bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction in CD11c+microglia correlates with clinical progression in chronic experimental autoimmune demyelination
Authors: Mayrhofer Florian , Dariychuk Zhanna , Zhen Anthony , Daugherty Daniel J. , Bannerman Peter , Hanson Angela M. , Pleasure David , Soulika Athena , Deng Wenbin , Chechneva Olga V. 
Published: August 2018

AbstractMultiple sclerosis (MS) is a chronic autoimmune demyelinating disease with high variability of clinical symptoms. In most cases MS appears as a relapsing-remitting disease course that at a later stage transitions into irreversible progressive decline of neurologic function. The mechanisms underlying MS progression remain poorly understood. Experimental autoimmune encephalomyelitis (EAE) is an animal model of MS. Here we demonstrate that mice that develop mild EAE after immunization with myelin oligodendrocyte glycoprotein 35-55 are prone to undergo clinical progression around 30 days after EAE induction. EAE progression was associated with reduction in CD11c+microglia and dispersed coalescent parenchymal infiltration. We found sex-dependent differences mediated by p38α signaling, a key regulator of inflammation. Selective reduction of CD11c+microglia in female mice with CD11c-promoter drivenp38αknockout (KO)correlated with increased rate of EAE progression. In protected animals, we found CD11c+microglia forming contacts with astrocyte processes at the glia limitans and immune cells retained within perivascular spaces. Together, our study provides evidence on the protective role of CD11c+microglia in controlling CNS immune cell parenchymal infiltration in autoimmune demyelination.
Full title: Label free quantitative proteomics ofQualea grandifloraMart. (Vochysiaceae) roots indicates an aluminium requirement for growth and development
Authors: Cury Natalia F. , Silva Renata C. C. , Melo Jessica R. , Andre Michelle S. F. , Fontes Wagner , Ricart Carlos A. O. , Castro Mariana S. , Silveira Conceição E. S. , de Sousa Marcelo V. , Pereira Luiz A. R. 
Published: August 2018

AbstractAluminium in acid soils is a hindrance to crop growth. Nonetheless, Brazilian Cerrado possesses many species such asQualea grandiflora, which are adapted to acid soils with large amounts of Al and accumulate this metal in its tissues and organs. Nonetheless, the mechanisms involved in these processes are poorly understood, mainly at molecular level. Thus, a root proteomic analysis was accomplished to identify Al-responsive proteins inQ. grandifloraplants. Concomitantly, a root growth analysis of plants grown with and without Al supplementation was conducted to determine the effects of Al on the whole plant. Subsequently, proteins from both treatments were identified and quantified by LC-MS/MS in a label-free fashion. From the 2,520 identified proteins, 410 were differentially abundant between the two treatments, which were associated with carbohydrate metabolism, redox activity, stress response and catabolism of organic compounds. Furthermore, Al was crucial for the growth and development ofQ. grandiflora. In fact, this species may have an Al-dependent metabolism. Moreover, it was possible to correlate plant growth to Al-upregulated proteins that were directly involved in cell wall synthesis, oxidative phosphorylation, genetic information processing, and amino acid metabolism. Additionally, this work provides an extensive dataset of Al-regulated protein inQ. grandiflora, which will be crucial to understanding the functions of Al in this species.
Regeneration-Associated Cells Improve Recovery from Myocardial Infarction through Enhanced Vasculogenesis, Anti-inflammation, and Cardiomyogenesis
Authors: Salybekov Amankeldi A. , Kawaguchi Akira T. , Masuda Haruchika , Vorateera Kosit , Okada Chisa , Asahara Takayuki 
Published: August 2018

ABSTRACTBackgroundConsidering the impaired function of regenerative cells in patients with comorbidities and associated risk factors, cell therapy to enhance the regenerative microenvironment was designed using regeneration-associated cells (RACs), including endothelial progenitor cells (EPCs) and anti-inflammatory cells.MethodsRACs were prepared by quality and quantity control culture of blood mononuclear cells (QQMNCs). The peripheral blood mononuclear cells (PBMNCs) were isolated from Lewis rats and conditioned for 5 days using a medium containing stem cell factors, thrombopoietin, Flt-3 ligand, vascular endothelial growth factor, and interleukin-6 to generate QQMNCs.ResultsIn vitro EPC colony forming assays demonstrated a 5.3-fold increase in the definitive colony-forming EPCs and vasculogenic EPCs, in comparison to naïve PBMNCs. Flow cytometry analysis revealed that QQMNCs were enriched with RACs, such as EPCs (28.9-fold, P<0.0019) and M2 macrophages (160.3-fold, P<0.0002). Cell transcriptome analysis revealed that angiogenesis (angpt1, angpt2, and vegfb), stem/progenitor (c-kit and sca-1) and anti-inflammation related (arg-1, erg-2, tgfb, and foxp3) genes were highly expressed in QQMNCs. For in vivo cell transplantation experiments, 1×105 cells were administered via the tail vein into syngeneic rat models of myocardial infarction (MI). Echocardiographic data showed that QQMNCs-transplanted group (QQ-Tx) preserved cardiac function and fraction shortening (45.5±4.6%) at 28-days post-MI in comparison with PBMNCs-transplanted (PB-Tx) (30.9±6.4%, P<0.0001) and Control (32.2±7.7%, P<0.0008) groups. Histological analysis revealed that QQ-Tx showed enhanced angiogenesis and reduced interstitial left ventricular fibrosis, along with a decrease in neutrophils and an increase in M2 macrophages in the acute phase of MI. Cell tracing studies revealed that intravenously administered QQMNCs preferentially homed to ischemic tissues via blood circulation, while PBMNCs did not. QQ-Tx showed markedly upregulated early cardiac transcriptional cofactors (Nkx2-5, 29.8-fold, and Gata-4, 5.2- fold) as well as c-kit (4.5-fold) while these markers were downregulated in PB-Tx. In QQ-Tx animals, de novo blood vessels formed a “Biological Bypass” as observed macroscopically and microscopically, while PB-Tx and Control-Tx groups never developed epicardial blood vessels but showed severe fibrotic adhesion to the surrounding tissues.ConclusionQQMNCs, as RACs derived from rat PBMNCs, conferred potent angiogenic and anti-inflammatory properties to the regenerative microenvironment, enhancing myocardiogenesis and functional recovery of rat MI hearts.
Determination of essential phenotypic elements of clusters in high-dimensional entities - DEPECHE
Authors: Theorell Axel , Bryceson Yenan Troi , Theorell Jakob 
Published: August 2018

AbstractTechnological advances have facilitated an exponential increase in the amount of information that can be derived from single cells, necessitating new computational tools that can make this highly complex data interpretable. Here, we introduce DEPECHE, a rapid, parameter free, sparse k-means-based algorithm for clustering of multi-and megavariate single-cell data. In a number of computational benchmarks aimed at evaluating the capacity to form biologically relevant clusters, including flow/mass-cytometry and single cell RNA sequencing data sets with manually curated gold standard solutions, DEPECHE clusters as well or better as the best performing state-of-the-art clustering algorithms. However, the main advantage of DEPECHE, compared to the state-of-the-art, is its unique ability to enhance interpretability of the formed clusters, in that it only retains variables relevant for cluster separation, thereby facilitating computational efficient analyses as well as understanding of complex datasets. An open source R implementation of DEPECHE is available athttps://github.com/theorell/DepecheR.Author summaryDEPECHE-a data-mining algorithm for mega-variate dataModern experimental technologies facilitate an array of single cells measurements,e.g.at the RNA-level, generating enormous datasets with thousands of annotated biological markers for each of thousands of cells. To analyze such datasets, researchers routinely apply automated or semi-automated techniques to order the cells into biologically relevant groups. However, even after such groups have been generated, it is often difficult to interpret the biological meaning of these groups since the definition of each group often dependends on thousands of biological markers. Therefore, in this article, we introduce DEPECHE, an algorithm designed to simultaneously group cells and enhance interpretability of the formed groups. DEPECHE defines groups only with respect to biological markers that contribute significantly to differentiate the cells in the group from the rest of the cells, yielding more succinct group definitions. Using the open source R software DepecheR on RNA sequencing data and mass cytometry data, the number of defining markers were reduced up to 1000-fold, thereby increasing interpretability vastly, while maintaining or improving the biological relevance of the groups formed compared to state-of-the-art algorithms.
Implicit and explicit learning in reactive and voluntary saccade adaptation
Authors: Es D.M. van , Knapen T. 
Published: August 2018

AbstractSaccades can either be elicited automatically by salient peripheral stimuli or can additionally depend on explicit cognitive goals. Similarly, it is thought that motor adaptation is driven by the combination of a more automatic, implicit process and a more explicit, cognitive process. However, the degree to which such implicit and explicit learning contribute to the adaptation of more reactive and voluntary saccades remains elusive. To study this question, we employed a global saccadic adaptation paradigm with both increasing and decreasing saccade amplitudes. We assessed the resulting adaptation using a dual state model of motor adaptation. This model decomposes learning into a fast and slow process, which are thought to constitute the explicit and implicit learning, respectively. Our results show that adaptation of reactive saccades is equally driven by fast and slow learning, while fast learning is nearly absent when adapting voluntary (i.e. scanning) saccades. This pattern of results was present both when saccade gain was increased or decreased. Our results suggest that the increased cognitive demands associated with voluntary compared to reactive saccade planning interfere specifically with explicit learning.
In Silico Identification and Experimental Validation of Novel KPC-2 β-lactamase Inhibitors
Authors: Klein R. , Linciano P. , Celenza G. , Bellio P. , Papaioannou S. , Blazquez J. , Cendron L. , Brenk R. , Tondi D. 
Published: August 2018

AbstractBacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, as putative hit candidates. We performed a structure-based in silico screening of commercially available compounds for non-β-lactam KPC-2 inhibitors. Thirty-two commercially available high-scoring, fragment-like hits were selected for in vitro validation and their activity and mechanism of action vs the target was experimentally evaluated using recombinant KPC-2. N-(3-(1H-tetrazol-5-yl)phenyl)-3-fluorobenzamide (11a), in light of its ligand efficiency (LE = 0.28 kcal/mol/non-hydrogen atom) and chemistry, was selected as hit to be directed to chemical optimization to improve potency vs the enzyme and explore structural requirement for inhibition in KPC-2 binding site. Further, the compounds were evaluated against clinical strains overexpressing KPC-2 and the most promising compound reduced the MIC of the β-lactam antibiotic meropenem by four fold.
Comparative Multi-scale Hierarchical Structure of the Tail, Plantaris, and Achilles Tendons in the Rat
Authors: Lee Andrea H. , Elliott Dawn M. 
Published: August 2018

AbstractRodent tendons are widely used to study human pathology, such as tendinopathy and repair, and to address fundamental physiological questions about development, growth, and remodeling. However, how the gross morphology and the multi-scale hierarchical structure of rat tendons, such as the tail, plantaris, and Achillles tendons, compare to that of human tendons are unknown. In addition, there remains disagreement about terminology and definitions. Specifically, the definition of fascicle and fiber are often dependent on the diameter size and not their characteristic features, which impairs the ability to compare across species where the size of the fiber and fascicle might change with animal size and tendon function. Thus, the objective of the study was to select a single species that is widely used for tendon research (rat) and tendons with varying mechanical functions (tail, plantaris, Achilles) to evaluate the hierarchical structure at multiple length scales. This study was designed including, histology, SEM, and confocal imaging. We confirmed that rat tendons do not contain fascicles, and thus the fiber is the largest tendon subunit in the rat. In addition, we provided a structurally-based definition of a fiber as a bundle of collagen fibrils that is surrounded by elongated cells, and this definition was supported by both histologically processed and unprocessed tendons. In all rat tendons studied, the fiber diameters were consistently 10-50 µm, and this diameter appears to be conserved across larger species. Specific recommendations were made for the strengths and limitations of each rat tendon as tendon research models. Understanding the hierarchical structure of tendon can advance the design and interpretation of experiments and development of tissue engineered constructs.
Computational performance and accuracy of Sentieon DNASeq variant calling workflow
Authors: Kendig Katherine I. , Baheti Saurabh , Bockol Matthew A. , Drucker Travis M. , Hart Steven N. , Heldenbrand Jacob R. , Hernaez Mikel , Hudson Matthew E. , Kalmbach Michael T. , Klee Eric W. , Mattson Nathan R. , Ross Christian A. , Taschuk Morgan , Wieben Eric D. , Wiepert Mathieu , Wildman Derek E. , Mainzer Liudmila S. 
Published: August 2018

AbstractAs reliable, efficient genome sequencing becomes more ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy. One such alternative is Sentieon DNASeq, a toolkit analogous to GATK but built on a highly optimized backend. We evaluated the DNASeq single-sample variant calling pipeline in comparison to that of GATK. Our results confirm the near-identical accuracy of the two software packages, showcase perfect scalability and great speed from Sentieon, and describe computational performance considerations for the deployment of Sentieon DNASeq.
Differences in bank profit persistence in Sub-Saharan Africa
Authors: Sarpong-Kumankoma Emmanuel , Abor Joshua , Aboagye Anthony Q.Q. , Amidu Mohammed 
Published: August 2018

Purpose
The purpose of this paper is to examine differences in determinants of bank profit persistence among Sub-Saharan African (SSA) countries.

Design/methodology/approach
Using system generalized method of moments and data from four SSA countries during the period 2006–2012, this study considers differences in determinants of bank profit persistence across countries.

Findings
Efficiency in cost management is a major determinant of profit persistence in all the countries. However, concentration is found to be insignificant in all the estimations, suggesting that efficiency may be a more important determinant of profit persistence than concentration. Economic freedom associates negatively with profit persistence in Ghana, but its effect is insignificant in Tanzania, Kenya and South Africa. Lending specialization translates into less profit persistence in South Africa, but greater persistence in Tanzania. Higher levels of financial development result in lower profit persistence in Kenya and Ghana, but does not matter in Tanzania and South Africa.

Practical implications
The level of profit persistence gives an indication of the effectiveness of competition policies, and the differences observed in their determinants in this study suggest the need for tailor-made policy responses in the different countries.

Originality/value
This study improves the understanding of why some banking market competition policies have not achieved the desired outcomes in some countries. It is evident that blanket rules or wholesale importation of policies from other countries may not work in different contexts.
Study on farmers land consolidation adaptation intention
Authors: Gessesse Abrham Tezera , Li Houjian , He Ge , Berhe Araya Alemie 
Published: August 2018

Purpose
The purpose of this paper is to examine the effects of media and social network in the development of farmers land consolidation (LC) awareness, perception and adaptation intention decisions.

Design/methodology/approach
A face-to-face interview was carried out with randomly selected farmers from three districts (Neijiang, Ya’an and Dujiangyan) of Sichuan province, China. A structural equation modeling (SEM) technique was used to test the conceptual framework of this study. The SEM was set to confirmatory factor analysis of the measurement and structural models for maximum likelihood estimate by means of IBM-AMOS to capture the models goodness-of-fit.

Findings
The result indicates that social network contributes a significant role in the development of farmers LC awareness, perception and adaptation intention decisions than media. The total (direct and indirect) effect of social network and media toward the farmers LC adaptation intention is 56.7 and 14 percent, respectively. When farmers are aware and perceived of LC and rehabilitation program, their adaptation intention improves significantly. Therefore, social network is a useful tool in improving the awareness, perception and adaptation intention decisions of Sichuan farmers compared to media.

Originality/value
This study tests the applicability of SEM techniques to understand the farmers LC adaptation intentions; and synthesizes the impact of social network and media in the development of the farmers LC awareness, perception as well as adaptation intentions. This study serves as an outline for assessing the adaptation intention of farmers toward sustainable land management.
Thermal breakdown in high voltage direct current cable insulations due to space charges
Authors: Jörgens Christoph , Clemens Markus 
Published: August 2018

Purpose
In high voltage direct current (HVDC), power cables heat is generated inside the conductor and the insulation during operation. A higher amount of the generated heat in comparison to the dissipated one, results in a possible thermal breakdown. The accumulation of space charges inside the insulation results in an electric field that contributes to the geometric electric field, which comes from the applied voltage. The total electric field decreases in the vicinity of the conductor, while it increases near the sheath, causing a possible change of the breakdown voltage.

Design/methodology/approach
Here, the thermal breakdown is studied, also incorporating the presence of space charges. For a developed electro-thermal HVDC cable model, at different temperatures, the breakdown voltage is computed through numerical simulations.

Findings
The simulation results show a dependence of the breakdown voltage on the temperature at the location of the sheath. The results also show only limited influence of the space charges on the breakdown voltage.

Research limitations/implications
The study is restricted to one-dimensional problems, using radial symmetry of the cable, and does not include any aging or long-term effect of space charges. Such aging effect can locally increase the electric field, resulting in a reduced breakdown voltage.

Originality/value
A comparison of the breakdown voltage with and without space charges is novel. The chosen approach allows for the first time to assess the influence of space charges and field inversion on the thermal breakdown.
Open factory events as triggers of interactive learning in organizations
Authors: Brunetti Federico , Bonfanti Angelo , Castellani Paola , Giaretta Elena 
Published: August 2018

Purpose
The purpose of this paper is to present and discuss an unconventional approach for developing organizational learning inside companies. The subject of this paper is the interactive mode of organizational learning – involving shared understanding and sense-making – which has proven useful in the current turbulent era and complex competitive environment.

Design/methodology/approach
The paper is based on an inductive and phenomenon-driven approach. The data collection method consists of interviews with involves informants. The empirical context of the research is Open Factory – the largest open-door event for industrial manufacturing in Italy.

Findings
Companies participating in Open Factory gained several benefits in terms of interactive learning. In particular, intra-organizational knowledge sharing, staff motivation, and more focused organizational identity were reported as the most relevant advantages.

Practical implications
Companies eager to enhance their interactive mode of organizational learning should seriously consider taking part in events such as Open Factory or should strive to create a similar event.

Originality/value
To the best of the authors’ knowledge, this paper is the first to describe and analyze open-door events for manufacturing companies as a source of organizational learning.