bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improve your Galaxy text life: The Query Tabular Tool
Authors: Johnson James E. , Kumar Praveen , Easterly Caleb , Esler Mark , Mehta Subina , Eschenlauer Arthur C. , Hegeman Adrian D. , Jagtap Pratik D. , Griffin Timothy  J. 
Published: October 2018

Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different ‘omic domains (e.g. genomics, proteomics, metabolomics). In these complex workflows, intermediate outputs are often generated as tabular text files, which must be transformed into customized formats which are compatible with the next software tools in the pipeline. Consequently, many text manipulation steps are added to an already complex workflow, overly complicating the process and decreasing usability, especially for non-expert bench researchers focused on obtaining results. In some cases, limitations to existing text manipulation are such that desired analyses can only be carried out using highly sophisticated processing steps beyond the reach of most users. As a solution, we have developed the Query Tabular Galaxy tool, which leverages a SQLite database generated from tabular input data. This database can be queried and manipulated to produce transformed and customized tabular outputs compatible with downstream processing steps. Regular expressions can also be utilized for even more sophisticated manipulations, such as find and replace and other filtering actions. Using several Galaxy-based multi-omic workflows as an example, we demonstrate how the Query Tabular tool dramatically streamlines and simplifies the creation of multi-step analyses, efficiently enabling complicated textual manipulations and processing. This tool should find broad utility for users of the Galaxy platform seeking to develop and use sophisticated workflows involving text manipulation on tabular outputs.
Excision with primary midline closure compared with Limberg flap in the treatment of sacrococcygeal pilonidal disease: a randomised clinical trial
Authors: Arnous M , Elgendy H , Thabet W , Emile SH , Elbaz SA , Khafagy W 
Published: October 2018

BackgroundAlthough several surgical techniques for treatment of sacrococcygeal pilonidal sinus (SPND) have been described, there is no consensus on the optimal surgical procedure. In this study we compared excision with primary closure and Limberg flap in the treatment of SPND.MethodsThis was a prospective randomised clinical trial in patients with SPND who were randomly allocated to one of two groups: group I (excision and primary closure) and group II (Limberg flap technique). The primary outcome of the trial was recurrence of SPND whereas postoperative complications, return to work and cosmetic results were the secondary outcomes.ResultsSixty patients were included, with a mean age of 24.1 years and mean body mass index (BMI) of 26.8 kg/m2. Group 1 had significantly shorter operation time than group II. Both groups had similar hospital stay and comparable complication rates (43.3% vs 30%; P = 0.4). Group I had significantly higher recurrence rate (20% vs 0; P < 0.02) and significantly better cosmetic satisfaction score than group II. Being hairy (P = 0.04), positive family history (P = 0.03), diabetes mellitus (P = 0.005) and history of previous surgery for SPND (P = 0.01) were the significant predictors for recurrence.ConclusionsThe Limberg flap is an effective technique for the treatment of SPND with very low recurrence rate and comparable complication rate and hospital stay to excision and primary closure. Excision and primary closure offered the advantages of quicker healing time, earlier resumption of daily activities, better cosmetic results, which may render it more suitable for patients with low risk for recurrence.
Will we ever cure nasal polyps?
Authors: Ta NH 
Published: October 2018

BACKGROUND Nasal polyposis is a benign hyperplastic growth of nasal mucosa. There is a paucity of evidence on the prevalence and incidence of nasal polyposis. Although nasal polyps can be asymptomatic, they can cause a spectrum of nasal problems including nasal obstruction, rhinorrhoea, nasal congestion, anosmia resulting in ageusia. Nasal polyps are mostly associated with chronic rhinosinusitis, The current management of chronic rhinosinusitis with nasal polyps is controversial and is not curative. METHODS A Medline search was conducted, using the keywords ‘rhinosinusitis’, ‘sinusitis’, ‘classification’ and ‘’aetiology. FINDINGS The current treatment of nasal polyposis in chronic rhinosinusitis with nasal polyps is still challenging. Emerging research through endotypes profiling aims to better understand the complexities of this heterogeneous disease to personalise treatment and provide a cure. Randomised controlled trials aim to provide robust evidence for current management options.
A prospective clinical, cost and environmental analysis of a clinician-led virtual urology clinic
Authors: Miah S , Dunford C , Edison M , Eldred-Evans D , Gan C , Shah TT , Lunn P , Winkler M , Ahmed HU , Gibbons N , Hrouda D 
Published: October 2018

Introduction A virtual clinic is a form of telemedicine where contact between clinical teams and patients occur without face-to-face consultation. Our study aims to quantify the clinical, financial and environmental benefits of our virtual urology clinic. Material and methods We collected data prospectively from our weekly follow-up virtual clinic over a continuous four-month period between July and September 2017. Results In total, we reviewed 409 patients. Following virtual clinic consultation, 68.5% of our patients were discharged from further follow-up. The majority of our patients (male 57.7%, female 55.5%) were of working age. The satisfaction scores were high, at 90.1%, and there were no reported adverse events as a result of using the virtual clinic. Our calculated cost savings were £18,744, with a predicted 12-month cost saving of £56,232. The creation of additional face-to-face clinic capacity has created an estimated 12-month increase in tariff generation for our unit of £72,072. In total, 4623 travel miles were avoided by patients using the virtual clinic, with an estimated avoided carbon footprint of 0.35–1.45 metric tonnes of CO2e, depending on mode of transport. Our predicted 12-month avoided carbon footprint is 1.04–4.04 metric tonnes of CO2e. Conclusions Our virtual clinic model has demonstrated a trifecta of positive outcomes, namely, clinical, financial and environmental benefits. The environmental importance and benefits of a virtual clinic should be promoted as a social enterprise value when engaging stakeholders in setting up such a urological service. We propose the adoption of our virtual clinic model in those urological units considering this method of telemedicine.
Suture choice to reduce occurrence of surgical site infection, hernia, wound dehiscence and sinus/fistula: a network meta-analysis
Authors: Zucker BE , Simillis C , Tekkis P , Kontovounisios C 
Published: October 2018

Background There are many options and little guiding evidence when choosing suture types with which to close the abdominal wall fascia. This network meta-analysis investigated the effect of suture materials on surgical site infection, hernia, wound dehiscence and sinus/fistula occurrence after abdominal surgery. The aim was to provide clarity on whether previous recommendations on suture choice could be followed with confidence. Methods and methods In February 2017, the Cochrane Central Register of Controlled Trials, Medline, EMBASE and Science Citation Index Expanded were searched for randomised controlled trials investigating the effect of suture choice on these four complications in closing the abdomen. A reference search of identified trials was performed. Prisma guidelines and the Cochrane risk of bias tool were followed in the data extraction and synthesis. Two review authors screened titles and abstracts of trials identified. A random effect model was used for the surgical site infection network based on the deviance information criterion statistics. Results Thirty-one trials were included (11,533 participants). No suture material reached the predetermined 90% probability threshold for determination of ‘best treatment’ for any outcome. Pairwise comparisons largely showed no differences between suture types for all outcomes measured. However, nylon demonstrated a reduction in the occurrence of incisional hernias with respect to two commonly used absorbable sutures: polyglycolic acid (odds ratio, OR 1.91; 95% confidence interval, CI, 1.01–3.63) and polyglyconate (OR 2.18; 95% CI 1.17–4.07). Conclusions No suture type can be considered the ‘best treatment’ for the prevention of surgical site infection, hernia, wound dehiscence and sinus/fistula occurrence.
Public Health Insurance and Prescription Medications for Mental Illness
Authors: Maclean Johanna Catherine , Cook Benjamin , Carson Nicholas , Pesko Michael F 
Published: October 2018

Abstract
Mental illnesses are prevalent in the United States and globally. Cost is a critical barrier to treatment receipt. We study the effects of the Affordable Care Act's recent expansion of Medicaid, a public insurance system for the poor in the U.S., on psychotropic prescription medications for mental illness. We estimate differences-in-differences models using administrative data on medications for which Medicaid was a third-party payer over the period 2011–2017. Our findings suggest that these expansions increased psychotropic prescriptions by 21.0%. We show that Medicaid, and not patients, financed these prescriptions. For states expanding Medicaid, the total cost of these prescriptions was $28.0 M by the second quarter of 2017. Expansion effects were experienced across most major mental illness categories and across states with different levels of patient need, system capacity, and expansion scope. We find no statistically significant evidence that Medicaid expansion reduced mental illness.
Bayesian Prediction Bounds for the Exponential-type Distribution Based on Generalized Progressive Hybrid Censoring Scheme
Authors: Kotb Mohammed S. 
Published: October 2018

AbstractThis paper deals with predicting censored data in a general form for the underlying distribution based on generalized progressive hybrid censoring scheme. A conjugate prior is used and the predictive reliability function is obtained in the one-sample case. The special case of linear exponential distributed observations is considered and completed with numerical results.
Nondestructive Extraction of Parameters of Multilayered Media Using Terahertz Pulse Technique
Authors: Singh Surya Prakash , Tiwari Nilesh K. , Akhtar M. Jaleel 
Published: October 2018

Abstract
In this work, an efficient non-invasive terahertz pulse technique is proposed and investigated to determine the thickness and refractive index of each layer in an optically thick stratified media. A closed form formulations are derived for simultaneous extraction of the thickness and complex refractive index of each layer with the help of primary reflected signals from the multilayered structure. The proposed technique is numerically tested using a full wave electromagnetic simulator and is experimental verified in the millimeter wave frequency range by utilizing the power peaks corresponding to the primary reflected signals. The numerical and measured results of multilayered samples under test are in good agreement with the reference data. The proposed terahertz pulse technique can be used for non-destructive testing of the multilayered system existing in various industries.
Pressure-Leaching Behavior of Nickel from Ni–Mo Ore in Aqueous Oxygenated Media
Authors: Zhigan Deng , Jiuyuan Bai , Chang Wei , Gang Fan , Xingbin LI , Minting Li , Cunxiong LI 
Published: October 2018

AbstractNi–Mo ore is a multi-metal complex and unique mineral resource that exists as a black shale. This ore contains more than 4 wt% Mo and at least 2 wt% Ni. Economic value is associated with deriving products from Ni–Mo ore that contains amorphous colloidal sulfides and that is highly active. Under low-temperature hydrothermal conditions (water at 120 °C or more) and in excess oxygen, amorphous sulfides are oxidized easily to metal-sulfate forms, which leads to nickel and molybdenum dissolution. In this study, the effects of agitation speed, temperature, oxygen partial pressure and particle size on the rate of nickel leaching were investigated. The leaching rate was nearly independent of agitation speed above 400 rpm and increased with a decrease in particle size. A temperature increase to 150 °C contributed significantly to the nickel leaching rate. Oxygen pressure influences nickel leaching, with an oxygen pressure of between 0.5 MPa and 0.7 MPa providing the greatest effect. The pressure-leaching behavior of nickel was fitted to a shrinking-core kinetic model. The mathematical analyses indicates that the dissolution process is chemical-reaction controlled during early dissolution, with an activation energy of 42.68 kJ/mol, and the reaction order with respect to the oxygen partial pressure was 0.79. Up to nearly 70 % nickel was dissolved into solution, and product layers of molybdenum and iron oxide were formed on the surface of the Ni–Mo ore particles, which prevented further nickel dissolution. Thereafter, nickel leaching was controlled by liquid-film diffusion, with an activation energy of 11.01 kJ/mol.
Effect of Natural and Artificial Light on Fe(III) Organic Complexes Photolysis: Case of Fe (III)-Malonate and Fe(III)-Malate
Authors: Dekkiche Besma Anfal , Seraghni Nassira , Debbache Nadra , Ghoul Imane , Sehili Tahar 
Published: October 2018

Abstract
The photolysis of iron(III) organic complexes in the presence of natural and simulated light was a concern for the role it plays within the environment in terms of producing hydroxyl radicals able to degrade organic products. In the present work, the study focused on two iron(III) organic complexes. The characterization of these complexes by spectrometry allowed to show their stability in environment with a stability constant equal to Log β = 13.13 for the complex Fe(III)-malonate, and Log β = 20.85 for the Fe(III)-malate complex. Photolysis of these complexes was carried out using a lamp at 365 nm at different pHs, and followed by several assay Fe(II), H2O2 and •OH. The complexes present different photo-reactivities, in the case of Fe(III)-malate, the photolysis is favored by the Fenton process and generates hydroxyl radicals, contrarily to Fe(III)-malonate photolysis which generates an oxidizing •CH2COOH radical without formation of H2O2 nor of •OH. The presence of oxygen and the addition of isopropanol and chloroform show different effects on the complex photolysis. Complexes mineralization at natural irradiation was also studied using chemical oxygen demand (COD).
Finite-Sample Theory and Bias Correction of Maximum Likelihood Estimators in the EGARCH Model
Authors: Demos Antonis , Kyriakopoulou Dimitra 
Published: October 2018

AbstractWe derive the analytical expressions of bias approximations for maximum likelihood (ML) and quasi-maximum likelihood (QML) estimators of the EGARCH (1,1) parameters that enable us to correct after the bias of all estimators. The bias-correction mechanism is constructed under the specification of two methods that are analytically described. We also evaluate the residual bootstrapped estimator as a measure of performance. Monte Carlo simulations indicate that, for given sets of parameters values, the bias corrections work satisfactory for all parameters. The proposed full-step estimator performs better than the classical one and is also faster than the bootstrap. The results can be also used to formulate the approximate Edgeworth distribution of the estimators.
Complexity of Knee Extensor Torque: Effect of Aging and Contraction Intensity
Authors: Fiogbé Elie , Vassimon-Barroso Verena , Catai Aparecida Maria , de Melo Ruth Caldeira , Quitério Robison José , Porta Alberto , Takahashi Anielle Cristhine de Medeiros 
Published: October 2018

Abstract
Fiogbé, E, Vassimon-Barroso, V, Catai, AM, de Melo, RC, Quitério, RJ, Porta, A, and Takahashi, ACdM. Complexity of knee extensor torque: effect of aging and contraction intensity. J Strength Cond Res 35(4): 1050–1057, 2021—Assessing the knee extensors' torque complexity in older adults is relevant because these muscles are among the most involved in functional daily activities. This study aimed to investigate the effects of aging and isometric contraction intensity on knee extensor torque complexity. Eight young (24 ± 2.8 years) and 13 old adults (63 ± 2.8 years) performed 3 maximal (maximum voluntary contraction [MVC], duration = 10 seconds) and submaximal isometric contractions (SICs, targeted at 15, 30, and 40% of MVC, respectively) of knee extensors. Torque signals were sampled continuously, and the metrics of variability and complexity were calculated basing on the SIC torque data. The coefficient of variation (CV) was used to quantify the torque variability. The torque complexity was determined by calculating the corrected approximate entropy (CApEn) and sample entropy (SampEn) and its normalized versions (NCApEn and NSampEn). Young subjects produced greater isometric torque than older adults, and the CV was similar between both groups except at the highest force level (40% MVC) where young subjects' value was higher. The major novel finding of this investigation was that although the knee extensor torque complexity is reduced in older adults, its relationship with contraction intensity is similar to young subjects. This means that despite the age-related decrease of the interactions between the components of the neuromuscular system, the organization of force control remains preserved in older adults, at least up to just below the force midrange.
A Hollow Cylinder Radial-Seepage Apparatus for Evaluating Permeability of Sheared Compacted Clay
Authors: Wang Gang , Wei Xing , Zou Ting 
Published: October 2018

Abstract
Compacted clay is widely used to control seepage in earth and rock-fill dams in favor of its low permeability. The clay at certain locations of dams often experience large shear strain due to differential settlement, which may lead to changes in seepage resistance. A new apparatus was developed to examine the permeability evolution of compacted clay during shearing. The apparatus tests a hollow cylindrical specimen holding by a set of inner and outer laminar rings. The specimen can thus be compressed in the height direction and sheared in the circumferential direction. The permeability is measured by radial seepage from the inner side to the outer side of the hollow cylinder. A series of tests on heavily compacted specimens of a core-wall clay were conducted to demonstrate the performance of the new apparatus. The permeability of unsheared specimens under different surcharge pressures and hydraulic gradients was investigated firstly, and the observed phenomenon agreed well with those in conventional permeameters. Then the permeability evolution during shearing was investigated under constant surcharge pressures. It was found that the compacted specimens deformed non-uniformly with a well-developed shear band, and the permeability of the shear band determines the overall seepage resistance. The permeability of the shear band increases during shearing under low surcharge pressure, whereas under high surcharge pressure, it varies insignificantly. Such behavior is related to different structural changes of shear bands under low and high surcharge pressures. The preliminary test results highlighted an important fact, that the heavy-compacted clay under low surcharge pressure could generate low seepage resistance shear bands when subjected to a large shear, leading to a high risk of concentrated leakage and erosion. The new apparatus could prove useful for clarifying stress conditions triggering low seepage resistance shear bands in compacted clays.
A Tensile Strength Apparatus with the Facility to Monitor Negative Pore-Water Pressure
Authors: Murray Ian , Tarantino Alessandro , Francescon Fernando 
Published: October 2018

Abstract
This article presents a new testing method for investigating the behavior of clayey geomaterials subjected to a tensile (negative) total stress. The method includes the use of high-capacity tensiometers to measure the pore–water pressure of the test specimen, an aspect which has not been demonstrated in any other direct tensile testing method. This addition allows interpretation of failure data in terms of effective stress rather than total stress, which is the approach that should be pursued in the saturated range. The test specimen shape and loading method have been modified from those commonly seen in existing literature to ensure that the direction of the major principal stress in the failure zone coincides with the direction of the externally applied tensile force, allowing for a more accurate analysis of tensile failure. Results are shown for saturated specimens and compared to results obtained for the same soil in uniaxial compression, using a modified version of the presented uniaxial tensile method, and a triaxial compression test. It is demonstrated that crack initiation occurs by shear failure if the data are interpreted in terms of effective stress rather than total stress and that the failure mechanisms under tension do not differ from compression.
A Simple Measurement of Membrane Penetration in Gravel Triaxial Tests Based on Eliminating Soil Skeleton Plastic Deformation with Cyclic Confining Pressure Loading
Authors: Liu Jingmao , Zou Degao , Kong Xianjing , Ning Fanwei , Han Jianhua 
Published: October 2018

Abstract
Previous investigations of membrane penetration mainly focused on uniform sandy soils, and few studied gravelly soils. A common problem in most previous investigations was that unverified assumptions were made to evaluate or mitigate the membrane penetration of a cylindrical specimen in triaxial test. In this study, a simple measurement of the membrane penetration of gravelly soils was proposed, based on small-amplitude cyclic confining pressure Δσ3 loading, in which the cyclic membrane penetration amplitude ΔVm is recoverable, and the cyclic soil skeleton volume deformation amplitude ΔVk gradually decreases with increasing number of cycles and becomes elastic. The accuracy in the proposed method is related to the accuracy in measuring ΔVk. Because of the natural limitations in measurements of the radial strain of a cylindrical specimen, ΔVk is calculated based on the isotropic assumption. The proposed method provides sufficiently accurate ΔVm values for gravelly soils because of the small portion of ΔVk in the total cyclic volume change amplitude ΔVc (=ΔVm+ΔVk), and the accuracy increases as the coarse fraction increases. Furthermore, the method can be easily implemented for individual specimens to remove inconsistences in specimen preparation. The test results indicate that ΔVm values corresponding to the same Δσ3 exponentially decrease with the confining pressure σ3. Membrane penetration increases with increases in the void ratio and coarse fraction, but the trend is becoming weak with decreasing coarse fraction and void ratio, respectively. It also demonstrated that there exists a clear difference between the results of Nicholson’s empirical formula and the test results.