bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of the impact of PSI:Biology according to the annotations of the determined structures
Authors: DePietro Paul J , Julfayev Elchin S , McLaughlin William A 
Published: October 2013

Abstract

Background
Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure.

Results
One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure.

Conclusions
We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i.e. the numbers of structures and impact of publication records, to monitor the progress of PSI:Biology towards its goals of examining structure to function connections of high biomedical relevance. The metric provides an objective means to quantify the overall impact of PSI:Biology as it uses biomedical annotations from external sources.
Attenuating effect of standardized fruit extract of punica granatum L in rat model of tibial and sural nerve transection induced neuropathic pain
Authors: Jain Vivek , Pareek Ashutosh , Bhardwaj Yashumati Ratan , Singh Nirmal 
Published: October 2013

Abstract

Background
Injury to a nerve is the most common reason of acquired peripheral neuropathy. Therefore, searching for effective substance to recover of nerve after injury is need of present era. The current study investigates the protective potential of Standardized Fruit Extract of Punica granatum L (PFE) [Ellagic acid (41.6%), Punicalagins (10%), Granatin (5.1%)] in Tibial & Sural Nerve Transection (TST) induced neuropathic pain in rats.

Methods
TST was performed by sectioning tibial and sural nerve portions of the sciatic nerve and leaving the common peroneal nerve intact. Acetone drop, pin-prick, hot plate, paint brush & Walking Track tests were performed to assess cold allodynia; mechanical heat, hyperalgesia and dynamic mechanical allodynia & tibial functional index respectively. The levels of TNF-α, TBARS, GSH and Nitrite were measured in the sciatic nerve as an index of inflammation & oxidative stress.

Results
TST led to significant development of cold allodynia; mechanical and heat hyperalgesia; dynamic mechanical allodynia; functional deficit in walking along with rise in the levels of TBARS, TNF-α, GSH and Nitrite. Administrations of PFE (100 & 300 mg/kg oral), significantly attenuate TST induced behavioral & biochemical changes. Pretreatments of BADGE (120 mg/kg IP) a PPAR-γ antagonist and nitric oxide precursor L-arginine (100 mg/kg IP) abolished the protective effect of PFE. Whereas, pretreatment of L-NAME (5 mg/kg IP) a NOS inhibitor significantly potentiated PFE’s protective effect of PFE.

Conclusion
PFE shown to have attenuating effect in TST induced neuropathic pain which may be attributed to potential PPAR-gamma agonistic activity, nitric oxide inhibitory, anti-inflammatory and anti oxidative actions.
Regulation of stem cell self-renewal and differentiation by Wnt and Notch are conserved throughout the adenoma-carcinoma sequence in the colon
Authors: Prasetyanti Pramudita Ramadhina , Zimberlin Cheryl Doreen , Bots Michael , Vermeulen Louis , De Sousa E Melo Felipe , Medema Jan Paul 
Published: October 2013

Abstract

Background
Colon cancer stem cells are shown to be the self-renewing cells within a tumor that give rise to all lineages of more differentiated tumor cells. In this respect they are remarkably similar to their non-malignant counterparts that orchestrate the intestinal lining. This suggests that, despite the numerous genetic aberrations and morphological changes that have occurred during cancer initiation and progression, a remnant homeostatic regulation persists.

Findings
Using a number of human and mouse intestinal-derived organoid cultures from normal, adenoma and cancerous tissues, we show here that Notch signals coordinate self-renewal and lineage determination not only in normal, but also at the adenoma and carcinoma stage in both mice and humans. Moreover, the Wnt pathway, which carries activating mutations in virtually all colon cancers, is not as previously predicted constitutively active in adenomas and carcinomas, but still displays a heterogeneous activity pattern that determined stemness in all stages of disease.

Conclusion
These data for the first time provide a comprehensive overview of Wnt and Notch-mediated signaling in the different stages of the adenoma-carcinoma sequence and demonstrates that these morphogenic pathways, despite mutations, remain crucial determinants of both architecture and hierarchy in normal and malignant intestinal tissue.
The Campylobacter jejuniCiaD effector protein activates MAP kinase signaling pathways and is required for the development of disease
Authors: Samuelson Derrick R , Eucker Tyson P , Bell Julia A , Dybas Leslie , Mansfield Linda S , Konkel Michael E 
Published: October 2013

Abstract

Background
Enteric pathogens utilize a distinct set of proteins to modulate host cell signaling events that promote host cell invasion, induction of the inflammatory response, and intracellular survival. Human infection with Campylobacter jejuni, the causative agent of campylobacteriosis, is characterized by diarrhea containing blood and leukocytes. The clinical presentation of acute disease, which is consistent with cellular invasion, requires the delivery of the Campylobacter invasion antigens (Cia) to the cytosol of host cells via a flagellar Type III Secretion System (T3SS). We identified a novel T3SS effector protein, which we termed CiaD that is exported from the C. jejuni flagellum and delivered to the cytosol of host cells.

Results
We show that the host cell kinases p38 and Erk 1/2 are activated by CiaD, resulting in the secretion of interleukin-8 (IL-8) from host cells. Additional experiments revealed that CiaD-mediated activation of p38 and Erk 1/2 are required for maximal invasion of host cells by C. jejuni. CiaD contributes to disease, as evidenced by infection of IL-10 knockout mice. Noteworthy is that CiaD contains a Mitogen-activated protein (MAP) kinase-docking site that is found within effector proteins produced by other enteric pathogens. These findings indicate that C. jejuni activates the MAP kinase signaling pathways Erk 1/2 and p38 to promote cellular invasion and the release of the IL-8 pro-inflammatory chemokine.

Conclusions
The identification of a novel T3SS effector protein from C. jejuni significantly expands the knowledge of virulence proteins associated with C. jejuni pathogenesis and provides greater insight into the mechanism utilized by C. jejuni to invade host cells.
Correlation of Nav1.8 and Nav1.9 Sodium Channel Expression with Neuropathic Pain in Human Subjects with Lingual Nerve Neuromas
Authors: Bird Emma V , Christmas Claire R , Loescher Alison R , Smith Keith G , Robinson Peter P , Black Joel A , Waxman Stephen G , Boissonade Fiona M 
Published: October 2013

Background Voltage-gated sodium channels Nav1.8 and Nav1.9 are expressed preferentially in small diameter sensory neurons, and are thought to play a role in the generation of ectopic activity in neuronal cell bodies and/or their axons following peripheral nerve injury. The expression of Nav1.8 and Nav1.9 has been quantified in human lingual nerves that have been previously injured inadvertently during lower third molar removal, and any correlation between the expression of these ion channels and the presence or absence of dysaesthesia investigated. Results Immunohistochemical processing and quantitative image analysis revealed that Nav1.8 and Nav1.9 were expressed in human lingual nerve neuromas from patients with or without symptoms of dysaesthesia. The level of Nav1.8 expression was significantly higher in patients reporting pain compared with no pain, and a significant positive correlation was observed between levels of Nav1.8 expression and VAS scores for the symptom of tingling. No significant differences were recorded in the level of expression of Nav1.9 between patients with or without pain. Conclusions These results demonstrate that Nav1.8 and Nav1.9 are present in human lingual nerve neuromas, with significant correlations between the level of expression of Nav1.8 and symptoms of pain. These data provide further evidence that changes in expression of Nav1.8 are important in the development and/or maintenance of nerve injury-induced pain, and suggest that Nav1.8 may be a potential therapeutic target.
Biochemical and molecular heterogeneity among isolates of Yersinia ruckeri from rainbow trout (Oncorhynchus mykiss, Walbaum) in north west Germany
Authors: Huang Yidan , Runge Martin , Michael Geovana Brenner , Schwarz Stefan , Jung Arne , Steinhagen Dieter 
Published: October 2013

Abstract

Background
Enteric Redmouth Disease (ERM), caused by Yersinia ruckeri, is one of the most important infectious diseases in rainbow trout (Oncorhynchus mykiss) aquaculture in Europe. More recently, non-motile vaccine resistant isolates appear to have evolved and are causing disease problems throughout Europe, including Germany. The aim of this study was to analyse the variation of biochemical and molecular characteristics of Y. ruckeri isolates collected in north west Germany as a basis for strain differentiation. The isolates originated mainly from rainbow trout and were characterised by biochemical profiling, 16S rDNA sequencing, repetitive sequence-based PCRs, including (GTG)5-PCR, BOX-PCR, ERIC-PCR and REP-PCR, and pulsed-field gel electrophoresis (PFGE).

Results
In total, 83 isolates were characterised, including 48 isolates collected during a field study in north west Germany. All isolates were confirmed as Y. ruckeri by the API 20E system. Five isolates were additionally confirmed as Y. ruckeri by Y. ruckeri-specific PCR and 16S rDNA sequencing. Only 17 isolates hydrolyzed Tween 80/20. Sixty-six isolates (79.5%) were non-motile. Two different patterns were obtained by REP-PCR, five patterns by ERIC-PCR, four patterns by (GTG)5-PCR and three patterns by BOX-PCR. NotI-directed PFGE resulted in 17 patterns that differed from each other by 25–29 fragments. Isolates from the field study clustered together as PFGE type C. According to the results of API 20E, repetitive sequence-based PCRs and PFGE, these isolates could be subdivided into 27 different groups.

Conclusions
The detailed molecular and phenotypic characterisation scheme developed in this study could be used to help trace the dissemination of Y. ruckeri isolates, and thus may represent part of improved disease monitoring plans in the future.
Risk factors for intra-abdominal hypertension and abdominal compartment syndrome among adult intensive care unit patients: a systematic review and meta-analysis
Authors: Holodinsky Jessalyn K , Roberts Derek J , Ball Chad G , Blaser Annika Reintam , Starkopf Joel , Zygun David A , Stelfox Henry Thomas , Malbrain Manu L , Jaeschke Roman C , Kirkpatrick Andrew W 
Published: October 2013

Abstract
Introduction
Although intra-abdominal hypertension (IAH) and abdominal compartment syndrome (ACS) are associated with substantial morbidity and mortality among critically ill adults, it remains unknown if prevention or treatment of these conditions improves patient outcomes. We sought to identify evidence-based risk factors for IAH and ACS in order to guide identification of the source population for future IAH/ACS treatment trials and to stratify patients into risk groups based on prognosis.

Methods
We searched electronic bibliographic databases (MEDLINE, EMBASE, PubMed, and the Cochrane Database from 1950 until January 21, 2013) and reference lists of included articles for observational studies reporting risk factors for IAH or ACS among adult ICU patients. Identified risk factors were summarized using formal narrative synthesis techniques alongside a random effects meta-analysis.

Results
Among 1,224 citations identified, 14 studies enrolling 2,500 patients were included. The 38 identified risk factors for IAH and 24 for ACS could be clustered into three themes and eight subthemes. Large volume crystalloid resuscitation, the respiratory status of the patient, and shock/hypotension were common risk factors for IAH and ACS that transcended across presenting patient populations. Risk factors with pooled evidence supporting an increased risk for IAH among mixed ICU patients included obesity (four studies; odds ratio (OR) 5.10; 95% confidence interval (CI), 1.92 to 13.58), sepsis (two studies; OR 2.38; 95% CI, 1.34 to 4.23), abdominal surgery (four studies; OR 1.93; 95% CI, 1.30 to 2.85), ileus (two studies; OR 2.05; 95% CI, 1.40 to 2.98), and large volume fluid resuscitation (two studies; OR 2.17; 95% CI, 1.30 to 3.63). Among trauma and surgical patients, large volume crystalloid resuscitation and markers of shock/hypotension and metabolic derangement/organ failure were risk factors for IAH and ACS while increased disease severity scores and elevated creatinine were risk factors for ACS in severe acute pancreatitis patients.

Conclusions
Although several IAH/ACS risk factors transcend across presenting patient diagnoses, some appear specific to the population under study. As our findings were somewhat limited by included study methodology, the risk factors reported in this study should be considered candidate risk factors until confirmed by a large prospective multi-centre observational study.
Metalloid Sn clusters: properties and the novel synthesis via a disproportionation reaction of a monohalide
Authors: Schrenk Claudio , Schnepf Andreas 
Published: October 2013

AbstractMetalloid cluster compounds of tin of the general formulae SnnRm with n>m (R=organic ligand), where beside ligand-bound tin atoms also “naked” tin atoms, that only bind to other tin atoms, are present, represent a novel class of cluster compounds in tin chemistry. As the “naked” tin atoms inside these clusters exhibit an oxidation state of 0, the average oxidation state of the tin atoms within such metalloid tin clusters is in between 0 and 1. Thus, these cluster compounds may be seen as intermediates on the way to the elemental state. Therefore, interesting properties are expected for these compounds, which might complement results from nanotechnology. During the last years, different syntheses of such novel cluster compounds have been introduced, leading to several metalloid tin cluster compounds, which exhibit new and partly unusual structure and bonding properties. In this review, recent results in this novel field of group 14 chemistry are discussed, whereby special attention is focused on the novel synthetic route applying a disproportionation reaction of metastable Sn(I) halides.
La geografía del caos
Authors: Sanginés Pedro Agustín Salmerón 
Published: October 2013

En este ensayo se pretende aclarar el cambiante mapa político-militar de México durante el verano y el otoño de 1914. Se busca mostrar la fuerza, las posiciones y los recursos de los grupos revolucionarios durante el proceso de gestación de la ruptura que provocaría la guerra civil en noviembre de 1914, guerra que enfrentó a convencionistas contra constitucionalistas. Además, se intenta cruzar el mapa económico y demográfico con el mapa militar, así como recurrir a fuentes originales para hacer una nueva valoración de esa coyuntura, contraria a las tradicionalmente aceptadas.
The aim of this paper is to clarify the changing political and military map of Mexico during the summer and autumn of 1914. I intend to show the strength, positions and resources of the revolutionary groups during the emergence of the rupture that would cause civil war between convencionistas and constitutionalistas in November 1914. Furthermore, I attempt to cross over the economic and demographic map with the military map using original sources to make a new assessment of the situation, contrary to the one traditionally accepted.
The Subcommander and the Sardinian
Authors: Henck Nick 
Published: October 2013

Numerous scholars have adopted a Gramscian framework when analyzing the Zapatistas and Subcommander Marcos. Some, however, have gone beyond the evidence, claiming that Marcos was influenced by Gramsci. Inspection of the Subcommander’s discourse provides no proof that he has been directly influenced by the Sardinian; instead, indigenous thought and practice appear more influential in having shaped Marcos’s political philosophy. Marcos’s independence from Gramsci distances him from other contemporary Central American guerrillas and has wider implications concerning the timing and extent of Gramsci’s diffusion in Mexico. Gramsci did, however, contribute to an atmosphere of “antiauthoritarian eclecticism” among the Latin American new left from which Marcos emerged.Muchos estudiosos han adoptado el marco teórico gramsciano para analizar a los zapatistas y al Subcomandante Marcos. Pero algunos han pasado por alto la evidencia y afirman que Marcos recibió influencia de Gramsci. Al inspeccionar el discurso del Subcomandante no se encuentran pruebas de que haya recibido influencia directa del pensador de Sardinia; en cambio, el pensamiento y la práctica indígenas aparecen como influencias más notorias en la conformación de la filosofía política de Marcos. La independencia de este último respecto de Gramsci lo aparta de otras guerrillas contemporáneas centroamericanas y tiene implicaciones más amplias en lo que toca al momento y alcance de la difusión de Gramsci en México. Lo cierto es que éste contribuyó a una atmósfera de “eclecticismo antiautoritario” entre la nueva izquierda latinoamericana de la que surgió Marcos.
La historia encarnada, Llanto de Carmen Boullosa
Authors: Muñoz Elizabeth Cummins 
Published: October 2013

En su novela Llanto, novelas imposibles (1992), Carmen Boullosa explora el uso del cuerpo como una herramienta epistemológica para indagar en las tensiones entre el discurso tradicional de la historia mexicana y la lógica literaria de la novela moderna. Desde su momento posmoderno, la autora reconoce que la historiografía tradicional ya no es fiable y quiere encontrar el significado perdido mediante la dramatización literaria del cuerpo histórico y su entorno físico. Al fracasar como novela histórica moderna, su proyecto cumple con un rito íntimo y personal en el que la ausencia del pasado indígena colectivo se asimila por un proceso de duelo individual que está firmemente localizado en el cuerpo y representado por el llanto.
In her novel Llanto, novelas imposibles (1992), Carmen Boullosa explores the body as an epistemological means to examine the tensions between the traditional discourse of Mexican history and the literary logic of the modern novel. From her postmodern stance, she recognizes that traditional historiography is no longer reliable and wants to recover meaning through a literary dramatization of the historical body and its physical environment. Her project fails as a modern historical novel, but undergoes an intimate and personal rite in which the absence of the collective indigenous past is assimilated through an individual grieving process firmly located in the body and represented by tears.
Divergence of Iron Metabolism in Wild Malaysian Yeast
Authors: Lee Hana N , Mostovoy Yulia , Hsu Tiffany Y , Chang Amanda H , Brem Rachel B 
Published: October 2013

Abstract
Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.