bluuebunny/crossref_metadata_2025_split huggingface dataset:
NEAT: a framework for building fully automated NGS pipelines and analyses
Authors: Schorderet Patrick 
Published: February 2016

Abstract
Background
The analysis of next generation sequencing (NGS) has become a standard task for many laboratories in the life sciences. Though there exists several tools to support users in the manipulation of such datasets on various levels, few are built on the basis of vertical integration. Here, we present the NExt generation Analysis Toolbox (NEAT) that allows non-expert users including wet-lab scientists to comprehensively build, run and analyze NGS data through double-clickable executables without the need of any programming experience.

Results
In comparison to many publicly available tools including Galaxy, NEAT provides three main advantages: (1) Through the development of double-clickable executables, NEAT is efficient (completes within <24 hours), easy to implement and intuitive; (2) Storage space, maximum number of job submissions, wall time and cluster-specific parameters can be customized as NEAT is run on the institution’s cluster; (3) NEAT allows users to visualize and summarize NGS data rapidly and efficiently using various built-in exploratory data analysis tools including metagenomic and differentially expressed gene analysis.
To simplify the control of the workflow, NEAT projects are built around a unique and centralized file containing sample names, replicates, conditions, antibodies, alignment-, filtering- and peak calling parameters as well as cluster-specific paths and settings. Moreover, the small-sized files produced by NEAT allow users to easily manipulate, consolidate and share datasets from different users and institutions.

Conclusions
NEAT provides biologists and bioinformaticians with a robust, efficient and comprehensive tool for the analysis of massive NGS datasets. Frameworks such as NEAT not only allow novice users to overcome the increasing number of technical hurdles due to the complexity of manipulating large datasets, but provide more advance users with tools that ensure high reproducibility standards in the NGS era. NEAT is publically available at https://github.com/pschorderet/NEAT.
Early pneumonia and timing of antibiotic therapy in patients after nontraumatic out-of-hospital cardiac arrest
Authors: Hellenkamp Kristian , Onimischewski Sabrina , Kruppa Jochen , Faßhauer Martin , Becker Alexander , Eiffert Helmut , Hünlich Mark , Hasenfuß Gerd , Wachter Rolf 
Published: February 2016

Abstract
Background
While early pneumonia is common in patients after out-of-hospital cardiac arrest (OHCA), little is known about the impact of pneumonia and the optimal timing of antibiotic therapy after OHCA.

Methods
We conducted a 5-year retrospective cohort study, including patients who suffered from OHCA and were treated with therapeutic hypothermia. ICU treatment was strictly standardized with defined treatment goals and procedures. Medical records, chest radiographic images and microbiological findings were reviewed.

Results
Within the study period, 442 patients were admitted to our medical ICU after successfully resuscitated cardiac arrest. Of those, 174 patients fulfilled all inclusion and no exclusion criteria and were included into final analysis. Pneumonia within the first week could be confirmed in 39 patients (22.4 %) and was confirmed or probable in 100 patients (57.5 %), without a difference between survivors and non-survivors (37.8 % vs. 23.1 % confirmed pneumonia, p = 0.125). In patients with confirmed pneumonia a tracheotomy was performed more frequently (28.2 vs. 12.6 %, p = 0.026) compared to patients without confirmed pneumonia. Importantly, patients with confirmed pneumonia had a longer ICU- (14.0 [8.5-20.0] vs. 8.0 [5.0-14.0] days, p < 0.001) and hospital stay (23.0 [11.5-29.0] vs. 15.0 [6.5-25.0] days, p = 0.016).
A positive end expiratory pressure (PEEP) > =10.5 mbar on day 1 of the hospital stay was identified as early predictor of confirmed pneumonia (odds ratio 2.898, p = 0.006). No other reliable predictor could be identified.
Median time to antibiotic therapy was 8.7 [5.4-22.8] hours, without a difference between patients with or without confirmed pneumonia (p = 0.381) and without a difference between survivors and non-survivors (p = 0.264). Patients receiving antibiotics within 12 hours after admission had a shorter ICU- (8.0 [4.0-14.0] vs. 10.5 [6.0-16.0] vs. 13.5 [8.0-20.0] days, p = 0.004) and hospital-stay (14.0 [6.0-25.0] vs. 16.5 [11.0-27.0] vs. 21.0 [17.0-28.0] days, p = 0.007) compared to patients receiving antibiotics after 12 to 36 or more than 36 hours, respectively.

Conclusions
Early pneumonia may extend length of ICU- and hospital-stay after OHCA and its occurrence is difficult to predict. A delayed initiation of antibiotic therapy in OHCA patients may increase the duration of the ICU- and hospital-stay.
BET protein inhibitor JQ1 inhibits growth and modulates WNT signaling in mesenchymal stem cells
Authors: Alghamdi Saeed , Khan Irfan , Beeravolu Naimisha , McKee Christina , Thibodeau Bryan , Wilson George , Chaudhry G. Rasul 
Published: February 2016

Abstract
Background
Efficacy and safety of anticancer drugs are traditionally studied using cancer cell lines and animal models. The thienodiazepine class of BET inhibitors, such as JQ1, has been extensively studied for the potential treatment of hematological malignancies and several small molecules belonging to this class are currently under clinical investigation. While these compounds are well known to inhibit cancer cell growth and cause apoptosis, their effects on stem cells, particularly mesenchymal stem cells (MSCs), which are important for regeneration of damaged cells and tissues, are unknown. In this study we employed umbilical cord derived MSCs as a model system to evaluate the safety of JQ1.

Methods
Cord derived MSCs were treated with various doses of JQ1 and subjected to cell metabolic activity, apoptosis, and cell cycle analyses using MTT assay, Annexin-V/FITC and PI staining, and flow cytometry, respectively. The effect of JQ1 on gene expression was determined using microarray and quantitative real-time reverse transcriptase polymerase chain reaction analysis. Furthermore, protein expression of apoptotic and neuronal markers was carried out using western blot and immunostaining, respectively.

Results
Our results showed that JQ1 inhibited cell growth and caused cell cycle arrest in G1 phase but did not induce apoptosis or senescence. JQ1 also down-regulated genes involved in self-renewal, cell cycle, DNA replication, and mitosis, which may have negative implications on the regenerative potential of MSCs. In addition, JQ1 interfered with signaling pathways by down regulating the expression of WNT, resulting in limiting the self-renewal. These results suggest that anticancer agents belonging to the thienodiazepine class of BET inhibitors should be carefully evaluated before their use in cancer therapy.

Conclusions
This study revealed for the first time that JQ1 adversely affected MSCs, which are important for repair and regeneration. JQ1 specifically modulated signal transduction and inhibited growth as well as self-renewal. These findings suggest that perinatal MSCs could be used to supplement animal models for investigating the safety of anticancer agents and other drugs.
Cochlear implant and congenital cholesteatoma
Authors: Mierzwinski J. , Fishman AJ , Grochowski T. , Drewa S. , Drela M. , Winiarski P. , Bielecki I. 
Published: February 2016

Background The occurence of cholesteatoma and cochlear implant is rare. Secondary cholesteatomas may develop as a result of cochlear implant surgery. Primarily acquired cholesteatoma is not typically associated with congenital sensorineural hearing loss or cochlear implant in children. The occurrence of congenital cholesteatoma during cochlear implant surgery has never been reported before, partly because all patients are preoperatively submitted to imaging studies which can theoretically exclude the disease. Case presentation We have reported a rare case of congenital cholesteatoma, found during sequential second side cochlear implantation in a 3-year-old child. The child underwent a computed tomography (CT) scan and magnetic resonance imaging (MRI) at 12 months of age, before the first cochlear implant surgery, which excluded middle ear pathology. The mass was removed as an intact pearl, without visible or microscopic violation of the cholesteatoma capsule. All the areas where middle ear structures were touching the cholesteatoma were vaporized with a laser and the cochlear implant was inserted uneventfully. Further follow-up excluded residual disease. Conclusion We believe that primary, single stage placement of a cochlear implant (CI) with simultaneous removal of the congenital cholesteatoma can be performed safely. However, to prevent recurrence, the capsule of the cholesteatoma must not be damaged and complete laser ablation of the surface, where suspicious epithelial cells could remain, is recommended. In our opinion, cholesteatoma removal and cochlear implantation should be staged if these conditions are not met, and/or the disease is at a more advanced stage. It is suspected, that the incidence of congenital cholesteatoma in pediatric CI candidates is much higher that in average pediatric population.
Oral ketamine for the treatment of pain and treatment-resistant depression
Authors: Schoevers Robert A. , Chaves Tharcila V. , Balukova Sonya M. , Rot Marije aan Het , Kortekaas Rudie 
Published: February 2016

BackgroundRecent studies with intravenous (i.v.) application of ketamine show remarkable but short-term success in patients with MDD. Studies in patients with chronic pain have used different ketamine applications for longer time periods. This experience may be relevant for psychiatric indications.AimsTo review the literature about the dosing regimen, duration, effects and side-effects of oral, intravenous, intranasal and subcutaneous routes of administration of ketamine for treatment-resistant depression and pain.MethodSearches in PubMed with the terms ‘oral ketamine’, ‘depression’, ‘chronic pain’, ‘neuropathic pain’, ‘intravenous ketamine’, ‘intranasal ketamine’ and ‘subcutaneous ketamine’ yielded 88 articles. We reviewed all papers for information about dosing regimen, number of individuals who received ketamine, number of ketamine days per study, results and side-effects, as well as study quality.ResultsOverall, the methodological strength of studies investigating the antidepressant effects of ketamine was considered low, regardless of the route of administration. The doses for depression were in the lower range compared with studies that investigated analgesic use. Studies on pain suggested that oral ketamine may be acceptable for treatment-resistant depression in terms of tolerability and side-effects.ConclusionsOral ketamine, given for longer time periods in the described doses, appears to be well tolerated, but few studies have systematically examined the longer-term negative consequences. The short- and longer-term depression outcomes as well as side-effects need to be studied with rigorous randomised controlled trials.
Ending political abuse of psychiatry: where we are at and what needs to be done
Authors: van Voren Robert 
Published: February 2016

SummaryThe number of reports of political activists falling victim to the political abuse of psychiatry is increasing. When the USSR first disintegrated, this practice virtually ceased to occur. What came in its place, however, was a disturbing collection of other forms of abuses, including human rights abuses, caused by a lack of resources, outdated treatment methods, a lack of understanding of individual human rights and a growing lack of tolerance in society. The number of cases of political abuse of psychiatry has increased since the 21st century began, particularly over the past few years in Russia, Belarus and Kazakhstan.
‘Locked rehabilitation’: a need for clarification
Authors: Dye Stephen , Smyth Lucy , Pereira Stephen 
Published: February 2016

SummaryRecently, the term ‘locked rehabilitation’ has spread from commissioning to now also clinical parlance. This is without any clear service description or category of patient which this service manages. Differences between this new term and an established definition of low secure services are examined and reasons for the introduction of this terminology are discussed. This is contextualised within service development, payment by results and measures of quality. It is argued that there is a need for ongoing measurements of types of patients admitted to, and treatments offered by, this ‘new’ ward, as well as those within psychiatric intensive and low secure care services.
β-cell Mass in Nondiabetic Autoantibody-Positive Subjects: An Analysis Based on the Network for Pancreatic Organ Donors Database
Authors: Diedisheim Marc , Mallone Roberto , Boitard Christian , Larger Etienne 
Published: February 2016

Abstract

Context:
Little information is available about β-cell mass in antibody-positive (Ab+) nondiabetic subjects.

Objective:
We have investigated whether the publicly available virtual slides of the Network for Pancreatic Organ Donors with Diabetes (nPOD) project can be used to assess β-cell mass and distribution in nondiabetic antibody-negative (Ab−) and antibody-positive (Ab+) subjects and in patients with recent-onset type 1 diabetes (T1D).

Subjects and Methods:
We developed a semi-automated quantification method and applied it to 415 insulin-stained slides from 69 Ab− subjects, 101 slides from 18 Ab+ subjects, and 46 slides from eight recent-onset (&lt;3 y) T1D subjects. Among these subjects, 48, 17, and seven had an available pancreatic mass, respectively, and were used for the quantification of β-cell mass.

Results:
In Ab− subjects, the β-cell and endocrine mass were 0.66 ± 0.42 and 1.0 ± 0.65 g, respectively. Nonexocrine tissue represented 29% of pancreatic area, a proportion that increased with age. Proportional β-cell area relative to total pancreatic area was higher in the tail compared with head (0.83 vs 0.71%; P &lt; .001). In Ab+ subjects, β-cell mass and β-cell area were similar to those of Ab− individuals, whereas these parameters were dramatically decreased in recent-onset T1D patients.

Conclusion:
The virtual slides of the nPOD project can be used for quantification projects. In Ab+ nondiabetic subjects, the β-cell mass was not decreased. However, as this cohort is largely composed of donors from the general population, with a single autoantibody, future studies with a larger number of donors with multiple autoantibodies and predisposing human leucocyte antigen genes are required to better define the dynamics of β-cell destruction in the preclinical phases of T1D.
The German Side of Things
Authors: Imlay Talbot 
Published: February 2016

This review of recent scholarship on the German occupation of France during the Second World War discusses four subjects: the role of the German military authorities, anti-Jewish policy, economic policy, and relations between occupiers and occupied. The review argues that recent scholarship on the German occupation offers a potential complement to the scholarship on Vichy, which has been dominated by a focus on the French. There is, however, a danger of simply replacing a focus on the French with one on the Germans. The review points to the need for more exploration of the intertwined experiences of occupiers and occupied. This intertwining was evident in the economic and industrial realms and perhaps even more so in the social realm, in which significant numbers of French and Germans interacted with one another on a regular basis.Cet article passe en revue plusieurs études récentes sur l'histoire de l'occupation allemande de la France pendant la Deuxième Guerre mondiale. Il traite de quatre sujets en particulier: le rôle des autorités militaires allemandes; la politique antisémite; la politique économique; et les rapports entre les occupés et les occupants. L'argument de l'article est que les études récentes sur l'occupation offrent un éventuel complément aux études sur Vichy, qui sont marquées par une concentration sur les Français. En même temps, il est à craindre que les études récentes remplacent tout simplement une concentration sur les Français par une autre sur les Allemands. L'article avance la nécessité d'examiner les rapports entrecroisés des occupés et des occupants. Cet entrecroisement était évident dans les domaines de l'économie et de l'industrie et peut-être davantage dans celui du social—un domaine dans lequel un grand nombre de Français et Allemands ont dû s'affronter au quotidien.
Double-Fluorescent-Labeled Single-Chain Antibodies Showing Antigen-Dependent Fluorescence Ratio Change
Authors: Yoshikoshi Kensuke , Watanabe Takayoshi , Hohsaka Takahiro 
Published: February 2016

Abstract
Fluorescence ratio probes are useful tools for quantitative detection of target molecules even if the concentration of probe molecules is unknown. However, a general and widely applicable method for design and synthesis of fluorescence ratio probes has never been established. Here, we developed double-labeled single-chain antibody fragment (scFv) derivatives showing antigen-dependent fluorescence ratio change based on fluorescence resonance energy transfer (FRET) and antigen-dependent fluorescence quenching. Double-labeled scFvs were synthesized by incorporating fluorescent nonnatural amino acids labeled with TAMRA and Rhodamine Green (RhG) as a FRET donor and acceptor pair into N- and C-termini of scFv, respectively, using four-base and amber codons in a cell-free translation system. The resulting double-labeled antibody fragments showed significant fluorescence ratio change upon the antigen-binding. This result was explained by FRET occurring from RhG to TAMRA but TAMRA being quenched by Trp residues in the absence of antigen. The binding of the antigen canceled the quenching of TAMRA without changing FRET efficiency. Double-labeled antibody fragments developed here will be useful as diagnostic and imaging tools.
Is there a Link between Supply Chain Strategies and Firm Performance? Evidence from Large-Scale Manufacturing Firms in Kenya
Authors: Nyaoga Richard Bitange , Magutu Peterson Obara , Aduba Josiah 
Published: February 2016

The purpose of this study was to establish the relationship between supply chain strategies and performance of large-scale manufacturing firms in Kenya by addressing three primary gaps in the literature. The research gaps include the research findings and results on the relationship between supply chain strategies and firm performance that have been contradicting and no attempt to clear the contradictions; biased and unbalanced analysis of the different measures of firm performance, and failure to use weighted scores to measure firm performance. Resource-Based View guided this study. A sample of one hundred and thirty-eight (138) firms was drawn using proportionate sampling from a population of six hundred and twenty-seven (627) large-scale manufacturing firms in Kenya. The response rate was seventy-five (75) percent. The correlation analysis and regression analysis models were used to test the hypotheses. The study findings indicate that Supply chain strategies are useful predictors of the firm’s performance as supply chain strategies explain 76.7 % of the changes in the firm’s performance.DOI:10.12660/joscmv8n2p1-22 URL: http://dx.doi.org/10.12660/joscmv8n2p1-22
Characterization of cross-functional integration level: A multi case study in Agribusiness Organizations
Authors: Ferreira Ana Cristina , Pimenta Marcio Lopes , Bertan Franciele Olivo 
Published: February 2016

A point that has generated discussion in the literature is the level of integration required for the coordination of activities between areas. However, there is a lack of theoretical definitions and field studies that explain this phenomenon in depth. Thus, this study aims to characterize the level of cross-integration, the factors that generate it and the impacts on organizational performance. For this, interviews with managers of Operations, R&D and Marketing/Commercial areas, from two multinational companies based in Minas Gerais were performed. The results indicate that the level of integration can be analyzed as a combination of three factors: 1) absence of overlapping of perceptions about integration factors over the processes, balance between formality and informality, and absence of manifest conflicts of interest. This is a setting that provides a deeper definition than those obtained in the studied literature, which basically present integration mechanisms, without detailing how these should be applied in order to generate higher levels of integration. DOI:10.12660/joscmv8n2p36-51URL: http://dx.doi.org/10.12660/joscmv8n2p36-51
A Stochastic Two-Echelon Supply Chain Model for the Petrol Station Replenishment Problem
Authors: Mubiru Kizito Paul 
Published: February 2016

In this paper, a new mathematical model is developed to optimize replenishment policies and inventory costs of a two-echelon supply chain system of kerosene product under demand uncertainty. The system consists of a fuel depot at the upper echelon and four petrol stations at the lower echelon. The petrol stations face stochastic stationary demand where inventory replenishment periods are uniformly fixed over the echelons. Adopting a Markov decision process approach, the states of a Markov chain represent possible states of demand for the inventory item. The replenishment cost, holding cost and shortage costs are combined with demand and inventory positions in order to generate the inventory cost matrix over the echelons. The matrix represents the long run measure of performance for the decision problem. The objective is to determine in each echelon of the planning horizon an optimal replenishment policy so that the long run inventory costs are minimized for a given state of demand. Using weekly equal intervals, the decisions of when to replenish additional units are made using dynamic programming over a finite period planning horizon. A numerical example demonstrates the existence of an optimal state-dependent replenishment policy and inventory costs over the echelons. DOI:10.12660/joscmv8n2p67-76URL: http://dx.doi.org/10.12660/joscmv8n2p67-76
Evaluation of immunologic response of salivary sIg-A in pediatric tuberculosis patients to antigen Ag38-rec of Mycobacterium tuberculosis Indonesian strain
Authors: Raras Tri Yudani Mardining , Pritta Santi Diah Erma , Kusuma HMS Chandra 
Published: February 2016

Objective: We studied the immune response of salivary secretory immunoglobulin A (sIg-A) from a pediatric tuberculosis (TB) group (scoring > and =6) and non-TB group (scoring <6) against recombinant Ag38 (Ag38-rec) fromMycobacterium tuberculosis Indonesian strain.Materials and Methods: Seventy-eight children were divided into three groups; those with TB (n=26), those with suspected TB (n=26), and healthy children (n=26), their saliva was collected, and salivary sIg-A was challenged with purified Ag38-rec using the dot blot method. A change of color from white to dark blue indicated a positive reaction.Results: The immune response of sIg-A of children with TB and those with suspected TB to Ag38-rec was not significantly different. In the TB group, Ag38-rec showed a higher sensitivity than protein purified derivative (PPD) (70.8% vs. 62.5%), but a lower specificity (26.9% vs. 34.62%). However, within both groups (scoring > and =6) as well as non-TB group (scoring <6) Ag38-rec was able to identify children with a positive TST (tuberculin skin test) better than PPD.Conclusion: The antigen Ag38-rec could not distinguish between children with TB (scores > and =6 and <6). However, it demonstrated the potential of Ag38-rec for use in screening for TB infection among children with suspect TB (scores <6).