possible the systematic sampling of the single mutation landscape for many proteins, defined as the change in protein fitness as the result of point mutation sequence changes. In a more limited number of cases, and for small proteins only, we also have nearly full coverage of all possible double mutants. By comparing the phenotypic effect of two simultaneous mutations with that of the individual amino acid changes, we can evaluate epistatic effects that reflect non-additive cooperative processes. The observation that epistatic residue pairs often are in contact in the 3D structure led to the hypothesis that a systematic epistatic screen contains sufficient information to identify the 3D fold of a protein. To test this hypothesis, we examined experimental double mutants for evidence of epistasis and identified residue contacts at 86% accuracy, including secondary structure elements and evidence for an alternative all-α-helical conformation. Positively epistatic contacts – corresponding to compensatory mutations, restoring fitness – were the most informative. Folded models generated from top-ranked epistatic pairs, when compared with the known structure, were accurate within 2.4 Å over 53 residues, indicating the possibility that 3D protein folds can be determined experimentally with good accuracy from functional assays of mutant libraries, at least for small proteins. These results suggest a new experimental approach for determining protein structure.
Dummy-atom modelling of stacked and helical nanostructures from solution scattering data
Authors: Burian Max , Amenitsch Heinz
Published: May 2018

The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a `projection scheme': by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif. This building block is fitted by allowing random dummy-atom movements without an underlying grid. The proposed method is verified using a variety of analytical models, and examples are presented of successful shape reconstruction from experimental data sets. To make the algorithm available to the scientific community, it is implemented in a graphical computer program that encourages user interaction during the fitting process and also includes an option for shape reconstruction of globular particles.
The corrosion resistance of low concentration ruthenium laser alloyed 304L stainless steel exposed to sulphuric acid at 25°C
Authors: Van der Merwe Josias Willem , Nelwalani Ndivhuwo Brayner
Published: May 2018

Purpose

This paper aims to study the effect of small ruthenium additions through laser surface alloying of 304L stainless steel on the corrosion resistance when exposed to a 1 M sulphuric acid solution at 25°C.

Design/methodology/approach

In this study, the characteristics of laser-alloyed surface layers enriched with low concentrations of ruthenium, less than 0.3 Wt.%, were evaluated. Samples were manufactured by performing laser surface alloying on a 304L stainless steel and using a 304 stainless steel powder enriched with ruthenium. The welded surfaces were cross-sectioned and the microstructure and chemical composition were analysed; in addition, the depth of penetration was determined. The corrosion characteristics of these surface welds were investigated through electrochemical analysis such as open circuit potential measurements and potentiodynamic scans.

Findings

It was found that with the addition of ruthenium levels of more than 0.2 Wt.%, the corrosion characteristics when exposed to 1 M sulphuric acid improved in the enriched welded zone.

Research limitations/implications

This study investigated the improvement of the surface layer of the 304L stainless steel because of the cost involved when ruthenium is alloyed in the bulk and showed that an improved corrosion resistance can be achieved in sulphuric acid at room temperature.

Practical implications

The hardness of the laser alloying was not significantly affected by the ruthenium, but more by the laser parameters.

Originality/value

This paper considers the improvement of 304L stainless steel through laser alloying with ruthenium.
A systemic exploration of drivers for and constraints on construction productivity enhancement
Authors: Javed Arshad Ali , Pan Wei , Chen Le , Zhan Wenting
Published: May 2018

Purpose

The purpose of this paper is to investigate the complex interdependence of the factors in driving or hindering construction productivity at the industry, project and activity levels in a systemic manner.

Design/methodology/approach

A mixed-methods design, which combines a critical literature review, an interview-based survey with 32 industry experts and five focus group meetings participated in by 109 representatives of a wide range of industry stakeholder groups, was employed to identify the drivers for and constraints on construction productivity enhancement in Hong Kong and explore the interrelated insights into the drivers and constraints.

Findings

The study conceptualised and validated a systemic framework for examining construction industry productivity, and developed three causal loop diagrams (CLDs) for illustrating the dynamic structures that underpin the complex systems of the drivers and constraints.

Research limitations/implications

Although the scope of the study was limited to Hong Kong, the results could be interpreted for critical learning in other urban contexts.

Practical implications

The systemic perspective of construction productivity and the CLDs of the drivers and constraints support the systems thinking of industry stakeholders in the formulation of holistic strategies for long-term construction industry productivity enhancement.

Originality/value

The study conceptualises construction productivity from a systemic perspective and provides empirically supported CLDs to facilitate future investigations into the complex system of construction productivity.
Improving contractor social networking on IBS infrastructure maintenance projects: a review
Authors: Ismail Zul-Atfi Bin
Published: May 2018

Purpose

A key factor adversely affecting contractor social networking performance is the improper handling and information management of contractor’s services delivery on websites. Contractor social networking is particularly problematic on industrialised building system (IBS) infrastructure maintenance projects where contractor’s certified quality product and firms are not matched with maintenance specialisation services. The paper aims to discuss this issue.

Design/methodology/approach

This paper reports on the early stages of research which is developing a new information and communications technology (ICT)-based approach to managing contractor social networking on IBS infrastructure maintenance schemes. As a precursor to this work, the paper reviews current contractor social networking websites practices on IBS infrastructure maintenance projects and explores the ICT tools and techniques currently being employed on such projects.

Findings

The findings reveal the need for more sophisticated contractor social networking websites solutions which accord with the needs of IBS infrastructure maintenance schemes.

Originality/value

The paper concludes by presenting a research framework for developing such a system in the future.