bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concise Review: Reprogramming, Behind the Scenes: Noncanonical Neural Stem Cell Signaling Pathways Reveal New, Unseen Regulators of Tissue Plasticity With Therapeutic Implications
Authors: Poser Steven W. , Chenoweth Josh G. , Colantuoni Carlo , Masjkur Jimmy , Chrousos George , Bornstein Stefan R. , McKay Ronald D. , Androutsellis-Theotokis Andreas 
Published: September 2015

Abstract

Interest is great in the new molecular concepts that explain, at the level of signal transduction, the process of reprogramming. Usually, transcription factors with developmental importance are used, but these approaches give limited information on the signaling networks involved, which could reveal new therapeutic opportunities. Recent findings involving reprogramming by genetic means and soluble factors with well-studied downstream signaling mechanisms, including signal transducer and activator of transcription 3 (STAT3) and hairy and enhancer of split 3 (Hes3), shed new light into the molecular mechanisms that might be involved. We examine the appropriateness of common culture systems and their ability to reveal unusual (noncanonical) signal transduction pathways that actually operate in vivo. We then discuss such novel pathways and their importance in various plastic cell types, culminating in their emerging roles in reprogramming mechanisms. We also discuss a number of reprogramming paradigms (mouse induced pluripotent stem cells, direct conversion to neural stem cells, and in vivo conversion of acinar cells to β-like cells). Specifically for acinar-to-β-cell reprogramming paradigms, we discuss the common view of the underlying mechanism (involving the Janus kinase-STAT pathway that leads to STAT3-tyrosine phosphorylation) and present alternative interpretations that implicate STAT3-serine phosphorylation alone or serine and tyrosine phosphorylation occurring in sequential order. The implications for drug design and therapy are important given that different phosphorylation sites on STAT3 intercept different signaling pathways. We introduce a new molecular perspective in the field of reprogramming with broad implications in basic, biotechnological, and translational research.

Significance
Reprogramming is a powerful approach to change cell identity, with implications in both basic and applied biology. Most efforts involve the forced expression of key transcription factors, but recently, success has been reported with manipulating signal transduction pathways that might intercept them. It is important to start connecting the function of the classic reprogramming genes to signaling pathways that also mediate reprogramming, unifying the sciences of signal transduction, stem cell biology, and epigenetics. Neural stem cell studies have revealed the operation of noncanonical signaling pathways that are now appreciated to also operate during reprogramming, offering new mechanistic explanations.
Comparison of atmospheric profiles between microwave radiometer retrievals and radiosonde soundings
Authors: Xu Guirong , Xi Baike , Zhang Wengang , Cui Chunguang , Dong Xiquan , Liu Yuanyuan , Yan Guopao 
Published: September 2015

AbstractAtmospheric profiles of temperature (T), vapor density (ρv), and relative humidity (RH) retrieved from ground‐based microwave radiometer (MWR) measurements are compared with radiosonde soundings at Wuhan, China. The MWR retrievals were averaged in the ±30 min period centered at sounding times of 00 and 12 UTC. A total of 403 and 760 profiles under clear and cloudy skies were selected. Based on the comparisons, temperature profiles have better consistency than the ρv and RH profiles, lower levels are better than upper levels, and the cloudy are better than the clear‐sky profiles. Three cloud types (low, middle, and high) were identified by matching the infrared radiation thermometer‐detected cloud base temperature to the MWR‐retrieved temperature‐height profiles. Temperature profile under high cloud has the highest correlation coefficient (R) and the lowest bias and RMS, but under low cloud is in the opposite direction. The ρv profile under middle cloud has the highest R and the lowest bias but under high cloud has the lowest R, the largest bias, and RMS. Based on the radiosonde soundings, both clear and cloudy wind speeds and drifting distances increase with height but increase much faster under clear than cloudy above 4 km. The increased wind speeds and drifting distances with height have resulted in decreased correlation coefficient and increased temperature biases and RMSs with height for both clear and cloudy skies. The differences in R, bias, and RMS between clear and cloudy skies are primarily resulted from their wind speeds and drifting distances.
Lagrangian Optimization forLP: Theory and Algorithms
Authors: Desai Jitamitra , Wang Kai 
Published: September 2015

AbstractWe present a methodological framework for solving large‐scale linear programming (LP) problems via a Lagrangian optimization approach. Beginning with a formulation of the Lagrangian dual (LD) problem, we relate this approach to standard LP theory in two steps: first, we demonstrate that the optimal objective function value obtained by solving the Lagrangian dual is optimal to the original linear program; and second, theorems and propositions that characterize the mathematical properties of the Lagrangian dual and establish the equivalence of this approach to classical LP duality are included. Recognizing that the Lagrangian dual formulation is a nondifferentiable optimization problem, a subgradient algorithm is prescribed for solving the LD problem, and related dual convergence results are presented. Furthermore, to recover the primal solution of the original linear program, an improved primal‐dual proximal point algorithm along with its convergence properties is also described. Computational results for a small numerical example serve to illustrate the theoretical and algorithmic concepts elucidated in this article, and finally, a brief extension of this approach for solving integer programs can also be found at the end of this article.
Optical Sensors
Authors: Haus Jörg 
Published: September 2015

Abstract
In terms of dynamic range and noise, optical sensors have great advantages over their electronic or mechanical counterparts. In addition, the noncontact nature of all optical measurements avoids influences of the sensor on the measured value and, thus, measurement‐introduced systematic errors. This article gives an update to the overview published in the first edition of the Optics Encyclopedia (sometimes denoted as the “original article” in the text). It contains up‐to‐date specifications of sensor components along with additional sensor principles and applications.
In Situ Trapped and Immobilized Palladium Nanoparticles as Active and Clean Catalysts for Suzuki–Miyaura Reaction
Authors: Li Yan , Mao Fei , Chen Ting , Zhou Zhicheng , Wang Yong , Huang Jun 
Published: September 2015

AbstractActive palladium nanoparticles were trapped and immobilized in situ by Pd‐catalyzed Suzuki–Miyaura reaction to form heterogeneous Pd catalysts. This Pd@PhPad2 catalyst was found to be highly active, recyclable and clean for the Suzuki–Miyaura reaction. Both the anchored diadamantylphosphine ligand and the formation of polyphenylene polymer improved the activity and stability of the Pd@PhPad2 catalyst for Suzuki–Miyaura reaction. The Pd@PhPad2 catalyst was reusable, and no contamination (P ligand or Pd) was detected from the catalyst system for the coupling reaction.magnified image
Synthesis of Naphtho‐Fused Imidazo[1,2‐a]pyridines through Copper‐Catalyzed Cascade Reactions
Authors: Saini Hitesh Kumar , Kaswan Pinku , Pericherla Kasiviswanadharaju , Kumar Anil 
Published: September 2015

AbstractA highly efficient copper‐catalyzed one‐pot tandem protocol has been developed for the synthesis of naphtho‐fused imidazo[1,2‐a]pyridines. The transformation involves a Knoevenagel condensation followed by a chemoselective cross‐coupling reaction along with a carbon‐carbon bond cleavage. This protocol can tolerate a variety of functional groups and provided naphtho[1′,2′:4,5]imidazo[1,2‐a]pyridines in moderate to excellent (35–91 %) yields. The photophysical studies of the naphtho‐fused imidazo[1,2‐a]pyridines show a bathochromic shift between the band maxima of the absorption and emission spectra. These compounds emit with high fluorescence quantum yields.
Thick Methacrylate Sections Devoid of Lost Caps Simplify Stereological Quantifications Based on the Optical Fractionator Design
Authors: Hasselholt Stine , Lykkesfeldt Jens , Larsen Jytte Overgaard 
Published: September 2015

ABSTRACTIn neuroscience, the optical fractionator technique is frequently used for unbiased cell number estimations. Although unbiased in theory, the practical application of the technique is often biased by the necessity of introducing a guard zone at one side of the disector to counter lost caps and/or optical limitations. Restricting the disector within the section thickness potentially introduces bias in two ways. First, the need to measure section thickness in order to obtain the disector height/section thickness fraction is challenging since both microcator measurements, microtome block advance, and measurements on re‐embedded sections are potentially biased. Second, disector placement is not uniform random within the section thickness resulting in a bias in most sections with inhomogeneous cell distribution along the z axis. Re‐embedded 2‐hydroxyethylmethacrylate (hereafter methacrylate) sections were inspected for lost caps to evaluate the possibility of whole section thickness counting with the optical fractionator technique and hippocampal granular cell nucleoli density differences along the z axis were assessed with a z axis analysis. No lost caps were found in the examined re‐embedded tissue and an inhomogeneous cell distribution through the section thickness was observed. In thick methacrylate sections devoid of lost caps sampling through the entire section thickness could be an acceptable alternative to the use of guard zones and the consequent biases associated with section thickness measurement and non‐random placement of disectors. Anat Rec, 298:2141–2150, 2015. © 2015 Wiley Periodicals, Inc.
Paradoxical Effects of Partial Leptin Deficiency on Bone in Growing Female Mice
Authors: Philbrick Kenneth A. , Turner Russell T. , Branscum Adam J. , Wong Carmen P. , Iwaniec Urszula T. 
Published: September 2015

ABSTRACTMorbidly obese, leptin‐deficient ob/ob mice display low bone mass, mild osteoclast‐rich osteopetrosis, and increased bone marrow adiposity. While partial leptin deficiency results in increased weight, the skeletal manifestations of partial leptin deficiency are less well defined. We therefore analyzed femora and lumbar vertebrae in growing (7‐week‐old) female C57BL/6 wildtype (WT) mice, partial leptin‐deficient ob/+ mice, and leptin‐deficient ob/ob mice. The bones were evaluated by dual energy absorptiometry, microcomputed tomography and histomorphometry. As expected, ob/+ mice were heavier, had more white adipose tissue, and lower serum leptin than WT mice, but were lighter and had less white adipose tissue than ob/ob mice. With a few exceptions, cancellous bone architecture, cell (osteoblast, osteoclast, and adipocyte), and dynamic measurements did not differ between WT and ob/+ mice. In contrast, compared to WT and ob/+ mice, ob/ob mice had lower cancellous bone volume fraction, and higher bone marrow adiposity in the femur metaphysis, and higher cancellous bone volume fraction in lumbar vertebra. Paradoxically, ob/+ mice had greater femoral bone volume than either WT or ob/ob mice. There was a positive correlation between body weight and femur volume in all three genotypes. However, the positive effect of weight on bone occurred with lower body weight in leptin‐producing mice. The paradoxical differences in bone size among WT, ob/+, and ob/ob mice may be explained if leptin, in addition to stimulating bone growth and cancellous bone turnover, acts to lower the set‐point at which increased body weight leads to a commensurate increase in bone size. Anat Rec, 298:2018–2029, 2015. © 2015 Wiley Periodicals, Inc.
Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids
Authors: Torr Kirk M. , Love Karen T. , Simmons Blake A. , Hill Stefan J. 
Published: September 2015

ABSTRACTPretreating lignocellulosic biomass with certain ionic liquids results in structural and chemical changes that make the biomass more digestible by enzymes. In this study, pine wood was pretreated with 1‐ethyl‐3‐methylimidazolium chloride/acetate ([C2mim]Cl and [C2mim][OAc]) at different temperatures to investigate the relative importance of substrate features, such as accessible surface area, cellulose crystallinity, and lignin content, on enzymatic digestibility. The ionic liquid pretreatments resulted in glucan conversions ranging from 23% to 84% on saccharification of the substrates, with [C2mim][OAc] being more effective than [C2mim]Cl. The pretreatments resulted in no delignification of the wood, some loss of cellulose crystallinity under certain conditions, and varying levels of increased surface area. Enzymatic digestibility closely correlated with accessible surface area and porosity measurements obtained using Simons' staining and thermoporosimetry techniques. Increased accessible surface area was identified as the principal structural feature responsible for the improved enzymatic digestibility. Biotechnol. Bioeng. 2016;113: 540–549. © 2015 Wiley Periodicals, Inc.
Development of a synthetic receptor protein for sensing inflammatory mediators interferon‐γ and tumor necrosis factor‐α
Authors: Aurand T. Christopher , March John C. 
Published: September 2015

ABSTRACTIntestinal inflammation has been implicated in a number of diseases, including diabetes, Crohn's disease, and irritable bowel syndrome. Important components of inflammation are interferon‐γ (IFN‐γ) and tumor necrosis factor‐α (TNF‐α), which are elevated both on the luminal and submucosal sides of the intestinal epithelial barrier in several diseases. Here, we developed a novel Escherichia coli based detection system for IFN‐γ and TNF‐α comprised of a chimeric protein and a simple signal transduction construct, which could be deployed on the luminal side of the intestine. OmpA of E. coli was engineered to detect IFN‐γ or TNF‐α through the replacement of extracellular loops with peptide fragments from OprF of P. aeruginosa. OmpA/OprF chimeras were developed, capable of binding IFN‐γ or TNF‐α. The specific peptide fragments that bind IFN‐γ were identified. IFN‐γ or TNF‐α binding the OmpA/OprF chimera induced the pspA promoter, driving β‐galactosidase production. The OmpA/OprF chimera had a detection limit of 300 pM for IFN‐γ and 150 pM for TNF‐α. This work will further the development of bacteria based therapeutics for the treatment of inflammatory diseases of the gut. Biotechnol. Bioeng. 2016;113: 492–500. © 2015 Wiley Periodicals, Inc.
Cobalt‐Containing Nitrogen‐Doped Carbon Aerogels as Efficient Electrocatalysts for the Oxygen Reduction Reaction
Authors: Kreek Kristiina , Sarapuu Ave , Samolberg Lars , Joost Urmas , Mikli Valdek , Koel Mihkel , Tammeveski Kaido 
Published: September 2015

AbstractThe electrocatalysis of the oxygen reduction reaction (ORR) on cobalt‐containing nitrogen‐doped carbon aerogels (CAs) was studied in alkaline solution. CA‐based catalyst materials with varied compositions were prepared through the sol‐gel polymerisation of organic precursors (resorcinol derivatives and melamine), followed by insertion of Co by using an ion‐exchange process and pyrolysis. The concentrations of the precursors had a large effect on the structure and physicochemical properties of the materials, as characterised by using SEM, XRD, XPS, atomic adsorption spectroscopy, and N2‐adsorption analysis. The electrocatalytic activity of Co‐containing N‐doped CAs for the ORR was higher than that of nitrogen‐free CA, and this activity increased with increasing Co content. The most active catalyst materials supported the four‐electron reduction of O2 and short‐term stability tests indicated their high durability. Co‐containing N‐doped CAs can be regarded as a promising class of material for the cathode catalysts of alkaline membrane fuel cells.
GPU accelerated sparse matrix‐vector multiplication and sparse matrix‐transpose vector multiplication
Authors: Tao Yuan , Deng Yangdong , Mu Shuai , Zhang Zhenzhong , Zhu Mingfa , Xiao Limin , Ruan Li 
Published: September 2015

SummaryMany high performance computing applications require computing both sparse matrix‐vector product (SMVP) and sparse matrix‐transpose vector product (SMTVP) for better overall performance. Under such a circumstance, it is critical to maintain a similarly high throughput for these two computing patterns with the underlying sparse matrix encoded in a single storage format. The compressed sparse block (CSB) format proposed by Buluç et al. allows computing both problems on multi‐core CPUs with nearly identical throughputs. On the other hand, a direct porting of CSB to graphics processing units (GPUs), which have been recently recognized as a powerful general purpose computing platform, turns out to be inefficient. In this work, we propose a new data structure, designated as expanded CSB (eCSB), to minimize the throughput gap between SMVP and SMTVP computations on GPUs, while at the same time enable a high computing throughput. We also use a hybrid storage format to store elements in each block, which can be selected dynamically at runtime. Experimental results show that the proposed techniques implemented on a Kepler GPU delivers similar throughput on both SMVP and SMTVP and the throughput is up to 13 times faster than that of the CPU‐based CSB implementation. In addition, our eCSB procedure outperforms the previous GPU results by up to 188% and 914% in computing SMVP and SMTVP, and we validate the effectiveness of eCSB by means of wall‐clock time of bi‐conjugate gradient algorithm; our eCSB is 25% faster than Compressed Sparse Rows (CSR) and 6% faster than HYB, respectively. Copyright © 2014 John Wiley & Sons, Ltd.
Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and interlaboratory testing, life stage, and species
Authors: Raimondo Sandy , Lilavois Crystal R. , Lee Larisa , Augspurger Tom , Wang Ning , Ingersoll Chris G. , Bauer Candice , Hammer Edward , Barron Mace G. 
Published: September 2015

Abstract

The authors developed a toxicity database for unionid mussels to examine the extent of intra- and interlaboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the 2 life stages; and the variation in sensitivity among commonly tested mussels (Lampsilis siliquoidea, Utterbackia imbecillis, and Villosa iris), commonly tested cladocerans (Daphnia magna and Ceriodaphnia dubia), and fish (Oncorhynchus mykiss, Pimephales promelas, and Lepomis macrochirus). The results of these analyses indicate that intralaboratory variability for median effect concentrations (EC50) averaged about 2-fold for both life stages, whereas interlaboratory variability averaged 3.6-fold for juvenile mussels and 6.3-fold for glochidia. The EC50s for juveniles and glochidia were within a factor of 2 of each other for 50% of paired records across chemicals, with juveniles more sensitive than glochidia by more than 2-fold for 33% of the comparisons made between life stages. There was a high concurrence of sensitivity of commonly tested L. siliquoidea, U. imbecillis, and V. iris to that of other mussels. However, this concurrence decreased as the taxonomic distance of the commonly tested cladocerans and fish to mussels increased. The compiled mussel database and determination of data variability will advance risk assessments by including more robust species sensitivity distributions, interspecies correlation estimates, and availability of taxon-specific empirically derived application factors for risk assessment. Environ Toxicol Chem 2016;35:750–758. Published 2015 Wiley Periodicals Inc on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Impact on survival of addition of etoposide to primary chemotherapy in diffuse large B‐cell lymphoma: a Swedish Lymphoma Registry study
Authors: Wästerlid Tove , Hartman Linda , Székely Elisabeth , Jerkeman Mats 
Published: September 2015

AbstractNo randomised study in the rituximab era has been performed specifically to evaluate addition of etoposide to treatment of diffuse large B‐cell lymphoma (DLBCL). The aim of this study was to compare the outcome with three chemotherapy regimens (R‐CHOP‐21, R‐CHOP‐14 and R‐CHOEP‐14) in a population‐based cohort in terms of overall survival, adjusted for clinical prognostic factors. Through the Swedish Lymphoma Registry, 3443 patients with DLBCL were identified 2007–2012. Among all patients, there was no evidence of a difference between the regimens, after adjustment for prognostic factors. However, when restricted to patients aged up to 65, R‐CHOEP‐14 was associated with superior outcome compared to both R‐CHOP‐21 (hazard ratio: 0.49, 95% confidence interval: 0.3–0.9, p = 0.028) and R‐CHOP‐14 (hazard ratio: 0.64, 95% confidence interval: 0.4–1.0, p = 0.06), when adjusted for prognostic factors. Results were consistent in an additional stratified analysis with patients grouped according to age and IPI‐score. In conclusion, we could show that R‐CHOEP‐14 was associated with superior overall survival in patients with DLBCL aged up to 65 years, indicating that this may be a valid treatment option for this patient population. To further investigate which patient groups that may benefit the most from treatment intensification, R‐CHOEP‐14 should be compared to R‐CHOP‐21 in a randomised setting. Copyright © 2015 John Wiley & Sons, Ltd.