bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embryonic remnants of intercentra and cervical ribs in turtles
Authors: Werneburg Ingmar , Maier Wolfgang , Joyce Walter G. 
Published: September 2013

Summary
A broad sample of extant turtles possesses a series of paired bones in the neck that are situated between the cervical vertebrae. These paired bones were originally proposed to be cervical rib remnants, but have more recently been interpreted as vestiges of intercentra. Here, we document, for the first time, the neck development of a pleurodire turtle, Emydura subglobosa, and identify blastematous structures, which partially recapitulate the ribs and intercentra of the plesiomorphic tetrapod condition. We identify blastematous “bridges” between intercentra and the corresponding ribs, which we homologize with the vestiges visible in extant turtles and with the remnant parapophyseal articulation processes of the intercentra of some stem taxa. Only the unpaired, median part of the intercentrum of the atlas is retained in adult turtles, but intercentra are recapitulated along the entire vertebral column during development; they are embedded in the cervical myosepta and serve as attachment sites for neck musculature. We also identify two rib rudiments in the occipital region, which may indicate that at least two vertebrae are integrated into the cranium of turtles in particular, and of amniotes in general.
CSF p-Tau levels in the prediction of Alzheimer's disease
Authors: Kandimalla Ramesh J. L. , Prabhakar Sudesh , Wani Willayat Yousuf , Kaushal Alka , Gupta Nidhi , Sharma Deep Raj , Grover V. K. , Bhardwaj Neerja , Jain Kajal , Gill Kiran Dip 
Published: September 2013

Summary
The two hallmarks of Alzheimer's disease (AD) are neurofibrillary tangles and amyloid plaques. Neurofibrillary tangles are formed due to the hyperphosphorylation of tau protein. There is an urgent need to develop a reliable biomarker for the diagnosis of AD. Cerebrospinal fluid (CSF) is surrounding the brain and reflects the major neuropathological features in the AD brain. Diagnosis, disease progression and drug actions rely on the AD biomarkers. Mainly CSF tau and phosphorylated tau (p-Tau) have been observed to serve the purpose for early AD. Keeping in view the early appearance of p-Tau in CSF, we analyzed p-Tau levels in 23 AD, 23 Non AD type dementia (NAD), 23 Neurological control (NC) and 23 Healthy control (HC) North Indian patients. The levels of p-Tau were found to be increased in AD patients (67.87±18.05 pg/ml, SEM 3.76) compared with NAD (47.55±7.85 pg/ml, SEM 1.64), NC (34.42±4.51 pg/ml, SEM 0.94) and HC (27.09±7.18 pg/ml, SEM 1.50). The resulting sensitivity for AD with NAD was 80.27% whereas with respect to the NAD, NC and HC was 85.40%. Therefore elevated levels of p-Tau in AD can be exploited as a predictive biomarker in North Indian AD patients.
Approximability of Robust Network Design
Authors: Olver Neil , Shepherd F. Bruce 
Published: September 2013

We consider robust (undirected) network design (RND) problems where the set of feasible demands may be given by an arbitrary convex body. This model, introduced by Ben-Ameur and Kerivin [Ben-Ameur W, Kerivin H (2003) New economical virtual private networks. Comm. ACM 46(6):69–73], generalizes the well-studied virtual private network (VPN) problem. Most research in this area has focused on constant factor approximations for specific polytope of demands, such as the class of hose matrices used in the definition of VPN. As pointed out in Chekuri [Chekuri C (2007) Routing and network design with robustness to changing or uncertain traffic demands. SIGACT News 38(3):106–128], however, the general problem was only known to be APX-hard (based on a reduction from the Steiner tree problem). We show that the general robust design is hard to approximate to within polylogarithmic factors. We establish this by showing a general reduction of buy-at-bulk network design to the robust network design problem. Gupta pointed out that metric embeddings imply an O(log n)-approximation for the general RND problem, and hence this is tight up to polylogarithmic factors. In the second part of the paper, we introduce a natural generalization of the VPN problem. In this model, the set of feasible demands is determined by a tree with edge capacities; a demand matrix is feasible if it can be routed on the tree. We give a constant factor approximation algorithm for this problem that achieves factor of 8 in general, and 2 for the case where the tree has unit capacities. As an application of this result, we consider so-called H-tope demand polytopes. These correspond to demands which are routable in some graph H. We show that the corresponding RND problem has an O(1)-approximation if H admits a stochastic constant-distortion embedding into tree metrics.
Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays
Authors: Lefever Steve , Pattyn Filip , Hellemans Jan , Vandesompele Jo 
Published: September 2013

BACKGROUND
Genome-sequencing studies have led to an immense increase in the number of known single-nucleotide polymorphisms (SNPs). Designing primers that anneal to regions devoid of SNPs has therefore become challenging. We studied the impact of one or more mismatches in primer-annealing sites on different quantitative PCR (qPCR)-related parameters, such as quantitative cycle (Cq), amplification efficiency, and reproducibility.

METHODS
We used synthetic templates and primers to assess the effect of mismatches at primer-annealing sites on qPCR assay performance. Reactions were performed with 5 commercially available master mixes. We studied the effects of the number, type, and position of priming mismatches on Cq value, PCR efficiency, reproducibility, and yield.

RESULTS
The impact of mismatches was most pronounced for the number of mismatched nucleotides and for their distance from the 3′ end of the primer. In addition, having ≥4 mismatches in a single primer or having 3 mismatches in one primer and 2 in the other was required to block a reaction completely. Finally, the degree of the mismatch effect was concentration independent for single mismatches, whereas concentration independence failed at higher template concentrations as the number of mismatches increased.

CONCLUSIONS
Single mismatches located &gt;5 bp from the 3′ end have a moderate effect on qPCR amplification and can be tolerated. This finding, together with the concentration independence for single mismatches and the complete blocking of the PCR reaction for ≥4 mismatches, can help to chart mismatch behavior in qPCR reactions and increase the rate of successful primer design for sequences with a high SNP density or for homologous regions of sequence.
Antibodies Targeting Human OX40 Expand Effector T Cells and Block Inducible and Natural Regulatory T Cell Function
Authors: Voo Kui S. , Bover Laura , Harline Megan L. , Vien Long T. , Facchinetti Valeria , Arima Kazuhiko , Kwak Larry W. , Liu Yong J. 
Published: September 2013

AbstractCurrent cancer vaccines induce tumor-specific T cell responses without sustained tumor regression because immunosuppressive elements within the tumor induce exhaustion of effector T cells and infiltration of immune-suppressive regulatory T cells (Tregs). Therefore, much effort has been made to generate agonistic Abs targeting members of the TNFR superfamily, such as OX40, 4-1BB, and GITR, expressed on effector T cells and Tregs, to reinvigorate T cell effector function and block Treg-suppressive function. In this article, we describe the development of a panel of anti-human OX40 agonistic mouse mAbs that could promote effector CD4+ and CD8+ T cell proliferation, inhibit the induction of CD4+ IL-10 -producing type 1 regulatory T cells, inhibit the expansion of ICOS+IL-10+ Tregs, inhibit TGF-β–induced FOXP3 expression on naive CD4+ T cells, and block natural Treg–suppressive function. We humanized two anti–human OX40 mAb clones, and they retained the potency of their parental clones. These Abs should provide broad opportunities for potential combination therapy to treat a wide realm of cancers and preventative vaccines against infectious diseases.
IFIT2 Is an Effector Protein of Type I IFN–Mediated Amplification of Lipopolysaccharide (LPS)-Induced TNF-α Secretion and LPS-Induced Endotoxin Shock
Authors: Siegfried Alexandra , Berchtold Susanne , Manncke Birgit , Deuschle Eva , Reber Julia , Ott Thomas , Weber Michaela , Kalinke Ulrich , Hofer Markus J. , Hatesuer Bastian , Schughart Klaus , Gailus-Durner Valérie , Fuchs Helmut , Hrabě de Angelis Martin , Weber Friedemann , Hornef Mathias W. , Autenrieth Ingo B. , Bohn Erwin 
Published: September 2013

Abstract
Type I IFN signaling amplifies the secretion of LPS-induced proinflammatory cytokines such as TNF-α or IL-6 and might thus contribute to the high mortality associated with Gram-negative septic shock in humans. The underlying molecular mechanism, however, is ill defined. In this study, we report the generation of mice deficient in IFN-induced protein with tetratricopeptide repeats 2 (Ifit2) and demonstrate that Ifit2 is a critical signaling intermediate for LPS-induced septic shock. Ifit2 expression was significantly upregulated in response to LPS challenge in an IFN-α receptor– and IFN regulatory factor (Irf)9–dependent manner. Also, LPS induced secretion of IL-6 and TNF-α by bone marrow–derived macrophages (BMDMs) was significantly enhanced in the presence of Ifit2. In accordance, Ifit2-deficient mice exhibited significantly reduced serum levels of IL-6 and TNF-α and reduced mortality in an endotoxin shock model. Investigation of the underlying signal transduction events revealed that Ifit2 upregulates Irf3 phosphorylation. In the absence of Irf3, reduced Ifn-β mRNA expression and Ifit2 protein expression after LPS stimulation was found. Also, Tnf-α and Il-6 secretion but not Tnf-α and Il-6 mRNA expression levels were reduced. Thus, IFN-stimulated Ifit2 via enhanced Irf3 phosphorylation upregulates the secretion of proinflammatory cytokines. It thereby amplifies LPS-induced cytokine production and critically influences the outcome of endotoxin shock.
Fibrosis and Subsequent Cytopenias Are Associated with Basic Fibroblast Growth Factor–Deficient Pluripotent Mesenchymal Stromal Cells in Large Granular Lymphocyte Leukemia
Authors: Mailloux Adam W. , Zhang Ling , Moscinski Lynn , Bennett John M. , Yang Lili , Yoder Sean J. , Bloom Gregory , Wei Cody , Wei Sheng , Sokol Lubomir , Loughran Thomas P. , Epling-Burnette Pearlie K. 
Published: September 2013

Abstract
Cytopenias occur frequently in systemic lupus erythematosus, rheumatoid arthritis, Felty’s syndrome, and large granular lymphocyte (LGL) leukemia, but the bone marrow microenvironment has not been systematically studied. In LGL leukemia (n = 24), retrospective analysis of bone marrow (BM) histopathology revealed severe fibrosis in 15 of 24 patients (63%) in association with the presence of cytopenias, occurrence of autoimmune diseases, and splenomegaly, but was undetectable in control cases with B cell malignancies (n = 11). Fibrosis severity correlated with T cell LGL cell numbers in the BM, but not in the periphery, suggesting deregulation is limited to the BM microenvironment. To identify fibrosis-initiating populations, primary mesenchymal stromal cultures (MSCs) from patients were characterized and found to display proliferation kinetics and overabundant collagen deposition, but displayed normal telomere lengths and osteoblastogenic, chondrogenic, and adipogenic differentiation potentials. To determine the effect of fibrosis on healthy hematopoietic progenitor cells (HPCs), bioartificial matrixes from rat tail or purified human collagen were found to suppress HPC differentiation and proliferation. The ability of patient MSCs to support healthy HSC proliferation was significantly impaired, but could be rescued with collagenase pretreatment. Clustering analysis confirmed the undifferentiated state of patient MSCs, and pathway analysis revealed an inverse relationship between cell division and profibrotic ontologies associated with reduced basic fibroblast growth factor production, which was confirmed by ELISA. Reconstitution with exogenous basic fibroblast growth factor normalized patient MSC proliferation, collagen deposition, and HPC supportive function, suggesting LGL BM infiltration and secondary accumulation of MSC-derived collagen is responsible for hematopoietic failure in autoimmune-associated cytopenias in LGL leukemia.
Distinction and Temporal Stability of Conformational Epitopes on Myelin Oligodendrocyte Glycoprotein Recognized by Patients with Different Inflammatory Central Nervous System Diseases
Authors: Mayer Marie C. , Breithaupt Constanze , Reindl Markus , Schanda Kathrin , Rostásy Kevin , Berger Thomas , Dale Russell C. , Brilot Fabienne , Olsson Tomas , Jenne Dieter , Pröbstel Anne-Katrin , Dornmair Klaus , Wekerle Hartmut , Hohlfeld Reinhard , Banwell Brenda , Bar-Or Amit , Meinl Edgar 
Published: September 2013

Abstract
Autoantibodies targeting conformationally intact myelin oligodendrocyte glycoprotein (MOG) are found in different inflammatory diseases of the CNS, but their antigenic epitopes have not been mapped. We expressed mutants of MOG on human HeLa cells and analyzed sera from 111 patients (104 children, 7 adults) who recognized cell-bound human MOG, but had different diseases, including acute disseminated encephalomyelitis (ADEM), one episode of transverse myelitis or optic neuritis, multiple sclerosis (MS), anti-aquaporin-4 (AQP4)–negative neuromyelitis optica (NMO), and chronic relapsing inflammatory optic neuritis (CRION). We obtained insight into the recognition of epitopes in 98 patients. All epitopes identified were located at loops connecting the β strands of MOG. The most frequently recognized MOG epitope was revealed by the P42S mutation positioned in the CC′-loop. Overall, we distinguished seven epitope patterns, including the one mainly recognized by mouse mAbs. In half of the patients, the anti-MOG response was directed to a single epitope. The epitope specificity was not linked to certain disease entities. Longitudinal analysis of 11 patients for up to 5 y indicated constant epitope recognition without evidence for intramolecular epitope spreading. Patients who rapidly lost their anti-MOG IgG still generated a long-lasting IgG response to vaccines, indicating that their loss of anti-MOG reactivity did not reflect a general lack of capacity for long-standing IgG responses. The majority of human anti-MOG Abs did not recognize rodent MOG, which has implications for animal studies. Our findings might assist in future detection of potential mimotopes and pave the way to Ag-specific depletion.
Chemoattraction: Basic Concepts and Role in the Immune Response
Authors: Rodríguez‐Fernández José Luis , Cabañas Laura Gómez 
Published: September 2013

Abstract

Chemoattraction is defined as the unidirectional movement of a cell, in response to a chemical gradient of ligands. During chemoattraction, cells move in the direction from a low to a high concentration of the chemoattractant. Chemoattraction is called ‘chemotaxis’ when the ligand gradient is soluble and ‘haptotaxis’ when this gradient is bound to the substrate. Chemoattraction plays a fundamental role in the regulation of the precise location of leucocytes during the immune response and consequently is fundamental for the adequate functioning of leucocytes in the immune system. Classical chemoattractants and chemokines use guanine nucleotide‐binding protein‐coupled seven‐transmembrane‐spanning receptors to relay intracellular signals that regulate chemoattraction. Apart from chemoattraction, chemoattractants and chemoattractant receptors may play additional functions, scavenging, transcytosis or even antimicrobial activities that could also importantly contribute to a correct immune response.

Key Concepts:

Chemoattraction is defined as the unidirectional movement of a cell, in response to a chemical gradient of ligands.

Chemoattractive factor constitutes a diverse group of chemicals, including lipids, formylated peptides, proteolytic fragments of complement proteins and chemokines, with chemoattractive properties.

Alterations in the expression or function of chemokine receptors are involved in a variety of human pathologies.

Chemokines are small secreted proteins (8–14 kDa) that display a similar tertiary structure and potent chemoattractive abilities.

Chemokines regulate a variety of cell functions in addition to chemotaxis.
Size‐Exclusion Chromatography Coupled with Infrared Spectroscopy, Applications of
Authors: Rickard Mark A. 
Published: September 2013

Abstract
The combination of size‐ and composition‐based separations with infrared spectroscopic detectors is a powerful technique that provides detailed information about the molecular structure of polymers that is not accessible with standard detectors. Two approaches for coupling size‐exclusion chromatography (SEC) and liquid chromatography (LC) to infrared detectors are flow cells and solvent elimination interfaces. Flow cells are straightforward to interface with separations, but they are limited by interference from the solvent. Solvent elimination interfaces are more complex than flow cells, but they remove the problem of solvent interference and, therefore, provide more structural information and higher sensitivity. In addition, they are readily compatible with gradient separations. Selected applications of flow cells and solvent elimination interfaces for polymer characterization are described.
PubMed search strings for the study of agricultural workers' diseases
Authors: Mattioli Stefano , Gori Davide , Di Gregori Valentina , Ricotta Lara , Baldasseroni Alberto , Farioli Andrea , Zanardi Francesca , Galletti Stefania , Colosio Claudio , Curti Stefania , Violante Francesco S. 
Published: September 2013

AbstractBackgroundSeveral optimized search strategies have been developed in Medicine, and more recently in Occupational Medicine. The aim of this study was to identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of agricultural workers' diseases.MethodsWe selected the Medical Subjects Heading (MeSH) term agricultural workers' diseases and six MeSH terms describing farm work (agriculture, agrochemicals NOT pesticides, animal husbandry, pesticides, rural health, rural population) alongside 61 other promising terms. We estimated proportions of articles containing potentially pertinent information regarding occupational etiology to formulate two search strategies (one “more specific,” one “more sensitive”). We applied these strategies to retrieve information on the possible occupational etiology among agricultural workers of kidney cancer, knee osteoarthritis, and multiple sclerosis. We evaluated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these pathologies.ResultsThe “more specific” search string was based on the combination of terms that yielded the highest proportion (40%) of potentially pertinent abstracts. The “more sensitive” string was based on use of broader search fields and additional coverage provided by other search terms under study. Using the “more specific” string, the NNR to find one potentially pertinent article were: 1.1 for kidney cancer; 1.4 for knee osteoarthritis; 1.2 for multiple sclerosis. Using the sensitive strategy, the NNR were 1.4, 3.6, and 6.3, respectively.ConclusionThe proposed strings could help health care professionals explore putative occupational etiology for agricultural workers' diseases (even if not generally thought to be work related). Am. J. Ind. Med. 56:1473–1481, 2013. © 2013 The Authors. American Journal of Industrial Medicine published by Wiley Periodicals, Inc.
SOX12 and NRSN2 are candidate genes for 20p13 subtelomeric deletions associated with developmental delay
Authors: An Yu , Amr Sami S. , Torres Alcy , Weissman Laura , Raffalli Peter , Cox Gerald , Sheng Xiaoming , Lip Va , Bi Weimin , Patel Ankita , Stankiewicz Pawel , Wu Bai‐Lin , Shen Yiping 
Published: September 2013

Abstract20p13 telomeric/subtelomeric deletions are clinically significant but are currently under‐investigated. So far only five molecularly delineated cases have been reported in literature and no candidate genes have been sufficiently implicated. Here, we present six new deletion cases identified by chromosomal microarray analysis (CMA). We also review 32 cases combined from literature and databases. We found that most 20p13 deletion patients exhibit significant developmental delay. Dysmorphic features are common but a consistent pattern was not recognized. Reduced cognitive ability was frequent. Based on pathogenic deletions delineated in this study, we mapped the smallest overlapping region and identified two nervous system expressing genes (SOX12 and NRSN2) as candidate genes that may be involved in the developmental defects in 20p13 microdeletion. © 2013 Wiley Periodicals, Inc.
Electrochemical deposition of poly[N,N′‐ethylene–bis(salicylideneiminato)–nickel(II)] nanobelts as electrode materials for supercapacitors
Authors: Zhang Yakun , Li Jianling , Wang Xindong , Ye Feng , Yang Jun 
Published: September 2013

ABSTRACTN,N′‐ethylene–bis(salicylideneiminato)]–nickel(II) [Ni(salen)] was synthesized in situ onto the surface of multiwalled carbon nanotubes via a one‐step potentiostatic electrodeposition as one‐dimensional nanobelts. The synthetic process was free of any templates or additives. Potential played a key role in the formation of the poly[N,N′‐ethylene–bis(salicylideneiminato)]–nickel(II)] {poly[Ni(salen)]} nanobelts, and the electrical conductivities of the poly[Ni(salen)] decreased with increasing deposition time. The capacitance values of poly[Ni(salen)] were 272, 195, and 146 F/g at 0.05 mA/cm2 for deposition times of 10, 20, and 30 min, respectively. The capacitance of the sample with a particle structure was much lower than that of poly[Ni(salen)] with a nanobelt structure. The poly[Ni(salen)] nanobelts exhibited a better capacitive behavior than the poly[Ni(salen)] particles because the nanobelt structure made access for the charge and ion to the inner part of the electrode easier. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 39561.
Inhibitory effect of hydrogen bonding on thermal decomposition of the nanocrystalline cellulose/poly(propylene carbonate) nanocomposite
Authors: Hong Jia‐Li , Zhang Xing‐Hong , Wei Ren‐Jian , Wang Qi , Fan Zhi‐Qiang , Qi Guo‐Rong 
Published: September 2013

ABSTRACTBiodegradable poly(propylene carbonate, PPC) is a typical noncrystalline polymer from the copolymerization of carbon dioxide (CO2) with propylene oxide (PO). But it is easy to be degraded to propylene carbonate (PC) via backbiting route during heat process (above 170°C), which limits its application. This work reports the introduction of biodegradable nanocrystalline cellulose (NCC) which was exfoliated from microcrystalline cellulose (MCC) by acid hydrolysis into PPC, affording a biodegradable PPC/NCC nanocomposite with improved thermal decomposition temperatures (the initial decomposition temperature, T5wt% was up to 265°C). Impressively, the thermal decomposition of PPC to PC at 200°C within 4.0 h was dramatically inhibited by introducing NCC, which was evident by 1H NMR spectra. This could be attributed to the hydrogen bonding interaction between NCC and PPC. Moreover, the film of PPC/NCC nanocomposite had not deformed when it was heated at 110°C for 4 h. In application, such biodegradable nanocomposite is a promising disposable package material. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 39847.