bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sphincteroplasty and perineoplasty with skin advancement flap in management of traumatic cloacal defect
Authors: Anaraki Fakhrolsadat , Etemad Omid 
Published: September 2016

Abstract
Background Traumatic cloacal defect (TCD) is the condition that occurs in 0.3% of women who have experienced the third/fourth-degree perineal laceration during traumatic Natural Vaginal Delivery (NVD). This condition has many undesirable effects in their lives. Surgery is the best way to repair this deformity and will improve the quality of life in these patients.
Design In this study, we prospectively studied 19 patients who were referred to the hospital with symptoms of TCD within years 2011 and 2015 with the mean of 2.6-yrs follow-up. They all underwent sphincteroplasty and perineoplasty with skin advancement flap.
Results Of all 19 patients, incontinence to solid faeces in 16 patients (84%), incontinence to liquid stool in 15 patients (78%) and incontinence to flatus in 4 patients (21%) were completely resolved. The FI score was decreased from the mean of 12.7 to 2.6. Sexual function was significantly improved in all of them and dyspareunia was completely disappeared in 9 patients (50%). The quality of life score was increased from the mean of 45 to 95. Post-operation complications were occurred in 3 of patients (wound infection in 2-cases and recto-vaginal fistula in another).
Conclusion Our findings show that sphincteroplasty and perineoplasty with skin advancement flap is an effective surgical technique to repair the perineal body due to its benefits and few complications. In this study, there was significant improvement in quality of life of almost all patients after this reconstructive surgery. Consulting with a colorectal surgeon is recommended for these cases.
The spin-up of a linearly stratified fluid in a sliced, circular cylinder
Authors: Munro R. J. , Foster M. R. 
Published: September 2016

A linearly stratified fluid contained in a circular cylinder with a linearly sloped base, whose axis is aligned with the rotation axis, is spun-up from a rotation rate $\unicode[STIX]{x1D6FA}-\unicode[STIX]{x0394}\unicode[STIX]{x1D6FA}$ to $\unicode[STIX]{x1D6FA}$ (with $\unicode[STIX]{x0394}\unicode[STIX]{x1D6FA}\ll \unicode[STIX]{x1D6FA}$) by Rossby waves propagating across the container. Experimental results presented here, however, show that if the Burger number $S$ is not small, then that spin-up looks quite different from that reported by Pedlosky & Greenspan (J. Fluid Mech., vol. 27, 1967, pp. 291–304) for $S=0$. That is particularly so if the Burger number is large, since the Rossby waves are then confined to a region of height $S^{-1/2}$ above the sloped base. Axial vortices, ubiquitous features even at tiny Rossby numbers of spin-up in containers with vertical corners (see van Heijst et al.Phys. Fluids A, vol. 2, 1990, pp. 150–159 and Munro & Foster Phys. Fluids, vol. 26, 2014, 026603, for example), are less prominent here, forming at locations that are not obvious a priori, but in the ‘western half’ of the container only, and confined to the bottom $S^{-1/2}$ region. Both decay rates from friction at top and bottom walls and the propagation speed of the waves are found to increase with $S$ as well. An asymptotic theory for Rossby numbers that are not too large shows good agreement with many features seen in the experiments. The full frequency spectrum and decay rates for these waves are discussed, again for large $S$, and vertical vortices are found to occur only for Rossby numbers comparable to $E^{1/2}$, where $E$ is the Ekman number. Symmetry anomalies in the observations are determined by analysis to be due to second-order corrections to the lower-wall boundary condition.
On the length scales of hypersonic shock-induced large separation bubbles near leading edges
Authors: Sriram R. , Srinath L. , Devaraj Manoj Kumar K. , Jagadeesh G. 
Published: September 2016

The interaction of a hypersonic boundary layer on a flat plate with an impinging shock – an order of magnitude stronger than that required for incipient separation of the boundary layer – near sharp and blunt leading edges (with different bluntness radii from 2 to 6 mm) is investigated experimentally, complemented by numerical computations. The resultant separation bubble is of length comparable to the distance of shock impingement from the leading edge, rather than the boundary layer thickness at separation; it is termed large separation bubble. Experiments are performed in the IISc hypersonic shock tunnel HST-2 at nominal Mach numbers 5.88 and 8.54, with total enthalpies 1.26 and $1.85~\text{MJ}~\text{kg}^{-1}$ respectively. Schlieren flow visualization using a high-speed camera and surface pressure measurements using fast response sensors are the diagnostics. For the sharp leading edge case, the separation length was found to follow an inviscid scaling law according to which the scaled separation length $(L_{sep}/x_{r})M_{er}^{3}$ is found to be linearly related to the reattachment pressure ratio $p_{r}/p_{er}$; where $L_{sep}$ is the measured separation length, $x_{r}$ the distance of reattachment from the leading edge, $M$ the Mach number, $p$ the static pressure and the subscripts $r$ and $e$ denote the conditions at the reattachment location and at the edge of the boundary layer at the shock impingement location respectively. However, for all the blunt leading edges $(L_{sep}/x_{r})M_{er}^{3}$ was found to be a constant irrespective of Mach number and much smaller than the sharp leading edge cases. The possible contributions of viscous and non-viscous mechanisms towards the observed phenomena are explored.
On the errors involved in ice-thickness estimates II: errors in digital elevation models of ice thickness
Authors: LAPAZARAN J. J. , OTERO J. , MARTÍN-ESPAÑOL A. , NAVARRO F. J. 
Published: September 2016

ABSTRACTThis paper is the second (Paper II) in a set of studies concerning the errors involved in the estimate of ice thickness and ice volume. Here we present a detailed analysis of the errors involved in the generation of ice-thickness DEMs constructed, most often, from GPR data, complemented by boundary data and sometimes, additional synthetic data arising from estimates based on theoretical considerations supported by independent data. We describe a complete methodology of error analysis that, starting from the errors in the data, propagates them to the grid nodes. In turn, the interpolation error at the grid nodes is calculated using a novel procedure that also provides an estimate of the bias introduced by the interpolation process. Finally, both errors are combined at the grid nodes to produce a gridpoint-dependent error estimate, which is complemented by an overall error estimate providing an assessment of the quality of the DEM. This methodology is illustrated with the case study of Werenskioldbreen, a land-terminating polythermal glacier in Svalbard.
SINCERITY, HYPOCRISY, AND CONSPIRACY THEORY IN THE OCCUPIED PALESTINIAN TERRITORY
Authors: Allen Lori 
Published: September 2016

AbstractConcerns about lying and sincerity in politics are common in most societies, as are concerns about conspiracy theories. But in the occupied Palestinian territory, these concerns give rise to particular kinds of effects because of the conditions of Israeli occupation. Political theorists often interpret opacity claims and conspiracy theories as responses to social disorder. In occupied Palestine, disorder and instability are standard. Opacity claims and conspiracy theories therefore require a different kind of analysis. Through an examination of the semiotic ideology of sincerity, especially as it has emerged in the conflict between Fatah and Hamas, this article argues that opacity claims act as a form of nationalist pedagogy, at once reinforcing the basic principles of sincerity of action and word, and encouraging a wariness of political spin.
Geographic Information Systems (GIS) in International Relations
Authors: Branch Jordan 
Published: September 2016

AbstractGeographic Information Systems (GIS) are being applied with increasing frequency, and with increasing sophistication, in international relations and in political science more generally. Their benefits have been impressive: analyses that simply would not have been possible without GIS are now being completed, and the spatial component of international politics—long considered central but rarely incorporated analytically—has been given new emphasis. However, new methods face new challenges, and to apply GIS successfully, two specific issues need to be addressed: measurement validity and selection bias. Both relate to the challenge of conceptualizing nonspatial phenomena with the spatial tools of GIS. Significant measurement error can occur when the concepts that are coded as spatial variables are not, in fact, validly measured by the default data structure of GIS, and selection bias can arise when GIS systematically excludes certain types of units. Because these potential problems are hidden by the technical details of the method, GIS data sets and analyses can sometimes appear to overcome these challenges when, in fact, they fail to do so. Once these issues come to light, however, potential solutions become apparent—including some in existing applications in international relations and in other fields.
Insight from animal models of environmentally driven epigenetic changes in the developing and adult brain
Authors: Doherty Tiffany S. , Roth Tania L. 
Published: September 2016

AbstractThe efforts of many neuroscientists are directed toward understanding the appreciable plasticity of the brain and behavior. In recent years, epigenetics has become a core of this focus as a prime mechanistic candidate for behavioral modifications. Animal models have been instrumental in advancing our understanding of environmentally driven changes to the epigenome in the developing and adult brain. This review focuses mainly on such discoveries driven by adverse environments along with their associated behavioral outcomes. While much of the evidence discussed focuses on epigenetics within the central nervous system, several peripheral studies in humans who have experienced significant adversity are also highlighted. As we continue to unravel the link between epigenetics and phenotype, discerning the complexity and specificity of epigenetic changes induced by environments is an important step toward understanding optimal development and how to prevent or ameliorate behavioral deficits bred by disruptive environments.
Genome-wide DNA methylation in 1-year-old infants of mothers with major depressive disorder
Authors: Cicchetti Dante , Hetzel Susan , Rogosch Fred A. , Handley Elizabeth D. , Toth Sheree L. 
Published: September 2016

AbstractA genome-wide methylation study was conducted among a sample of 114 infants (M age = 13.2 months, SD = 1.08) of low-income urban women with (n = 73) and without (n = 41) major depressive disorder. The Illumina HumanMethylation450 BeadChip array with a GenomeStudio Methylation Module and Illumina Custom model were used to conduct differential methylation analyses. Using the 5.0 × 10–7p value, 2,119 loci were found to be significantly different between infants of depressed and nondepressed mothers. Infants of depressed mothers had greater methylation at low methylation sites (0%–29%) compared to infants of nondepressed mothers. At high levels of methylation (70%–100%), the infants of depressed mothers were predominantly hypomethylated. The mean difference in methylation between the infants of depressed and infants of nondepressed mothers was 5.23%. Disease by biomarker analyses were also conducted using GeneGo MetaCore Software. The results indicated significant cancer-related differences in biomarker networks such as prostatic neoplasms, ovarian and breast neoplasms, and colonic neoplasms. The results of a process networks analysis indicated significant differences in process networks associated with neuronal development and central nervous system functioning, as well as cardiac development between infants of depressed and nondepressed mothers. These findings indicate that early in development, infants of mothers with major depressive disorder evince epigenetic differences relative to infants of well mothers that suggest risk for later adverse health outcomes.
An endoplasmic reticulum stress-regulated lncRNA hosting a microRNA megacluster induces early features of diabetic nephropathy
Authors: Kato Mitsuo , Wang Mei , Chen Zhuo , Bhatt Kirti , Oh Hyung Jung , Lanting Linda , Deshpande Supriya , Jia Ye , Lai Jennifer Y.C. , O’Connor Christopher L. , Wu YiFan , Hodgin Jeffrey B. , Nelson Robert G. , Bitzer Markus , Natarajan Rama 
Published: September 2016

AbstractIt is important to find better treatments for diabetic nephropathy (DN), a debilitating renal complication. Targeting early features of DN, including renal extracellular matrix accumulation (ECM) and glomerular hypertrophy, can prevent disease progression. Here we show that a megacluster of nearly 40 microRNAs and their host long non-coding RNA transcript (lnc-MGC) are coordinately increased in the glomeruli of mouse models of DN, and mesangial cells treated with transforming growth factor-β1 (TGF- β1) or high glucose. Lnc-MGC is regulated by an endoplasmic reticulum (ER) stress-related transcription factor, CHOP. Cluster microRNAs and lnc-MGC are decreased in diabeticChop−/−mice that showed protection from DN. Target genes of megacluster microRNAs have functions related to protein synthesis and ER stress. A chemically modified oligonucleotide targeting lnc-MGC inhibits cluster microRNAs, glomerular ECM and hypertrophy in diabetic mice. Relevance to human DN is also demonstrated. These results demonstrate the translational implications of targeting lnc-MGC for controlling DN progression.
Single-molecule visualization of dynamic transitions of pore-forming peptides among multiple transmembrane positions
Authors: Li Ying , Qian Zhenyu , Ma Li , Hu Shuxin , Nong Daguan , Xu Chunhua , Ye Fangfu , Lu Ying , Wei Guanghong , Li Ming 
Published: September 2016

AbstractResearch on the dynamics of single-membrane proteins remains underdeveloped due to the lack of proper approaches that can probe in real time the protein’s insertion depth in lipid bilayers. Here we report a single-molecule visualization method to track both vertical insertion and lateral diffusion of membrane proteins in supported lipid bilayers by exploiting the surface-induced fluorescence attenuation (SIFA) of fluorophores. The attenuation follows a d−4 dependency, where d is the fluorophore-to-surface distance. The method is validated by observing the antimicrobial peptide LL-37 to transfer among five transmembrane positions: the surface, the upper leaflet, the centre, the lower leaflet and the bottom of the lipid bilayer. These results demonstrate the power of SIFA to study protein-membrane interactions and provide unprecedented in-depth understanding of molecular mechanisms of the insertion and translocation of membrane proteins.
Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli
Authors: Laganenka Leanid , Colin Remy , Sourjik Victor 
Published: September 2016

AbstractBacteria communicate by producing and sensing extracellular signal molecules called autoinducers. Such intercellular signalling, known as quorum sensing, allows bacteria to coordinate and synchronize behavioural responses at high cell densities. Autoinducer 2 (AI-2) is the only known quorum-sensing molecule produced by Escherichia coli but its physiological role remains elusive, although it is known to regulate biofilm formation and virulence in other bacterial species. Here we show that chemotaxis towards self-produced AI-2 can mediate collective behaviour—autoaggregation—of E. coli. Autoaggregation requires motility and is strongly enhanced by chemotaxis to AI-2 at physiological cell densities. These effects are observed regardless whether cell–cell interactions under particular growth conditions are mediated by the major E. coli adhesin (antigen 43) or by curli fibres. Furthermore, AI-2-dependent autoaggregation enhances bacterial stress resistance and promotes biofilm formation.
Nonlinear optical observation of coherent acoustic Dirac plasmons in thin-film topological insulators
Authors: Glinka Yuri D. , Babakiray Sercan , Johnson Trent A. , Holcomb Mikel B. , Lederman David 
Published: September 2016

AbstractLow-energy collective electronic excitations exhibiting sound-like linear dispersion have been intensively studied both experimentally and theoretically for a long time. However, coherent acoustic plasmon modes appearing in time-domain measurements are rarely observed due to Landau damping by the single-particle continua. Here we report on the observation of coherent acoustic Dirac plasmon (CADP) modes excited in indirectly (electrostatically) opposite-surface coupled films of the topological insulator Bi2Se3. Using transient second-harmonic generation, a technique capable of independently monitoring the in-plane and out-of-plane electron dynamics in the films, the GHz-range oscillations were observed without corresponding oscillations in the transient reflectivity. These oscillations were assigned to the transverse magnetic and transverse electric guided CADP modes induced by the evanescent guided Lamb acoustic waves and remained Landau undamped due to fermion tunnelling between the opposite-surface Dirac states.
The Architecture of the Cytoplasmic Region of Type III Secretion Systems
Authors: Makino Fumiaki , Shen Dakang , Kajimura Naoko , Kawamoto Akihiro , Pissaridou Panayiota , Oswin Henry , Pain Maria , Murillo Isabel , Namba Keiichi , Blocker Ariel J. 
Published: September 2016

AbstractType III secretion systems (T3SSs) are essential devices in the virulence of many Gram-negative bacterial pathogens. They mediate injection of protein effectors of virulence from bacteria into eukaryotic host cells to manipulate them during infection. T3SSs involved in virulence (vT3SSs) are evolutionarily related to bacterial flagellar protein export apparatuses (fT3SSs), which are essential for flagellar assembly and cell motility. The structure of the external and transmembrane parts of both fT3SS and vT3SS is increasingly well-defined. However, the arrangement of their cytoplasmic and inner membrane export apparatuses is much less clear. Here we compare the architecture of the cytoplasmic regions of the vT3SSs of Shigella flexneri and the vT3SS and fT3SS of Salmonella enterica serovar Typhimurium at ~5 and ~4 nm resolution using electron cryotomography and subtomogram averaging. We show that the cytoplasmic regions of vT3SSs display conserved six-fold symmetric features including pods, linkers and an ATPase complex, while fT3SSs probably only display six-fold symmetry in their ATPase region. We also identify other morphological differences between vT3SSs and fT3SSs, such as relative disposition of their inner membrane-attached export platform, C-ring/pods and ATPase complex. Finally, using classification, we find that both types of apparatuses can loose elements of their cytoplasmic region, which may therefore be dynamic.
Process-based design of dynamical biological systems
Authors: Tanevski Jovan , Todorovski Ljupčo , Džeroski Sašo 
Published: September 2016

AbstractThe computational design of dynamical systems is an important emerging task in synthetic biology. Given desired properties of the behaviour of a dynamical system, the task of design is to build an in-silico model of a system whose simulated be- haviour meets these properties. We introduce a new, process-based, design methodology for addressing this task. The new methodology combines a flexible process-based formalism for specifying the space of candidate designs with multi-objective optimization approaches for selecting the most appropriate among these candidates. We demonstrate that the methodology is general enough to both formulate and solve tasks of designing deterministic and stochastic systems, successfully reproducing plausible designs reported in previous studies and proposing new designs that meet the design criteria, but have not been previously considered.
A powerful weighted statistic for detecting group differences of directed biological networks
Authors: Yuan Zhongshang , Ji Jiadong , Zhang Xiaoshuai , Xu Jing , Ma Daoxin , Xue Fuzhong 
Published: September 2016

AbstractComplex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. Different physiological conditions such as cases and controls may manifest as different networks. Statistical comparison between biological networks can provide not only new insight into the disease mechanism but statistical guidance for drug development. However, the methods developed in previous studies are inadequate to capture the changes in both the nodes and edges and often ignore the network structure. In this study, we present a powerful weighted statistical test for group differences of directed biological networks, which is independent of the network attributes and can capture the changes in both the nodes and edges, as well as simultaneously accounting for the network structure through putting more weights on the difference of nodes locating on relatively more important position. Simulation studies illustrate that this method had better performance than previous ones under various sample sizes and network structures. One application to GWAS of leprosy successfully identifies the specific gene interaction network contributing to leprosy. Another real data analysis significantly identifies a new biological network, which is related to acute myeloid leukemia. One potential network responsible for lung cancer has also been significantly detected. The source R code is available on our website.
Phase-matched second harmonic generation with on-chip GaN-on-Si microdisks
Authors: Roland I. , Gromovyi M. , Zeng Y. , El Kurdi M. , Sauvage S. , Brimont C. , Guillet T. , Gayral B. , Semond F. , Duboz J. Y. , de Micheli M. , Checoury X. , Boucaud P. 
Published: September 2016

AbstractWe demonstrate phase-matched second harmonic generation in gallium nitride on silicon microdisks. The microdisks are integrated with side-coupling bus waveguides in a two-dimensional photonic circuit. The second harmonic generation is excited with a continuous wave laser in the telecom band. By fabricating a series of microdisks with diameters varying by steps of 8 nm, we obtain a tuning of the whispering gallery mode resonances for the fundamental and harmonic waves. Phase matching is obtained when both resonances are matched with modes satisfying the conservation of orbital momentum, which leads to a pronounced enhancement of frequency conversion.