bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive Responses of Mitochondria to Mild Copper Deprivation Involve Changes in Morphology, OXPHOS Remodeling and Bioenergetics
Authors: Ruiz Lina María , Jensen Erik L. , Bustos Rodrigo I. , Argüelloa Graciela , Gutierrez‐Garcia Ricardo , González Mauricio , Hernández Claudia , Paredes Rodolfo , Simon Felipe , Riedel Claudia , Ferrick David , Elorza Alvaro A. 
Published: January 2014

AbstractCopper is an essential cofactor of complex IV of the electron transfer chain, and it is directly involved in the generation of mitochondrial membrane potential. Its deficiency induces the formation of ROS, large mitochondria and anemia. Thus, there is a connection between copper metabolism and bioenergetics, mitochondrial dynamics and erythropoiesis. Copper depletion might end in cellular apoptosis or necrosis. However, before entering into those irreversible processes, mitochondria may execute a series of adaptive responses. Mitochondrial adaptive responses (MAR) may involve multiple and diverse mechanisms for preserving cell life, such as mitochondrial dynamics, OXPHOS remodeling and bioenergetics output. In this study, a mild copper deficiency was produced in an animal model through intraperitoneal injections of bathocuproine disulfonate in order to study the MAR. Under these conditions, a new type of mitochondrial morphology was discovered in the liver. Termed the “butternut squash” mitochondria, it coexisted with normal and swollen mitochondria. Western blot analyses of mitochondrial dynamics proteins showed an up‐regulation of MFN‐2 and OPA1 fusion proteins. Furthermore, isolated liver mitochondria displayed OXPHOS remodeling through a decrease in supercomplex activity with a concomitant increase at an individual level of complexes I and IV, higher respiratory rates at complex I and II levels, higher oligomycin‐insensitive respiration, and lower respiratory control ratio values when compared to the control group. As expected, total ATP and ATP/ADP values were not significantly different, since animal's health was not compromised. As a whole, these results describe a compensatory and adaptive response of metabolism and bioenergetics under copper deprivation. J. Cell. Physiol. 229: 607–619, 2014. © 2013 Wiley Periodicals, Inc.
Functional Role of Connexins and Pannexins in the Interaction Between Vascular and Nervous System
Authors: Gaete Pablo S. , Lillo Mauricio A. , Figueroa Xavier F. 
Published: January 2014

ABSTRACTThe microvascular network of the microcirculation works in tight communication with surrounding tissues to control blood supply and exchange of solutes. In cerebral circulation, microvascular endothelial cells constitute a selective permeability barrier that controls the environment of parenchymal brain tissue, which is known as the blood–brain barrier (BBB). Connexin‐ and pannexin‐formed channels (gap junctions and hemichannels) play a central role in the coordination of endothelial and smooth muscle cell function and connexin‐mediated signaling in endothelial cells is essential in the regulation of BBB permeability. Likewise, gap junction communication between astrocyte end‐feet also contributes to maintain the BBB integrity, but the participation of hemichannels in this process cannot be discarded. Sympathetic and sensory perivascular nerves are also involved in the control and coordination of vascular function through the release of vasoconstrictor or vasodilator signals and by the regulation of gap junction communication in the vessel wall. Conversely, ATP release through pannexin‐1‐formed channels mediates the α1‐adrenergic signaling. Furthermore, here we show that capsaicin‐induced CGRP release from mesenteric perivascular sensory nerves induces pannexin‐1‐formed channel opening, which in turn leads to reduction of pannexin‐1 and endothelial nitric oxide synthase (eNOS) expression along the time. Interestingly, blockade of CGRP receptors with CGRP8–37 increased eNOS expression by ∼5‐fold, suggesting that capsaicin‐sensitive sensory nerves are involved in the control of key signaling proteins for vascular function. In this review, we discuss the importance of connexin‐based channels in the control of BBB integrity and the functional interaction of vascular connexins and pannexins with the peripheral nervous system. J. Cell. Physiol. 229: 1336–1345, 2014. © 2014 Wiley Periodicals, Inc.
Anomalies, trends and variability in atmospheric fields related to hailstorms in north‐eastern Spain
Authors: García‐Ortega E. , Hermida L. , Hierro R. , Merino A. , Gascón E. , Fernández‐González S. , Sánchez J. L. , López L. 
Published: January 2014

ABSTRACTHailstorms have become a serious meteorological risk in mid‐latitude countries because of their small‐scale development and short time span, and their forecasting remains problematic. Moreover, the lack of reliable hailstorm databases is an important handicap for Numerical Weather Prediction (NWP) model validation, time trend studies and establishment of hailstorm relationships with global warming and climate change. However, this can be overcome by ascertaining physical relationships between favourable synoptic patterns and mesoscale trigger factors for hailstorm development in a local study area.North‐eastern Spain is one of the European regions with largest number of hailstorm days (HD) observed in the summer. Since 2001, from May through September, reliable databases of hailstorm occurrence in the middle Ebro Valley have been constructed, which include intensity, temporal frequency and spatial coordinate data. June and July 2006 had the largest number of HD in 2001–2010. With the objective of analysing meteorological factors responsible for this anomaly, atmospheric patterns at low and mid‐tropospheric levels were studied. We determined a set of special synoptic configurations, with an evident deviation from climatic values generating anomalies of 850 hPa temperature relative to the characteristic values of 2001–2010 and 1950–2010. An analysis of these anomalies detected a positive trend of 850 hPa temperature and geopotential height in the western Mediterranean area. As a consequence, the characteristic synoptic circulation has changed since 1950, towards low‐level patterns favouring adequate thermodynamic environments for hailstorm development in north‐eastern Spain. Finally, after a cluster analysis, we studied periodicities in the monthly 850 hPa temperature field to improve knowledge for seasonal forecasting of hailstorms.
The Usual and the Unusual: Solving Remote Associates Test Tasks Using Simple Statistical Natural Language Processing Based on Language Use
Authors: Klein Ariel , Badia Toni 
Published: January 2014

AbstractIn this study we show how complex creative relations can arise from fairly frequent semantic relations observed in everyday language. By doing this, we reflect on some key cognitive aspects of linguistic and general creativity. In our experimentation, we automated the process of solving a battery of Remote Associates Test tasks. By applying Statistical Natural Language Processing techniques to a large web‐based corpus, we perform a frequency and collocation analysis of the test items. Results show that 37% of the 68 tasks were automatically solved, whereas human accuracy reached 43%. Our method outperformed humans in the tasks rated as difficult: 38% and 32%, respectively. Highly relevant is that the novel and adequate relations established in order to solve theRATwere not previously present in the corpus. The frequency based approach pervades all stages of our method: during the divergent stage, highly frequent collocations are listed, while the convergent stage starts by matching each task's triads output, shrinking that list, and finalizing it by choosing the least frequent, therefore more informative and often correct, result. Finally, we discuss the implications of our model in overcoming functional fixedness and understanding cognitive salience in the creative process.
Improving ryegrass‐clover pasture dry matter yield and urea efficiency with gibberellic acid
Authors: Zaman Mohammad , Ghani Anwar , Kurepin Leonid V , Pharis Richard P , Khan Shabana , Smith Terry J 
Published: January 2014

AbstractBACKGROUNDThe effects of spraying gibberellic acid (GA3) at 20 or 30 g ha−1, with or without application of urea, on pasture dry matter (DM) yield, herbage nitrogen (N) concentration and feed quality were investigated in 2011 and 2012 for managed pastoral systems in New Zealand across a range of sites, in both autumn and spring.RESULTSOn the Waikato site (autumn and spring, 2012), and at all five sites in 2011, liquid urea applied with GA3 at 20 or 30 g ha−1 consistently produced significantly higher pasture shoot DM yield, relative to liquid urea alone. Application of GA3 alone reduced feed quality by lowering metabolizable energy, crude protein and organic matter digestibility values. However, a reduced feed quality was not observed when GA3 was applied together with liquid urea. Liquid urea applied with GA3 also reduced total N and nitrate‐N concentration in herbage, relative to liquid urea applied alone.CONCLUSIONApplication of GA3 together with liquid urea provides an opportunity for the strategic use of urea to meet both production and environmental goals. © 2014 Society of Chemical Industry
Microstructure characterization of a decellularized vocal fold scaffold for laryngeal tissue engineering
Authors: Tse Justin R. , Long Jennifer L. 
Published: January 2014

Objectives/HypothesisOne potential treatment for vocal fold injury or neoplasia is to replace the entire vocal fold with a tissue‐engineered scaffold. This scaffold should ideally have similar mechanical properties and extracellular matrix composition as the native vocal fold. As one approach toward this goal, we decellularized human vocal folds and characterized their mechanical properties and extracellular matrix microstructure.Study DesignBasic science investigation.MethodsHuman vocal folds were dissected from the laryngeal framework and treated with sodium dodecyl sulfate (SDS) to remove all cells. Mechanical properties were measured by indentation before and after SDS treatment. The extracellular matrix components of collagen, laminin, elastin, and hyaluronic acid were also characterized before and after decellularization using histology and immunofluorescence.ResultsAfter 4 days of SDS treatment, we obtained a scaffold that retained the original geometry of the vocal fold but was devoid of cells. The elastic modulus of the vocal folds did not change significantly before and after decellularization. Upon qualitative inspection, the decellularized vocal folds retained the original collagen, elastin, and laminin content and orientation but lost the original hyaluronic acid.ConclusionsVocal folds can be decellularized using SDS without adversely affecting its mechanical stiffness and fibrous extracellular matrix. This preliminary study demonstrates the potential of a decellularized scaffold to serve as a tissue‐engineered construct for vocal fold replacement.Level of EvidenceNA Laryngoscope, 124:E326–E331, 2014
In vivo optical imaging of folate receptor‐β in head and neck squamous cell carcinoma
Authors: Sun Joel Y. , Shen Jiayin , Thibodeaux Joel , Huang Gang , Wang Yiguang , Gao Jinming , Low Philip S. , Dimitrov Dimiter S. , Sumer Baran D. 
Published: January 2014

Objectives/HypothesisFolate receptor (FR) expression, although known to be elevated in many types of cancer and inflammatory cells, has not been well characterized in head and neck squamous cell carcinoma (HNSCC). We hypothesized that tumor infiltrating inflammatory cells expressing FR‐β could allow fluorescent visualization of HNSCC tumors using folate conjugated dyes even when FR expression in cancer cells is low.Study DesignRetrospective review of clinical pathologic specimens and in vivo animal study.MethodsA tissue microarray with tumor and tumor‐free tissue from 22 patients with HNSCC was stained with antibodies to FR‐α and FR‐β. We characterized FR‐β+ cells by examining CD45, CD68, CD206, and transforming growth factor (TGF)‐β expression. To investigate fluorescent imaging, mice with orthotopic tumor xenografts were imaged in vivo after intravenous injections of folate conjugated fluorescein isothiocyanate (folate‐FITC) and were histologically evaluated ex vivo.ResultsAll tumor samples demonstrated significant FR‐β staining and negligible FR‐α staining. FR‐β+ cells found in tumors coexpressed CD68 and had increased expression of CD206 and TGF‐β characteristic of tumor‐associated macrophages. In the xenograft models, tumors showed strong in vivo fluorescence after folate‐FITC injection in contrast to surrounding normal tissues. Histologic examination of the xenograft tissue similarly showed folate‐FITC uptake in areas of inflammatory cellular infiltrate.ConclusionsAlthough HNSCC tumor cells do not express FR, HNSCC tumors contain a significant population of FR‐β–expressing macrophages. Folate conjugated fluorescent dye is able to specifically target and label tumor xenografts to permit macroscopic fluorescence imaging due to FR‐β expression on the infiltrating inflammatory cells.Level of EvidenceNA Laryngoscope, 124:E312–E319, 2014
Low‐frequency subthalamic nucleus stimulation in Parkinson's disease: A randomized clinical trial
Authors: Khoo Hui Ming , Kishima Haruhiko , Hosomi Koichi , Maruo Tomoyuki , Tani Naoki , Oshino Satoru , Shimokawa Toshio , Yokoe Masaru , Mochizuki Hideki , Saitoh Youichi , Yoshimine Toshiki 
Published: January 2014

ABSTRACTBackgroundLow‐frequency, bilateral stimulation of the subthalamic nucleus can improve axial symptoms of advanced Parkinson's disease (PD), but it is not particularly effective for segmental symptoms.MethodsThe optimal contacts for low‐frequency (60 Hz) and high‐frequency (130 Hz) single monopolar stimulation were determined. Then, in a randomized, double‐blind, prospective crossover manner, 60‐Hz and 130‐Hz stimulations via the respective optimal contacts were compared for immediate efficacy in improving the motor function of patients with PD.ResultsThe optimal contacts for 60‐Hz stimulation were situated more ventrally than those for 130‐Hz stimulation (P = 0.038). Under the respective optimal, single monopolar stimulation, 60 Hz provided superior efficacy over 130 Hz in improving the total Unified Parkinson's Disease Rating Scale motor score (P < 0.001) and the akinesia (P = 0.011) and axial motor signs (P = 0.012) subscores without compromising the therapeutic effect on tremor and rigidity.ConclusionsLow‐frequency stimulation via the optimal contacts is effective in improving overall motor function of patients with PD. © 2014 International Parkinson and Movement Disorder Society
A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes
Authors: Hansen Maren F. , Neckmann Ulrike , Lavik Liss A. S. , Vold Trine , Gilde Bodil , Toft Ragnhild K. , Sjursen Wenche 
Published: January 2014

AbstractThe purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon‐based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single‐GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false‐positive and true‐positive calls in homopolymeric regions by cross‐sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
A mathematical formulation and efficient heuristics for the dynamic container relocation problem
Authors: Hakan Akyüz M. , Lee Chung‐Yee 
Published: January 2014

AbstractThe container relocation problem (CRP) is concerned with emptying a single yard‐bay which contains J containers each following a given pickup order so as to minimize the total number of relocations made during their retrieval process. The CRP can be modeled as a binary integer programming (IP) problem and is known to be NP‐hard. In this work, we focus on an extension of the CRP to the case where containers are both received and retrieved from a single yard‐bay, and call it the dynamic container relocation problem. The arrival (departure) sequences of containers to (from) the yard‐bay is assumed to be known a priori. A binary IP formulation is presented for the problem. Then, we propose three types of heuristic methods: index based heuristics, heuristics using the binary IP formulation, and a beam search heuristic. Computational experiments are performed on an extensive set of randomly generated test instances. Our results show that beam search heuristic is very efficient and performs better than the other heuristic methods.Copyright © 2014 Wiley Periodicals, Inc. Naval Research Logistics 61: 101–118, 2014
Three orders of magnitude improved efficiency with high‐performance spectral crystal plasticity on GPU platforms
Authors: Mihaila Bogdan , Knezevic Marko , Cardenas Andres 
Published: January 2014

SUMMARYWe study efficient numerical implementations of crystal plasticity in the spectral representation, with emphasis on high‐performance computational aspects of the simulation. For illustrative purposes, we apply this approach to a Taylor homogenization model of fcc poly‐crystalline materials and show that the spectral representation of crystal plasticity is ideal for parallel implementations aimed at next‐generation large‐scale microstructure‐sensitive simulations of material deformation. We find that multi‐thread parallelizations of the algorithm provide two orders of magnitude acceleration of the calculation, whereas graphics processing unit‐based computing solutions allow for three orders of magnitude speedup factors over the conventional model. Copyright © 2014 John Wiley & Sons, Ltd.
Interleukin 6 Mediates the Therapeutic Effects of Adipose-Derived Stromal/Stem Cells in Lipopolysaccharide-Induced Acute Lung Injury
Authors: Zhang Shijia , Danchuk Svitlana D. , Bonvillain Ryan W. , Xu Beibei , Scruggs Brittni A. , Strong Amy L. , Semon Julie A. , Gimble Jeffrey M. , Betancourt Aline M. , Sullivan Deborah E. , Bunnell Bruce A. 
Published: January 2014

Abstract
Adipose-derived stromal/stem cells (ASCs) have anti-inflammatory as well as immunosuppressive activities and are currently the focus of clinical trials for a number of inflammatory diseases. Acute lung injury (ALI) is an inflammatory condition of the lung for which standard treatment is mainly supportive due to lack of effective therapies. Our recent studies have demonstrated the ability of both human ASCs (hASCs) and mouse ASCs (mASCs) to attenuate lung damage and inflammation in a rodent model of lipopolysaccharide-induced ALI, suggesting that ASCs may also be beneficial in treating ALI. To better understand how ASCs may act in ALI and to elucidate the mechanism(s) involved in ASC modulation of lung inflammation, gene expression analysis was performed in ASC-treated (hASCs or mASCs) and control sham-treated lungs. The results revealed a dramatic difference between the expression of anti-inflammatory molecules by hASCs and mASCs. These data show that the beneficial effects of hASCs and mASCs in ALI may result from the production of different paracrine factors. Interleukin 6 (IL-6) expression in the mASC-treated lungs was significantly elevated as compared to sham-treated controls 20 hours after delivery of the cells by oropharyngeal aspiration. Knockdown of IL-6 expression in mASCs by RNA interference abrogated most of their therapeutic effects, suggesting that the anti-inflammatory properties of mASCs in ALI are explained, at least in part, by activation of IL-6 secretion. Stem Cells 2014;32:1616–1628
NogoR1 and PirB Signaling Stimulates Neural Stem Cell Survival and Proliferation
Authors: Ramasamy Srinivas , Yu Fenggang , Hong Yu Yuan , Srivats Hariharan , Stewart Dawe Gavin , Ahmed Sohail 
Published: January 2014

Abstract
Neural stem cells (NSCs) and neural progenitors (NPs) in the mammalian neocortex give rise to the main cell types of the nervous system. The biological behavior of these NSCs and NPs is regulated by extracellular niche derived autocrine-paracrine signaling factors on a developmental timeline. Our previous reports [Plos One 2010;5:e15341; J Neurochem 2011;117:565–578] have shown that chondroitin sulfate proteoglycan and ApolipoproteinE are autocrine-paracrine survival factors for NSCs. NogoA, a myelin related protein, is expressed in the cortical ventricular zones where NSCs reside. However, the functional role of Nogo signaling proteins in NSC behavior is not completely understood. In this study, we show that NogoA receptors, NogoR1 and PirB, are expressed in the ventricular zone where NSCs reside between E10.5 and 14.5 but not at E15.5. Nogo ligands stimulate NSC survival and proliferation in a dosage-dependent manner in vitro. NogoR1 and PirB are low and high affinity Nogo receptors, respectively and are responsible for the effects of Nogo ligands on NSC behavior. Inhibition of autocrine-paracrine Nogo signaling blocks NSC survival and proliferation. In NSCs, NogoR1 functions through Rho whereas PirB uses Shp1/2 signaling pathways to control NSC behavior. Taken together, this work suggests that Nogo signaling is an important pathway for survival of NSCs. Stem Cells 2014;32:1636–1648
Concise Review: Bone Marrow-Derived Mesenchymal Stem Cells Change Phenotype Following In Vitro Culture: Implications for Basic Research and the Clinic
Authors: Bara Jennifer J. , Richards R. Geoff , Alini Mauro , Stoddart Martin J. 
Published: January 2014

Abstract
Mesenchymal stem cells (MSCs) are increasingly being used in tissue engineering and cell-based therapies in all fields ranging from orthopedic to cardiovascular medicine. Despite years of research and numerous clinical trials, MSC therapies are still very much in development and not considered mainstream treatments. The majority of approaches rely on an in vitro cell expansion phase in monolayer to produce large cell numbers prior to implantation. It is clear from the literature that this in vitro expansion phase causes dramatic changes in MSC phenotype which has very significant implications for the development of effective therapies. Previous reviews have sought to better characterize these cells in their native and in vitro environments, described known stem cell interactions within the bone marrow, and discussed the use of innovative culture systems aiming to model the bone marrow stem cell niche. The purpose of this review is to provide an update on our knowledge of MSCs in their native environment, focusing on bone marrow-derived MSCs. We provide a detailed description of the differences between naive cells and those that have been cultured in vitro and examine the effect of isolation and culture parameters on these phenotypic changes. We explore the concept of “one step” MSC therapy and discuss the potential cellular and clinical benefits. Finally, we describe recent work attempting to model the MSC bone marrow niche, with focus on both basic research and clinical applications and consider the challenges associated with these new generation culture systems. Stem Cells 2014;32:1713–1723