bluuebunny/crossref_metadata_2025 huggingface dataset:
A High-Throughput Pipeline Identifies Robust Connectomes But Troublesome Variability
Authors: Kiar Gregory , Bridgeford Eric W. , Gray Roncal William R. ,   Consortium for Reliability and Reproducibility (CoRR), Chandrashekhar Vikram , Mhembere Disa , Ryman Sephira , Zuo Xi-Nian , Margulies Daniel S. , Craddock R. Cameron , Priebe Carey E. , Jung Rex , Calhoun Vince D. , Caffo Brian , Burns Randal , Milham Michael P. , Vogelstein Joshua T.
Published: September 2017

Modern scientific discovery depends on collecting large heterogeneous datasets with many sources of variability, and applying domain-specific pipelines from which one can draw insight or clinical utility. For example, macroscale connectomics studies require complex pipelines to process raw functional or diffusion data and estimate connectomes. Individual studies tend to customize pipelines to their needs, raising concerns about their reproducibility, and adding to a longer list of factors that may differ across studies (including sampling, experimental design, and data acquisition protocols), resulting in failures to replicate. Mitigating these issues requires multi-study datasets and the development of pipelines that can be applied across them. We developed NeuroData’s MRI to Graphs (NDMG) pipeline using several functional and diffusion studies, including the Consortium for Reliability and Reproducibility, to estimate connectomes. Without any manual intervention or parameter tuning, NDMG ran on 25 different studies (≈ 6,000 scans) from 15 sites, with each scan resulting in a biologically plausible connectome (as assessed by multiple quality assurance metrics at each processing stage). For each study, the connectomes from NDMG are more similar within than across individuals, indicating that NDMG is preserving biological variability. Moreover, the connectomes exhibit near perfect consistency for certain connectional properties across every scan, individual, study, site, and modality; these include stronger ipsilateral than contralateral connections and stronger homotopic than heterotopic connections. Yet, the magnitude of the differences varied across individuals and studies—much more so when pooling data across sites, even after controlling for study, site, and basic demographic variables (i.e., age, sex, and ethnicity). This indicates that other experimental variables (possibly those not measured or reported) are contributing to this variability, which if not accounted for can limit the value of aggregate datasets, as well as expectations regarding the accuracy of findings and likelihood of replication. We, therefore, provide a set of principles to guide the development of pipelines capable of pooling data across studies while maintaining biological variability and minimizing measurement error. This open science approach provides us with an opportunity to understand and eventually mitigate spurious results for both past and future studies.
Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation
Authors: Li Xiao , Chen Xi , Wong Yin Ting , Wang Haitao , Feng Hemin , Zheng Xuejiao , Feng Jingyu , Baibado Joewel T. , Jesky Robert , Peng Yujie , Wang Zhedi , Xie Hui , Sun Wenjian , Zhang Zicong , Zhang Xu , He Ling , Zhang Nan , Zhang Zhijian , Tang Peng , Su Jun-Feng , Hu Ling-Li , Liu Qing , He Xiao-Bin , Tan Ailian , Sun Xia , Li Min , Wong Kelvin , Wang Xiaoyu , Guo Yi Ping , Xu Fuqiang , He Jufang
Published: September 2017

Memory is stored in neural networks via changes in synaptic strength mediated in part by NMDA-dependent long-term potentiation (LTP). There is evidence that entorhinal cortex enables neocortical neuroplasticity through cholecystokinin (CCK)-containing neocortical projections. Here we show that a CCKBantagonist blocks high-frequency stimulation (HFS)-induced LTP in the auditory cortex, whereas local infusion of CCK induces LTP. CCK-/-mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; administration of CCK rescued associative learning. HFS of CCK-containing entorhino-neocortical projection neurons in anesthetized mice enabled cue-cue associative learning. Furthermore, when one cue was pre-conditioned to footshock, the mouse showed a freezing response to the other cue, indicating that the mice had formed an association. HFS-induced neocortical LTP was completely blocked by either NMDA antagonist or CCK-BR antagonist, while application of either NMDA or CCK induced LTP after low-frequency stimulation (LFS). Moreover, in the presence of CCK LTP was still induced, even after blockade of NMDA receptors. Local application of NMDA induced CCK release in the neocortex. To identify how NMDA receptor switches LTP, a stimulation protocol of 25 pulse-pairs was adopted to replace HFS; NMDA-dependent LTP was induced with the inter-pulse intervals between 10 and 100 ms, but not with those of 5 and 200 ms. LTP-mediated plasticity was linked to localization of the NMDA receptor subunit NR2a on cortical CCK terminals originating in the entorhinal cortex. These novel findings suggest that presynaptic NMDA receptors on CCK terminals control the release of CCK, which enables neocortical LTP and formation of cue-cue associative memory.

One Sentence Summary

Presynaptic NMDA receptors switches the release of CCK from entorhinal neurons, which enables neocortical LTP and formation of sound-sound associative memory.
Global determinants of navigation ability
Authors: Coutrot A. , Silva R. , Manley E. , de Cothi W. , Sami S. , Bohbot V. D. , Wiener J. M. , Hölscher C. , Dalton R.C. , Hornberger M. , Spiers H. J.
Published: September 2017

Countries vary in their geographical and cultural properties. Only a few studies have explored how such variations influence how humans navigate or reason about space [1–7]. We predicted that these variations impact human cognition, resulting in an organized spatial distribution of cognition at a planetary-wide scale. To test this hypothesis we developed a mobile-app-based cognitive task, measuring non-verbal spatial navigation ability in more than 2.5 million people, sampling populations in every nation state. We focused on spatial navigation due to its universal requirement across cultures. Using a clustering approach, we find that navigation ability is clustered into five distinct, yet geographically related, groups of countries. Specifically, the economic wealth of a nation was predictive of the average navigation ability of its inhabitants, and gender inequality was predictive of the size of performance difference between males and females. Thus, cognitive abilities, at least for spatial navigation, are clustered according to economic wealth and gender inequalities globally, which has significant implications for cross-cultural studies and multi-centre clinical trials using cognitive testing.
STDP forms associations between memory traces in networks of spiking neurons
Authors: Pokorny Christoph , Ison Matias J. , Rao Arjun , Legenstein Robert , Papadimitriou Christos , Maass Wolfgang
Published: September 2017

Memory traces and associations between them are fundamental for cognitive brain function. Neuron recordings suggest that distributed assemblies of neurons in the brain serve as memory traces for spatial information, real-world items, and concepts. How-ever, there is conflicting evidence regarding neural codes for associated memory traces. Some studies suggest the emergence of overlaps between assemblies during an association, while others suggest that the assemblies themselves remain largely unchanged and new assemblies emerge as neural codes for associated memory items. Here we study the emergence of neural codes for associated memory items in a generic computational model of recurrent networks of spiking neurons with a data-constrained rule for spike-timing-dependent plasticity (STDP). The model depends critically on two parameters, which control the excitability of neurons and the scale of initial synaptic weights. By modifying these two parameters, the model can reproduce both experimental data from the human brain on the fast formation of associations through emergent overlaps between assemblies, and rodent data where new neurons are recruited to encode the associated memories. Hence our findings suggest that the brain can use both of these two neural codes for associations, and dynamically switch between them during consolidation.
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation ofERAP2transcripts under balancing selection
Authors: Ye Chun Jimmie , Chen Jenny , Villani Alexandra-Chloé , Gate Rachel E. , Subramaniam Meena , Bhangale Tushar , Lee Mark N. , Raj Towfique , Raychowdhury Raktima , Li Weibo , Rogel Noga , Simmons Sean , Imboywa Selina H. , Chipendo Portia I. , McCabe Cristin , Lee Michelle H. , Frohlich Irene Y. , Stranger Barbara E. , De Jager Philip L. , Regev Aviv , Behrens Tim , Hacohen Nir
Published: September 2017

While the impact of common genetic variants on gene expression response to cellular stimuli has been analyzed in depth, less is known about how stimulation modulates the genetic control of isoform usage. Analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to viral infection and stimulation with type I interferon. We identified more than a thousand single nucleotide polymorphisms associated with isoform usage (isoQTLs), > 40% of which are independent of expression QTLs for the same gene. Compared to eQTLs, isoQTLs are enriched for splice sites and untranslated regions, and depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs in stimulated cells explain a significant proportion of the disease heritability attributed to common genetic variants. At theIRF7locus, we found alternative promoter usage in response to influenza as a possible mechanism by which DNA variants previously associated with immune-related disorders mediate disease risk. At theERAP2locus, we shed light on the function of the major haplotype that has been maintained under long-term balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with absence ofERAP2expression while the minor haplotype, known to increase Crohn’s disease risk, is associated with highERAP2expression. Surprisingly, in response to influenza infection, the major haplotype results in the expression of two uncharacterized, alternatively transcribed, spliced and translated short isoforms. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in the innate immune response, and in the case ofERAP2, may confer a historical fitness advantage in response to virus.
FlashFry: a fast and flexible tool for large-scale CRISPR target design
Authors: McKenna Aaron , Shendure Jay
Published: September 2017

FlashFry is a fast and flexible command-line tool for characterizing large numbers of CRISPR target sequences. While several CRISPR web application exist, genome-wide knockout studies, noncoding deletion scans, and other large-scale studies or methods development projects require a simple and lightweight framework that can quickly discover and score thousands of candidates guides targeting an arbitrary DNA sequence. With FlashFry, users can specify an unconstrained number of mismatches to putative off-targets, richly annotate discovered sites, and tag potential guides with commonly used on target and off-target scoring metrics. FlashFry runs at speeds comparable to widely used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file.

Availability

FlashFry is written in Scala and bundled as a stand-alone Jar file, easily run on any system with an installed Java virtual machine (JVM). The tool is freely licensed under version 3 of the GPL, and code, documentation, and tutorials are available on the GitHub page:http://aaronmck.github.io/FlashFry/
Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
Authors: Lachmann Alexander , Torre Denis , Keenan Alexandra B. , Jagodnik Kathleen M. , Lee Hyojin J. , Wang Lily , Silverstein Moshe C. , Ma’ayan Avi
Published: September 2017

RNA-sequencing (RNA-seq) is currently the leading technology for genome-wide transcript quantification. While the volume of RNA-seq data is rapidly increasing, the currently publicly available RNA-seq data is provided mostly in raw form, with small portions processed non- uniformly. This is mainly because the computational demand, particularly for the alignment step, is a significant barrier for global and integrative retrospective analyses. To address this challenge, we developed all RNA-seq and ChIP-seq sample and signature search (ARCHS4), a web resource that makes the majority of previously published RNA-seq data from human and mouse freely available at the gene count level. Such uniformly processed data enables easy integration for downstream analyses. For developing the ARCHS4 resource, all available FASTQ files from RNA-seq experiments were retrieved from the Gene Expression Omnibus (GEO) and aligned using a cloud-based infrastructure. In total 137,792 samples are accessible through ARCHS4 with 72,363 mouse and 65,429 human samples. Through efficient use of cloud resources and dockerized deployment of the sequencing pipeline, the alignment cost per sample is reduced to less than one cent. ARCHS4 is updated automatically by adding newly published samples to the database as they become available. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene landing pages that provide average expression across cell lines and tissues, top co-expressed genes, and predicted biological functions and protein-protein interactions for each gene based on prior knowledge combined with co-expression. Benchmarking the quality of these predictions, co-expression correlation data created from ARCHS4 outperforms co-expression data created from other major gene expression data repositories such as GTEx and CCLE.

ARCHS4 is freely accessible at:http://amp.pharm.mssm.edu/archs4
An efficient and novel technique for solving continuously variable fractional order mass-spring-damping system
Authors: Sahoo S. , Saha Ray S. , Das S.
Published: September 2017

Purpose

In this paper, the formulation and analytic solutions for fractional continuously variable order dynamic models, namely, fractional continuously mass-spring damper (continuously variable fractional order) systems, have been presented. The authors will demonstrate via two cases where the frictional damping given by fractional derivative, the order of which varies continuously – while the mass moves in a guide. Here, the continuously changing nature of the fractional-order derivative for dynamic systems has been studied for the first time. The solutions of the fractional continuously variable order mass-spring damper systems have been presented here by using a successive recursive method, and the closed form of the solutions has been obtained. By using graphical plots, the nature of the solutions has been discussed for the different cases of continuously variable fractional order of damping force for oscillator. The purpose of the paper is to formulate the continuously variable order mass-spring damper systems and find their analytical solutions by successive recursion method.

Design/methodology/approach

The authors have used the viscoelastic and viscous – viscoelastic dampers for describing the damping nature of the oscillating systems, where the order of the fractional derivative varies continuously.

Findings

By using the successive recursive method, here, the authors find the solution of the fractional continuously variable order mass-spring damper systems, and then obtain close-form solutions. The authors then present and discuss the solutions obtained in the cases with the continuously variable order of damping for an oscillator through graphical plots.

Originality/value

Formulation of fractional continuously variable order dynamic models has been described. Fractional continuous variable order mass-spring damper systems have been analysed. A new approach to find solutions of the aforementioned dynamic models has been established. Viscoelastic and viscous – viscoelastic dampers are described. The discussed damping nature of the oscillating systems has not been studied yet.
Haar wavelets operational matrix based algorithm for computational modelling of hyperbolic type wave equations
Authors: Pandit Sapna , Jiwari Ram , Bedi Karan , Koksal Mehmet Emir
Published: September 2017

Purpose

The purpose of this study is to develop an algorithm for approximate solutions of nonlinear hyperbolic partial differential equations.

Design/methodology/approach

In this paper, an algorithm based on the Haar wavelets operational matrix for computational modelling of nonlinear hyperbolic type wave equations has been developed. These types of equations describe a variety of physical models in nonlinear optics, relativistic quantum mechanics, solitons and condensed matter physics, interaction of solitons in collision-less plasma and solid-state physics, etc. The algorithm reduces the equations into a system of algebraic equations and then the system is solved by the Gauss-elimination procedure. Some well-known hyperbolic-type wave problems are considered as numerical problems to check the accuracy and efficiency of the proposed algorithm. The numerical results are shown in figures and Linf, RMS and L2 error forms.

Findings

The developed algorithm is used to find the computational modelling of nonlinear hyperbolic-type wave equations. The algorithm is well suited for some well-known wave equations.

Originality/value

This paper extends the idea of one dimensional Haar wavelets algorithms (Jiwari, 2015, 2012; Pandit et al., 2015; Kumar and Pandit, 2014, 2015) for two-dimensional hyperbolic problems and the idea of this algorithm is quite different from the idea for elliptic problems (Lepik, 2011; Shi et al., 2012). Second, the algorithm and error analysis are new for two-dimensional hyperbolic-type problems.
An algorithm inspired by social spiders for truss optimisation problems
Authors: Duarte Grasiele Regina , Lemonge Afonso Celso de Castro , da Fonseca Leonardo Goliatt
Published: September 2017

Purpose

The purpose of this paper is to evaluate the performance of social spider algorithm (SSA) to solve constrained structural optimisation problems and to compare its results with others algorithms such as genetic algorithm, particle swarm optimisation, differential evolution and artificial bee colony.

Design/methodology/approach

To handle the constraints of the problems, this paper couples to the SSA an efficient selection criteria proposed in the literature that promotes a tournament between two solutions in which the feasible or less infeasible solution wins. The discussion is conducted on the competitiveness of the SSA with other algorithms as well as its performance in constrained problems.

Findings

SSA is a population algorithm proposed for global optimisation inspired by the foraging of social spiders. A spider moves on the web towards the position of the prey, guided by vibrations that occur around it in different frequencies. The SSA was proposed to solve problems without constraints, but these are present in most of practical problems. This paper evaluates the performance of SSA to solve constrained structural optimisation problems and compares its results with other algorithms such as genetic algorithm, particle swarm optimisation, differential evolution and artificial bee colony.

Research limitations/implications

The proposed algorithm has no limitations, and it can be applied in other classes of constrained optimisation problems.

Practical implications

This paper evaluated the proposed algorithm with a benchmark of constrained structural optimisation problems intensely used in the literature, but it can be applied to solve real constrained optimisation problems in engineering and others areas.

Originality/value

This is the first paper to evaluate the performance of SSA in constrained problems and to compare its results with other algorithms traditional in the literature.
Reliability analysis of CNC turning center based on the assessment of trends in maintenance data
Authors: Patil Rajkumar Bhimgonda , Kothavale Basavraj S. , Waghmode Laxman Yadu , Joshi Shridhar G.
Published: September 2017

Purpose

The paper presents reliability, maintainability and life cycle cost (LCC) analysis of a computerized numerical control (CNC) turning center which is manufactured and used in India. The purpose of this paper is to identify the critical components/subsystems from reliability and LCC perspective. The paper further aims at improving reliability and LCC by implementing reliability-improvement methods.

Design/methodology/approach

This paper uses a methodology for the reliability analysis based on the assessment of trends in maintenance data. The data required for reliability and LCC analysis are collected from the manufacturers and users of CNC turning center over a period of eight years. ReliaSoft’s Weibull++9 software has been used for verifying goodness of fit and estimating parameters of the distribution. The LCC of the system is estimated for five cost elements: acquisition cost, operation cost, failure cost, support cost and net salvage value.

Findings

The analysis shows that the spindle bearing, spindle belt, spindle drawbar, insert, tool holder, drive battery, hydraulic hose, lubricant hose, coolant hose and solenoid valve are the components with low reliability. With certain design changes and implementation of reliability-based maintenance policies, system reliability is improved, especially during warranty period. The reliability of the CNC turning center is improved by nearly 45 percent at the end of warranty period and system mean time between failure is increased from 15,000 to 17,000 hours. The LCC analysis reveals that the maintenance cost, operating cost and support costs dominate the LCC and contribute to the tune of 87 percent of the total LCC.

Research limitations/implications

The proposed methodology provides an excellent tool that can be utilized in industries, where safety, reliability, maintainability and availability of the system play a vital role. The approach may be improved by collecting data from more number of users of the CNC turning centers.

Practical implications

The approach presented in this paper is generic and can be applied to analyze the repairable systems. A real case study is presented to show the applicability of the approach.

Originality/value

The proposed methodology provides a practical approach for the analysis of time-to-failure and time-to-repair data based on the assessment of trends in the maintenance data. The methodology helps in selecting a proper approach of the analysis such as Bayesian method, parametric methods and nonparametric methods.
Structural equation modeling for validating impact of 5S implementation on business excellence of manufacturing organizations
Authors: Randhawa Jugraj Singh , Ahuja Inderpreet Singh
Published: September 2017

Purpose

The purpose of this paper is to deploy structural equation modeling (SEM) technique to empirically validate the interrelationships amongst significant variables of 5S implementation and business excellence performance parameters (BEPP) in SEM_5S model.

Design/methodology/approach

The confirmatory factor analysis approach is utilized to generate the effective SEM_5S model by using AMOS 20.0 (analysis of moment structures) software. The data have been collected from different manufacturing organizations that have successfully deployed the 5S program by using well-designed questionnaire for the evaluation of SEM_5S model.

Findings

SEM of 5S various parameters has established that attributes like top management involvement initiatives, employee involvement initiatives, basic 5S initiatives (BFSI) and fifth S initiatives (Shitsuke) should be holistically emphasized during the implementation of 5S program, leading to attainment of high level of melioration in the BEPP. SEM has been deployed to evaluate the original and modification indices of the model, which further establishes the improvement in SEM’s effectiveness. The model establishes the significant impact of 5S implementation on business excellence of manufacturing organizations.

Originality/value

The outcomes of the study will help the organizational managers, HR executives and practitioners from manufacturing organizations to know about the significant factors which should be followed holistically to achieve overall organizational business excellence through strategic 5S initiatives.
An empirical investigation of critical success factors influencing the successful TQM implementation for firms with different strategic orientation
Authors: Kumar Vimal , Sharma R.R.K.
Published: September 2017

Purpose

It has been found that critical success factors (CSFs) are responsible for successful implementation of total quality management (TQM) system. The purpose of this paper is to make a comparative analysis of the importance of 20 TQM CSFs to the strategic choices of the firms such as innovators, prospectors, and defenders.

Design/methodology/approach

From extant literature review on TQM, 20 CSFs have been carried out. The empirical data for this study was drawn from a survey of 111 firms in India. One-way ANOVA approach has been applied for analysis.

Findings

The findings of the research show that the CSFs hold importance for different firm’s strategy. From these 20 CSFs, some CSFs may be critically important for all three types of firm, while others have their significant roles for innovators, prospectors, and defenders individually which are better prepared for TQM implementation.

Practical implications

The results of this study present the importance of knowing the appropriate CSFs to a strategy of the firms. The emphasis on CSFs will help organizations in accepting and rejecting TQM practices when they try to implement TQM and it is equally important in a global context. Apparently, it is evident that if there is a mismatch of strategy and CSFs with TQM practices it may interrupt the smooth operations of the company.

Originality/value

This research can be useful for those firms who are in the starting phase of TQM implementation with consideration of CSFs. Moreover, this research also attempts to inspire managers to consider the appropriate CSFs for implementing TQM effectively in their firms.
Uber: aggressive management for growth
Authors: Matherne Brett P. , O’Toole Jay
Published: September 2017

Synopsis

This case uses Uber Technologies Inc. to engage students in a serious conversation about how a firm both affects its stakeholders and is affected by its stakeholders as well as the role of strategic leadership in the amount of emphasis placed on ethical practices. Uber represents a visible high-growth startup that has received considerable positive and negative attention in the media; however, few people know of the extent of its aggressive management approach. Much of the publicity about Uber is both a direct consequence of and a direct consequence for stakeholder relationships. Students are asked to analyze Uber’s approach and offer suggestions for moving forward.

Research methodology

This case was created using secondary data sources. The issues for Uber that led the authors to write this case were not very flattering to Uber, and therefore, the authors decided to use secondary sources. Since Uber and many of its direct competitors were private companies, the authors collected as much financial data as the authors could from publicly available sources. Also, due to the contentious nature of some of the managerial tactics used within Uber, the use of secondary data sources was warranted.

Relevant courses and levels

This case was crafted with senior undergraduate students in strategic management as the primary audience, but is also relevant for MBA-level strategy courses as well. This case touches upon core content in the vast majority of undergraduate strategic management courses with a special emphasis on two concepts underrepresented in most strategic management textbooks, stakeholder theory and ethical decision making.
Varieties of contemporary democratic breakdown and regression: A comparative analysis
Authors: TOMINI LUCA , WAGEMANN CLAUDIUS
Published: September 2017

The goal of this article is to understand which combinations of explanatory conditions account for the qualitative differences within forms of democratic breakdown (i.e., transitionfromdemocracy to a hybrid or authoritarian regime) and democratic regression (i.e., transitionwithindemocracy through a loss of democratic quality). The analysis focuses particularly on the specific features of those processes of change ending up with a transition from democratic rule, compared to those producing a simple loss of democratic quality within the democratic regime. Applying two‐step fuzzy‐set Qualitative Comparative Analysis (fsQCA), the study aims to integrate different types of explanatory factors, offering a fresh and comprehensive perspective on this phenomenon.
The effect of neuromuscular blockade on the efficiency of facemask ventilation in patients difficult to facemask ventilate: a prospective trial
Authors: Soltész S. , Alm P. , Mathes A. , Hellmich M. , Hinkelbein J.
Published: September 2017

Facemask ventilation of the lungs can be an important rescue intervention in a ‘cannot intubate’ scenario. We assessed the effect of neuromuscular blockade on expiratory tidal volumes in patients with expected difficulty in mask ventilation. The lungs of patients with at least three predictors of difficulty in mask ventilation were ventilated using a facemask held with two hands, with mechanical ventilation set in a pressure‐controlled mode. Tidal volumes were recorded before and after the establishment of complete neuromuscular block. In 113 patients, median (IQR [range]) tidal volume increased from 350 (260–492 [80–850]) ml initially, by 48% to 517 (373–667 [100–1250]) ml 30 s after rocuronium administration, (p < 0.001). After the onset of the complete neuromuscular block, a median tidal volume of 600 (433–750 [250–1303]) ml was observed, corresponding to an increase of 71% from baseline values (p < 0.001), and 16% from values obtained 30 s after rocuronium administration, respectively; p = 0.003). No decrease in the tidal volume during the measurements was observed. We conclude that the administration of rocuronium at a dose of 0.6 mg.kg−1 was able to improve facemask ventilation in all cases with a potentially clinically relevant increase in tidal volume. The early use of a neuromuscular blocking agent can be considered as a therapeutic option in case of difficulty with mask ventilation.
Improvement of Decellularization Efficiency of Porcine Aorta Using Dimethyl Sulfoxide as a Penetration Enhancer
Authors: Guler Selcan , Aydin Halil M. , Lü Lan‐Xin , Yang Ying
Published: September 2017

Decellularization of tissues and organs enables researchers to obtain extracellular matrix (ECM) with the natural conformation and chemical composition of specific tissues. However, drawbacks exist such as the structural alteration of ECM or loss of some important components in ECM due to overexposure to chemicals during the decellularization process. In this study, porcine aorta was decellularized by sodium dodecyl sulfate (SDS). Dimethyl sulfoxide (DMSO) was used as a penetration enhancer in the decellularization process to enhance the penetration of SDS, consequently reducing the exposure time of SDS to treated tissues. It is revealed that by addition of DMSO to the decellularization process 64.4% more DNA was removed when compared with just SDS exposure within a 3 h reaction. Cross‐validation by DAPI staining showed that, in the presence of DMSO, the penetration of SDS was improved and almost all cells were removed from the aorta within the 3 h exposure time. Collagen staining revealed that just SDS treatment showed less polarized collagen fibers, while the DMSO addition groups revealed denser and organized collagen fibers. Moreover 77% glycosaminoglycan content was preserved by addition of DMSO in resultant tissues. Scanning electron microscopy analysis of decellularized aortic matrix showed that ECM components remained in the adventitia layer with the addition of DMSO treatment, while the layer was removed with just SDS treatment. Biocompatibility assays proved that after washing the decellularized samples with media supplemented with 3% antibiotic and antimycotic solution for 2 days there was no cytotoxic effect related to the SDS + DMSO decellularization protocol. This study demonstrates that the new decellularization protocol not only improves the removal efficiency of cellular components but also protects the crucial ECM components.
Acinetobacter baumannii isolated from hospital‐acquired infection: biofilm production and drug susceptibility
Authors: Krzyściak Paweł , Chmielarczyk Agnieszka , Pobiega Monika , Romaniszyn Dorota , Wójkowska‐Mach Jadwiga
Published: September 2017

Acinetobacter baumannii cause opportunistic nosocomial infections and is often multidrug resistant. It has ability to form biofilm. The possession of drug resistance mechanism and ability of biofilm formation seems to be the different way to enhancement of viability in stressful environment. In this study, we evaluate relation between these two factors. The biofilm formation was investigated in M63 medium with casein in microtiter plates, and the drug susceptibility was performed by disk diffusion methods. We found that 80–98% strains formed a biofilm. Strains showing sensitivity to amikacin and tobramycin from ICU produced more biofilm than strains showing resistance to these antibiotics. Ceftazidime‐sensitive strains formed a smaller biofilm than resistant. The logistic regression shows association between drug resistance and strains originating from ICU. In case of ceftazidime, strong biofilm formation and descending from ICU reduced the likelihood of drug sensitivity. For other drugs such as aminoglycosides, fluoroquinolones, trimethoprim/sulfamethoxazole, and tetracycline, we found opposite relation (but it was not statistically significance). However, generally it seems that strong biofilm producers from ICUs are often more susceptible to antibiotics. This situation can be explained by the fact that bacteria protected in biofilm do not need mechanisms responsible for resistance of planktonic cells.
The updated grading system of prostate carcinoma: an inter‐observer agreement study among general pathologists in an academic practice
Authors: Al Nemer Areej M. , Elsharkawy Tarek , Elshawarby Mohamed , Al‐Tamimi Dalal , Kussaibi Haitham , Ahmed Ayesha
Published: September 2017

In 2016, the grading criteria for Gleason scoring (GS) have been updated in the WHO classification of tumors of the prostate, and a new set of grade groups (GG) was introduced. As the inter‐observer discordance is a well‐known concern in Gleason grading before the update and no reproducibility study testing the grade groups exists, we planned to evaluate the inter‐observer agreement of the most updated grading system. Four pathologists assessed 126 cores of prostatic carcinoma, and Kappa (k) test was calculated. The agreements for both GS and GG were substantial (k = 0.753 and 0.752; respectively). Discerning GG 2 from 3 also attained reasonable outcome (k = 0.675). Based on our results, the updated grading system seems to be reproducible, with satisfactory inter‐observer concordance rate.
Determination of net energy content of soybean oil fed to growing pigs using indirect calorimetry
Authors: Li Enkai , LV Zhiqian , Liu Hu , Liu Ling , Li Yakui , Li Zhongchao , Wang Fenglai , Li Defa , Zhang Shuai
Published: September 2017

The objectives of this experiment were: (i) to determine the net energy (NE) of soybean oil (SBO) fed to growing pigs using indirect calorimetry (IC); and (ii) to evaluate the effects of inclusion rate of SBO on heat production, oxidative status and nutrient digestibility in growing pigs. Eighteen growing barrows were allotted to three diets based on completely randomized design with six replicate pigs (period) per diet. Diets included a corn‐soybean meal basal diet and two test diets containing 5% or 10% SBO at the expense of corn and soybean meal. During each period, pigs were individually housed in metabolism crates for 14 days, including 7 days to adapt to feed, metabolism crate and environmental conditions. On day 8, pigs were transferred to the open‐circuit respiration chambers for measurement of daily O2 consumption and CO2 and CH4 production. During this time, pigs were fed one of the three diets at 2.4 MJ metabolizable energy/kg body weight (BW)0.6/day. Total feces and urine were collected and daily total heat production (THP) was measured from days 9 to 13 and fasted on day 14 to evaluate their fasting heat production (FHP). The results show that trends of decreased apparent total tract digestibility of neutral detergent fiber (linear, P = 0.09) and acid detergent fiber (linear, P = 0.07) were observed as the content of dietary lipids increased. The average THP for the three diets were 1326, 1208 and 1193 kJ/kg BW0.6/day, respectively. The FHP of pigs averaged 843 kJ/kg BW0.6/day and was not affected by diet characteristics. A reduction of the respiratory quotients in the fed state as the inclusion level of SBO increased was observed. In conclusion, the NE values of SBO we determined by indirect calorimetry were 33.45 and 34.05 MJ/kg dry matter under two inclusion levels. THP could be largely reduced when SBO is added in the feed, but the THP of SBO included at 5% in a corn‐soybean meal diet is not different from the THP of SBO included at 10%.
Monte Carlo Methods for Nonparametric Regression with Heteroscedastic Measurement Error
Authors: McIntyre Julie , Johnson Brent A. , Rappaport Stephen M.
Published: September 2017

Nonparametric regression is a fundamental problem in statistics but challenging when the independent variable is measured with error. Among the first approaches was an extension of deconvoluting kernel density estimators for homescedastic measurement error. The main contribution of this article is to propose a new simulation-based nonparametric regression estimator for the heteroscedastic measurement error case. Similar to some earlier proposals, our estimator is built on principles underlying deconvoluting kernel density estimators. However, the proposed estimation procedure uses Monte Carlo methods for estimating nonlinear functions of a normal mean, which is different than any previous estimator. We show that the estimator has desirable operating characteristics in both large and small samples and apply the method to a study of benzene exposure in Chinese factory workers.
New‐age ideas about age‐old sex: separating meiosis from mating could solve a century‐old conundrum
Authors: Brandeis Michael
Published: September 2017

Ever since Darwin first addressed it, sexual reproduction reigns as the ‘queen’ of evolutionary questions. Multiple theories tried to explain how this apparently costly and cumbersome method has become the universal mode of eukaryote reproduction. Most theories stress the adaptive advantages of sex by generating variation, they fail however to explain the ubiquitous persistence of sexual reproduction also where adaptation is not an issue. I argue that the obstacle for comprehending the role of sex stems from the conceptual entanglement of two distinct processes – gamete production by meiosis and gamete fusion by mating (mixis). Meiosis is an ancient, highly rigid and evolutionary conserved process identical and ubiquitous in all eukaryotes. Mating, by contrast, shows tremendous evolutionary variability even in closely related clades and exhibits wonderful ecological adaptability. To appreciate the respective roles of these two processes, which are normally linked and alternating, we require cases where one takes place without the other. Such cases are rather common. The heteromorphic sex chromosomes Y and W, that do not undergo meiotic recombination are an evolutionary test case for demonstrating the role of meiosis. Substantial recent genomic evidence highlights the accelerated rates of change and attrition these chromosomes undergo in comparison to those of recombining autosomes. I thus propose that the most basic role of meiosis is conserving integrity of the genome. A reciprocal case of meiosis without bi‐parental mating, is presented by self‐fertilization, which is fairly common in flowering plants, as well as most types of apomixis. I argue that deconstructing sex into these two distinct processes – meiosis and mating – will greatly facilitate their analysis and promote our understanding of sexual reproduction.
Risk factors for unfavourable postoperative outcome in patients with Crohn's disease undergoing right hemicolectomy or ileocaecal resection. An international audit by ESCP and S‐ECCO
Authors:   2015 European Society of Coloproctology collaborating group
Published: September 2017

Aim

Patient‐ and disease‐related factors, as well as operation technique, all have the potential to impact on postoperative outcome in Crohn's disease. The available evidence is based on small series and often displays conflicting results. The aim was to investigate the effect of preoperative and intra‐operative risk factors on 30‐day postoperative outcome in patients undergoing surgery for Crohn's disease.

Method

This was an international prospective snapshot audit including consecutive patients undergoing right hemicolectomy or ileocaecal resection. The study analysed a subset of patients who underwent surgery for Crohn's disease. The primary outcome measure was the overall Clavien–Dindo postoperative complication rate. The key secondary outcomes were anastomotic leak, reoperation, surgical site infection and length of stay in hospital. Multivariable binary logistic regression analyses were used to produce odds ratios and 95% confidence intervals.

Results

In all, 375 resections in 375 patients were included. The median age was 37 and 57.1% were women. In multivariate analyses, postoperative complications were associated with preoperative parenteral nutrition (OR 2.36, 95% CI 1.10–4.97), urgent/expedited surgical intervention (OR 2.00, 95% CI 1.13–3.55) and unplanned intra‐operative adverse events (OR 2.30, 95% CI 1.20–4.45). The postoperative length of stay in hospital was prolonged in patients who received preoperative parenteral nutrition (OR 31, 95% CI 1.08–1.61) and those who had urgent/expedited operations (OR 1.21, 95% CI 1.07–1.37).

Conclusion

Preoperative parenteral nutritional support, urgent/expedited operation and unplanned intra‐operative adverse events were associated with unfavourable postoperative outcome. Enhanced preoperative optimization and improved planning of operation pathways and timings may improve outcomes for patients.
Lower Mekong Fish Passage Conference: Applying innovation to secure fisheries productivity
Authors: Baumgartner Lee J. , Boys Craig A. , Barlow Chris , Roy Mike
Published: September 2017

The Lower Mekong Basin (LMB) is one of the most biodiverse regions in the world. It contains almost 1,100 fish species and supports a regional population of almost 60 million people. Fish provide protein, essential micronutrients and income for many of these people. Further, over 85% of fish are migratory and undertake small‐ and large‐scale movements to access spawning, feeding and nursery habitat. In recent times, irrigation and hydropower development have threatened the long‐term sustainability of fisheries resources in the region, and there is a need to develop robust mitigation measures in order to protect and improve fish passage and fisheries productivity. Recognising this, a conference, with 160 delegates from 14 countries brought together global experts in the fields of riverine development, fish passage and aquatic ecosystem management to demonstrate how applied research has been used over the last decade to enhance policy and decision‐making across the LMB and to discuss future directions.
Alterations in the α2δ ligand, thrombospondin‐1, in a rat model of spontaneous absence epilepsy and in patients with idiopathic/genetic generalized epilepsies
Authors: Santolini Ines , Celli Roberta , Cannella Milena , Imbriglio Tiziana , Guiducci Michela , Parisi Pasquale , Schubert Julian , Iacomino Michele , Zara Federico , Lerche Holger ,   EuroEPINOMICS CoGIE Consortium,   Genetic Commission of Italian League Against Epilepsy (LICE), Moyanova Slavianka , Ngomba Richard Teke , van Luijtelaar Gilles , Battaglia Giuseppe , Bruno Valeria , Striano Pasquale , Nicoletti Ferdinando
Published: September 2017

Objectives

Thrombospondins, which are known to interact with the α2δ subunit of voltage‐sensitive calcium channels to stimulate the formation of excitatory synapses, have recently been implicated in the process of epileptogenesis. No studies have been so far performed on thrombospondins in models of absence epilepsy. We examined whether expression of the gene encoding for thrombospondin‐1 was altered in the brain of WAG/Rij rats, which model absence epilepsy in humans. In addition, we examined the frequency of genetic variants of THBS1 in a large cohort of children affected by idiopathic/genetic generalized epilepsies (IGE/GGEs).

Methods

We measured the transcripts of thrombospondin‐1 and α2δ subunit, and protein levels of α2δ, Rab3A, and the vesicular glutamate transporter, VGLUT1, in the somatosensory cortex and ventrobasal thalamus of presymptomatic and symptomatic WAG/Rij rats and in two control strains by real‐time polymerase chain reaction (PCR) and immunoblotting. We examined the genetic variants of THBS1 and CACNA2D1 in two independent cohorts of patients affected by IGE/GGE recruited through the Genetic Commission of the Italian League Against Epilepsy (LICE) and the EuroEPINOMICS‐CoGIE Consortium.

Results

Thrombospondin‐1 messenger RNA (mRNA) levels were largely reduced in the ventrobasal thalamus of both presymptomatic and symptomatic WAG/Rij rats, whereas levels in the somatosensory cortex were unchanged. VGLUT1 protein levels were also reduced in the ventrobasal thalamus of WAG/Rij rats. Genetic variants of THBS1 were significantly more frequent in patients affected by IGE/GGE than in nonepileptic controls, whereas the frequency of CACNA2D1 was unchanged.

Significance

These findings suggest that thrombospondin‐1 may have a role in the pathogenesis of IGE/GGEs.