bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnotaxonomical considerations and usage of ichthyofauna in a fishing community in Ceará State, Northeast Brazil
Authors: Pinto Márcia Freire , Mourão José da Silva , Alves Rômulo Romeu Nóbrega 
Published: March 2013

AbstractBackgroundArtisanal fishery is one of the most important economic activities for human populations living in coastal areas. The traditional knowledge that fishermen have of fishes is of utmost importance for the establishment of conservation strategies for many species. This study aimed to analyse the knowledge of and utilization of fishes by the artisanal fishermen in a fishing community on the coast of Ceará State (Northeast Brazil).MethodsIn 2011, a number of semi-structured interviews were performed with fishermen with more than 20 years of fishery experience. The interviews were about fisheries (collecting spots, artefacts, etc.) and fish use. The fishes cited by the fishermen were identified scientifically and ethnotaxonomically.ResultsConsidered masters of fishery, they cited 162 vernacular names of fishes, which corresponded to 290 different species, also including other animals such as dolphins, porpoises, whales and manatees. The criteria for the classification of the fishes were well known and utilised by the fishermen, and they were based on morphology, behaviour, habitat and the importance of commercial and fishing activities. Four hierarchical categories were identified in their classification system: kingdom, life-form, generic and specific. The fish nomenclature created by the fishermen was mostly composed of generic and monotypic names. The main uses of fish were for food and commercial purposes.ConclusionsThe results stress the richness and complexity of the knowledge of the artisanal fishermen of Redonda Beach, and they provide support for the possibility of future studies and for the development of management plans and the management of wildlife resources.
Resolving spatial inconsistencies in chromosome conformation measurements
Authors: Duggal Geet , Patro Rob , Sefer Emre , Wang Hao , Filippova Darya , Khuller Samir , Kingsford Carl 
Published: March 2013

Abstract

Background
Chromosome structure is closely related to its function and Chromosome Conformation Capture (3C) is a widely used technique for exploring spatial properties of chromosomes. 3C interaction frequencies are usually associated with spatial distances. However, the raw data from 3C experiments is an aggregation of interactions from many cells, and the spatial distances of any given interaction are uncertain.

Results
We introduce a new method for filtering 3C interactions that selects subsets of interactions that obey metric constraints of various strictness. We demonstrate that, although the problem is computationally hard, near-optimal results are often attainable in practice using well-designed heuristics and approximation algorithms. Further, we show that, compared with a standard technique, this metric filtering approach leads to (a) subgraphs with higher statistical significance, (b) lower embedding error, (c) lower sensitivity to initial conditions of the embedding algorithm, and (d) structures with better agreement with light microscopy measurements. Our filtering scheme is applicable for a strict frequency-to-distance mapping and a more relaxed mapping from frequency to a range of distances.

Conclusions
Our filtering method for 3C data considers both metric consistency and statistical confidence simultaneously resulting in lower-error embeddings that are biologically more plausible.
Peritoneal tuberculosis mimicking advanced ovarian carcinoma: an important differential diagnosis to consider
Authors: Gosein Maria A , Narinesingh Dylan , Narayansingh Gordon V , Bhim Nazreen A , Sylvester Pearse A 
Published: March 2013

Abstract

Background
Female patients who present with ascites, adnexal masses and elevated CA125 levels are typically presumed to have advanced ovarian carcinoma. This can lead to radical surgery with its associated morbidity. An important differential diagnosis to consider is tuberculous peritonitis which can present in a similar manner and responds well to medical treatment.

Case presentation
A 44 year old female presented with abdominal distension, weight loss and low grade fever. Her CA125 level was 909 U/ml. Imaging studies revealed an adnexal lesion and ascites. The lungs appeared normal and a Mantoux test was negative. Ovarian malignancy was highly suspected. Cytology of ascites was negative for malignant cells. The patient subsequently developed a large pleural effusion which was drained and negative for malignant cells and acid fast bacilli. Repeat imaging revealed a ‘tree in bud’ appearance of the lung parenchyma and dense ascites. Histology from diagnostic laparotomy revealed caseating granulomas with epithelioid cells and Langhan’s type giant cells. The patient responded well to antituberculosis therapy with normalization of CA125 levels, confirming the diagnosis of peritoneal tuberculosis.

Conclusion
CA125 levels lack specificity, with elevated levels encountered in many benign and malignant conditions, including tuberculosis. There are a few discriminating features that suggest a diagnosis of tuberculous peritonitis rather than ovarian carcinoma. Apart from chest findings which may not always be present, smooth peritoneal thickening and a dirty omentum on CT favours a diagnosis of peritoneal tuberculosis compared with nodular thickening of the peritoneum and omentum in peritoneal carcinomatosis. PCR and ADA testing of ascitic fluid can also be helpful. When these tests are negative or unavailable then diagnostic laparoscopy or laparotomy should be performed with the aid of frozen section to avoid unnecessary radical surgery in cases of peritoneal tuberculosis.
Methylene blue as an early diagnostic marker for oral precancer and cancer
Authors: Riaz Akhtar , Shreedhar Balasundari , Kamboj Mala , Natarajan S 
Published: March 2013

Abstract
Oral cancer is one of the most common neoplasm’s and is ranked eighth in the cancer incidence worldwide. Early detection is of critical importance because survival rates markedly improve. In vivo staining is a simple, inexpensive, and fairly sensitive method. Involved 120 patients (50 with Premalignant Lesion, 50 with OSCC and 20 controls) stained by Methylene Blue (MB). The results of MB uptake were compared with a simultaneous biopsy of these lesions. Pathologically confirmed precancers and cancers were the positive targets of this screening, while hyperkeratosis without dysplasia and no evidence of malignancy were sorted as negative subjects of screening. The results revealed sensitivity of 91.4%, specificity of 66.6%, positive predictive value 97.7% and negative predictive value 33% leading to diagnostic accuracy of MB stain to 90%. We state that MB staining is useful diagnostic tool in community oral cancer screening programmes for high-risk individuals.
Panax ginseng extract rich in ginsenoside protopanaxatriol offers combinatorial effects in nitric oxide production via multiple signaling pathways
Authors: Ahn Hee Yoon , Hong So Young , Kim Ji Yeon , Kwon Oran 
Published: March 2013

Abstract
The root of Panax ginseng C.A. Meyer has been shown to induce nitric oxide (NO) release resulting in a hypotensive effect. However, the main active component contributing to vascular endothelium relaxation remains uncertain. In this study, we hypothesized that multiple components of ginseng extract might have combinatory effects providing greater health benefits than a single ginsenosides. To test this hypothesis, we compared the NO-releasing and endothelial NO synthase (eNOS) activating potency of wide range of ginseng extracts (crude extract, CE; protopanaxatriol-enriched extract, TE; protopanaxadiol-enriched extract, DE) and individual ginsenosides (Rg1, Re and Rb1) in human umbilical vein endothelial cells. We found that TE had the highest potency in NO production, followed by CE, DE, and Rg1. We also observed that TE-treatment resulted in rapid activation of intracellular signaling pathways, immediate linear rise of NO, and increased eNOS activation. TE-induced activation of eNOS was abolished by pretreatment with wortmannin (inhibitor for PI3K-Akt), compound C (inhibitor for AMP activated protein kinase, AMPK) or L-NAME (inhibitor for NOS), whereas Rg1-induced eNOS phosphorylation was only partially attenuated. Further analysis revealed that TE, but not Rg1, results in AMPK phosphorylation at Thr172. These novel finding add evidence that the multiple components of Panax ginseng extract rich in protopanaxatriol offers combinatorial effects in NO production and vascular endothelium relaxation via multiple signaling pathways.
Optimization of monomethoxy poly(ethylene glycol) grafting on Langerhans islets capsule using response surface method
Authors: Aghajani-Lazarjani Hamideh , Vasheghani-Farahani Ebrahim , Hashemi-Najafabadi Sameereh , Shojaosadati Seyed Abbas , Zahediasl Saleh , Tiraihi Taki , Atyabi Fatemeh 
Published: March 2013

AbstractLangerhans islet transplantation is a much less invasive approach compared with the pancreas transplantation to ‘cure’ diabetes. However, destruction of transplanted islets by the immune system is an impediment for a successful treatment. Chemical grafting of monomethoxy poly(ethylene glycol) onto pancreatic islet capsule is a novel approach in islet immunoisolation. The aim of this study was to determine an optimized condition for grafting of monomethoxy poly(ethylene glycol) succinimidyl propionate (mPEG-SPA) on islets capsule. Independent variables such as reaction time, the percentage of longer mPEG in the mixture, and polymer concentration were optimized using a three-factor, three-level Box-Behnken statistical design. The dependent variable was IL-2 (interleukin-2) secretion of lymphocytes co-cultured with PEGylated or uncoated control islets for 7 days co-culturing. A mathematical relationship is obtained which explained the main and quadratic effects and the interaction of factors which affected IL-2 secretion. Response surface methodology predicted the optimized values of reaction time, the percentage of longer mPEG in the mixture, and polymer concentration of 60 min to be 63.7% mPEG10and 22 mg/mL, respectively, for the minimization of the secreted IL-2 as response. Islets which were PEGylated at this condition were transplanted to diabetic rats. The modified islets could survive for 24 days without the aid of any immunosuppressive drugs and it is the longest survival date reported so far. However, free islets (unmodified islets as control) are completely destroyed within 7 days. These results strongly suggest that this new protocol provides an effective clinical means of decreasing transplanted islet immunogenicity.
Abundant stage-dependent Ly49E expression by liver NK cells is not essential for their differentiation and function
Authors: Filtjens Jessica , Taveirne Sylvie , Van Acker Aline , Van Ammel Els , Vanhees Mandy , Kerre Tessa , Taghon Tom , Vandekerckhove Bart , Plum Jean , Leclercq Georges 
Published: March 2013

Abstract
The Ly49E receptor is abundantly expressed on immature liver NK cells, but not essential in NK cell differentiation and function.
The NKR Ly49E has several unique characteristics. Unlike most NKRs, Ly49E is highly expressed on fetal NK cells, whereas expression is decreased on bone marrow-derived NK cells in adult mice. To investigate a possible role for Ly49E in NK cell differentiation and function, we have generated an Ly49E KO mouse. Our results show that bone marrow and splenic NK cells are present in normal numbers in Ly49E KO mice, expressing an unaltered panel of NKRs and differentiation markers. Furthermore, cytokine production and cytotoxicity by these cells are unaffected. Surprisingly, WT DX5− liver NK cells express high Ly49E levels in fetal and adult mice. Ly49E+DX5− liver NK cells transferred into Rag-2−/−/gc−/− mice maintain high Ly49E expression in the liver and differentiate into DX5+ NK cells in spleen and bone marrow. Ly49E expression is not crucial for liver NK cell differentiation during ontogeny, as the DX5−/DX5+ ratio, the NKR repertoire, and the granzyme B and TRAIL levels are comparable in Ly49E KO versus WT mice, except for lower TRAIL expression on DX5− liver NK cells in 20-day-old mice. The TRAIL-, perforin-, and FasL-mediated cytolysis by liver NK cells is unaffected in Ly49E KO mice. Collectively, we show that in addition to high Ly49E expression on fetal NK cells versus low Ly49E expression on conventional NK cells in adult life, Ly49E remains highly expressed on DX5− liver NK cells. However, Ly49E expression does not have a crucial role in differentiation and/or function of these NK cells.
TLR agonists: our best frenemy in cancer immunotherapy
Authors: Kaczanowska Sabina , Joseph Ann Mary , Davila Eduardo 
Published: March 2013

Abstract
Review on the ability of different TLR agonists to orchestrate antitumor immune responses, or promote tumor growth, underscoring the impact of choosing among TLR agonists when applying these therapies in the clinic.
Various TLR agonists are currently under investigation in clinical trials for their ability to orchestrate antitumor immunity. The antitumor responses are largely attributed to their aptitude to stimulate APCs such as DCs which in turn, activate tumor-specific T cell responses. However, there is a potential for TLR signaling to occur on cells other than professional APCs that could negate antitumor responses or even worse, promote tumor growth. The impetus for this review is twofold. First, there is accumulating data demonstrating that the engagement of TLRs on different T cell subsets and different cancer types could promote tumor growth or conversely, contribute to antitumor responses. Second, the efficacy of TLR agonists as monotherapies to treat cancer patients has been limited. In this review, we discuss how TLR signaling within different T cell subsets and cancer cells can potentially impact the generation of antitumor responses. Based on evidence from preclinical models and clinical trials, we draw attention to several criteria that we believe must be considered when selecting TLR agonists for developing effective immunotherapeutic strategies against cancer.
Localized bacterial infection induces systemic activation of neutrophils through Cxcr2 signaling in zebrafish
Authors: Deng Qing , Sarris Milka , Bennin David A , Green Julie M , Herbomel Philippe , Huttenlocher Anna 
Published: March 2013

Abstract
Direct visualization and characterization of Cxcr2 signaling as a mediator of systemic neutrophil reaction to a local infection.
Neutrophils are the first line of defense against tissue damage and are rapidly mobilized to sites of bacterial infection. However, the signals that regulate neutrophil recruitment are not well defined. Here, using photolabel-enabled fate mapping in zebrafish larvae, we show that localized otic infection with Pseudomonas aeruginosa induces systemic activation and mobilization of neutrophils from the CHT through Cxcr2 signaling. We have cloned the zebrafish Cxcr1 and Cxcr2 receptors and show that Cxcr2 functions as a Cxcl8 receptor in live zebrafish. With the use of morpholino-mediated depletion, we show that infection-induced neutrophil mobilization from the CHT is mediated by Cxcr2 but not Cxcr1. By contrast, Cxcr2 depletion does not affect neutrophil recruitment to the chemoattractant LTB4. Taken together, our findings identify Cxcl8-Cxcr2 signaling as an infection-induced long-range cue that mediates neutrophil motility and mobilization from hematopoietic tissues, positioning Cxcr2 as a critical pathway that mediates infection-induced systemic activation of neutrophils.
Pituitary Stalk Interruption Syndrome and Isolated Pituitary Hypoplasia May Be Caused by Mutations in Holoprosencephaly-Related Genes
Authors: Tatsi Christina , Sertedaki Amalia , Voutetakis Antonis , Valavani Eleni , Magiakou Maria-Alexandra , Kanaka-Gantenbein Christina , Chrousos George P. , Dacou-Voutetakis Catherine 
Published: March 2013

Context:Holoprosencephaly (HPE) is a developmental defect characterized by wide phenotypic variability, ranging from minor midline malformations (eg, single central incisor) to severe deformities. In 10–15% of HPE patients, mutations in specific genes have been identified (eg, SHH, TGIF, SIX3). Pituitary stalk interruption syndrome (PSIS) constitutes a distinct abnormality of unknown pathogenesis, whereas isolated pituitary hypoplasia (IPH) has been linked to various developmental genes.Objective:Three of our patients with PSIS had a single central incisor, a malformation encountered in some HPE cases. Based on this observation, we initiated a search for mutations in HPE-associated genes in 30 patients with PSIS or IPH.Design and Participants:The entire coding region of the TGIF, SHH, and SIX3 genes was sequenced in patients with combined pituitary hormone deficiency associated with either PSIS or IPH and in healthy controls.Results:Two novel mutations in the HPE-related genes were detected (ie, c.799 C&gt;T, p.Q267X in the TGIF gene, and c.1279G&gt;A, p.G427R in the SHH gene) in 2 of our patients. The overall incidence of HPE-related gene mutations in our nonsyndromic and nonchromosomal patients was 6.6%. No molecular defect in the SIX3 gene was detected in our cohort.Conclusions:The data suggest that HPE-related gene mutations are implicated in the etiology of isolated pituitary defects (PSIS or IPH). Alternatively, PSIS or IPH may constitute mild forms of an expanded HPE spectrum.
From shape to cells: mouse models reveal mechanisms altering palate development in Apert syndrome
Authors: Martínez-Abadías Neus , Holmes Greg , Pankratz Talia , Wang Yingli , Zhou Xueyan , Jabs Ethylin Wang , Richtsmeier Joan T. 
Published: March 2013

SummaryApert syndrome is a congenital disorder characterized by severe skull malformations and caused by one of two missense mutations, S252W and P253R, on fibroblast growth factor receptor 2 (FGFR2). The molecular bases underlying differential Apert syndrome phenotypes are still poorly understood and it is unclear why cleft palate is more frequent in patients carrying the S252W mutation. Taking advantage of Apert syndrome mouse models, we performed a novel combination of morphometric, histological and immunohistochemical analyses to precisely quantify distinct palatal phenotypes in Fgfr2+/S252W and Fgfr2+/P253R mice. We localized regions of differentially altered FGF signaling and assessed local cell patterns to establish a baseline for understanding the differential effects of these two Fgfr2 mutations. Palatal suture scoring and comparative 3D shape analysis from high resolution μCT images of 120 newborn mouse skulls showed that Fgfr2+/S252W mice display relatively more severe palate dysmorphologies, with contracted and more separated palatal shelves, a greater tendency to fuse the maxillary-palatine sutures and aberrant development of the inter-premaxillary suture. These palatal defects are associated with suture-specific patterns of abnormal cellular proliferation, differentiation and apoptosis. The posterior region of the developing palate emerges as a potential target for therapeutic strategies in clinical management of cleft palate in Apert syndrome patients.
piggyBac as a high-capacity transgenesis and gene-therapy vector in human cells and mice
Authors: Li Rongbo , Zhuang Yuan , Han Min , Xu Tian , Wu Xiaohui 
Published: March 2013

Summary
The stable genomic integration and expression of a large transgene is a major hurdle in gene therapy. We show that the modified piggyBac (PB) transposon system can be used to introduce a 207 kb genomic DNA fragment containing the RORγ/γt locus into human cells and mice. PB-mediated transgenesis results in a single copy of a stably inherited and expressed transgene. These results indicate that PB could serve as an effective high-capacity vector for functional analysis of the mammalian genome and for gene therapy in human cells.
Loss of the E3 ubiquitin ligase LRSAM1 sensitizes peripheral axons to degeneration in a mouse model of Charcot-Marie-Tooth disease
Authors: Bogdanik Laurent P. , Sleigh James N. , Tian Cong , Samuels Mark E. , Bedard Karen , Seburn Kevin L. , Burgess Robert W. 
Published: March 2013

Summary
Charcot-Marie-Tooth disease (CMT) is a clinically and genetically heterogeneous condition characterized by peripheral axon degeneration with subsequent motor and sensory deficits. Several CMT gene products function in endosomal sorting and trafficking to the lysosome, suggesting that defects in this cellular pathway may present a common pathogenic mechanism for these conditions. LRSAM1 is an E3 ubiquitin ligase that is implicated in this process, and mutations in LRSAM1 have recently been shown to cause CMT. We have generated mouse mutations in Lrsam1 to create an animal model of this form of CMT (CMT2P). Mouse Lrsam1 is abundantly expressed in the motor and sensory neurons of the peripheral nervous system. Both homozygous and heterozygous mice have largely normal neuromuscular performance and only a very mild neuropathy phenotype with age. However, Lrsam1 mutant mice are more sensitive to challenge with acrylamide, a neurotoxic agent that causes axon degeneration, indicating the axons in the mutant mice are indeed compromised. In transfected cells, LRSAM1 primarily localizes in a perinuclear compartment immediately beyond the Golgi and shows little colocalization with components of the endosome to lysosome trafficking pathway, suggesting that other cellular mechanisms also merit consideration.
Osteoarticular tissue infection and development of skeletal pathology in murine brucellosis
Authors: Magnani Diogo M. , Lyons Elizabeth T. , Forde Toni S. , Shekhani Mohammed T. , Adarichev Vyacheslav A. , Splitter Gary A. 
Published: March 2013

Summary
Brucellosis, a frequent bacterial zoonosis, can produce debilitating chronic disease with involvement of multiple organs in human patients. Whereas acute brucellosis is well studied using the murine animal model, long-term complications of host-pathogen interaction remain largely elusive. Human brucellosis frequently results in persistent, chronic osteoarticular system involvement, with complications such as arthritis, spondylitis and sacroiliitis. Here, we focused on identifying infectious sites in the mouse that parallel Brucella melitensis foci observed in patients. In vivo imaging showed rapid bacterial dispersal to multiple sites of the murine axial skeleton. In agreement with these findings, immunohistochemistry revealed the presence of bacteria in bones and limbs, and in the lower spine vertebrae of the axial skeleton where they were preferentially located in the bone marrow. Surprisingly, some animals developed arthritis in paws and spine after infection, but without obvious bacteria in these sites. The identification of Brucella in the bones of mice corroborates the findings in humans that these osteoarticular sites are important niches for the persistence of Brucella in the host, but the mechanisms that mediate pathological manifestations in these sites remain unclear. Future studies addressing the immune responses within osteoarticular tissue foci could elucidate important tissue injury mediators and Brucella survival strategies.