Miracle-dz/UniFAR-FTUs huggingface dataset:
Population dynamics of rapid fixation in cytotoxic T lymphocyte escape mutants of influenza A

The dynamics of cellular immunity against pathogens, and its interaction with the human MHC system, is a key area for empirical research, both within individual hosts and in population genetic surveys. However, in contrast with humoral immunity, the dynamics of cellular immunity have not been modeled at the population level. Here, we address this lacuna with a model of recently observed dramatic invasions of cytotoxic T lymphocyte escape mutants in human influenza A. In particular, we offer an explanation for the rapid fixation of a HLA-B27 restricted cytotoxic T lymphocyte escape mutant on the nucleoprotein that emerged in the 1993–1994 season. We find that the dynamics within a single season of influenza do not provide a realistic description, but a model of the full annual dynamics can offer a possible explanation. Our model is deterministic for the winter epidemic, and stochastic for the summer period. An escape mutant that leads to a slightly longer infection in a small proportion of hosts has a substantial advantage through summer persistence. Furthermore, if a small number of founding cases are responsible for initiating each epidemic, then this effect of rapid mutant fixation is amplified.
COMPOSIÇÃO E ABUNDÂNCIA DO ZOOPLÂNCTON EM UM CÓRREGO URBANO

Resumo : O conhecimento das especies zooplanctonicas tem sido um poderoso instrumento para avaliar modificacoes nos ecossistemas aquaticos, os quais sao submetidos a grandes impactos causados pelas atividades antropicas. A distribuicao e estrutura do zooplâncton em ecossistemas de agua doce sao influenciadas pelo tipo de habitat e pela estabilidade no ambiente. Este rapido inventario tem como objetivo analisar a comunidade zooplanctonica que caracteriza o corrego Santa Maria do Leme no municipio de Sao Carlos, SP a fim de complementar a avaliacao da qualidade da agua e detectar os efeitos de ambientes loticos sobre esta comunidade. Foram registradas as medidas da temperatura da agua, pH, condutividade e oxigenio dissolvido. O zooplâncton foi amostrado com rede de plâncton (68 µm). As amostras foram fixadas com formol na concentracao final 4% e os organismos foram identificados e contados, calculando-se entao a densidade e os indices de diversidade, dominância e equitabilidade. Foram identificadas 18 especies, sendo que para Protozoa e Meroplâncton foi registrada a maior riqueza (seis especies cada); para Rotifera registrou-se tres especies, Cladocera (duas especies) e Copepoda (um taxon). A analise da comunidade zooplanctonica entre os pontos no corrego Santa Maria do Leme revelou um padrao diferenciado na abundância e diversidade de especies, sendo a densidade e a riqueza de especies maiores no ponto P1. Os protozoarios e rotiferos dominaram tanto em termos de riqueza quanto de densidade. O micro-habitat proporcionado pela instabilidade dos locais garantiu uma maior quantidade de materia orgânica em suspensao, favorecendo o microzooplâncton. Palavras-chave : Corrego urbano. Degradacao. Diversidade de especies.
[IGFBP-2 mRNA expression in gastric cancer tissues and its roles in proliferation, differentiation and peritoneal metastasis of gastric cancer].

OBJECTIVE To detect the expression of IGFBP-2 mRNA in gastric cancer tissues and its roles in neoplasia and peritoneal metastasis of gastric cancer. METHODS The IGFBP-2 mRNA expression levels in the fresh tissues from normal mucosa, primary cancer and peritoneal metastasis of 35 patients with gastric cancer were determined by the quantitative real time RT-PCR method, and the samples were sliced up and stained with hematoxylin-eosin for pathologyical examination. RESULTS The levels of IGFBP-2 mRNA expression in gastric primary cancer tissues were significantly higher than those in the tissues from normal mucosa and peritoneal metastasis (P<0.05). Yet, IGFBP-2 mRNA expression levels showed no difference between the tissues of normal mucosa and peritoneal metastasis (P>0.05). CONCLUSION The expression of IGFBP-2 mRNA possibly plays an important role in proliferation, differentiation and peritoneal metastasis of gastric cancer, and it might be useful in a new method for clinical prognostication and treatment of gastric cancer peritoneal metastasis.
Enhanced expression of a transmembrane phosphotyrosine phosphatase (LAR) in keratoconus cultures and corneas.

The purpose of the study was to identify genes that are differentially expressed in normal versus keratoconus corneas. Total RNA isolated from corneal stromal cell cultures was reverse-transcribed and then amplified by the polymerase chain reaction (PCR) using defined, arbitrary primers. The products were displayed on polyacrylamide gels and bands that were differentially expressed were excised, re-amplified and subcloned. The resulting clones were sequenced and utilized as probes for Northern blots with cultured cell RNA or Southern blots of corneal cDNA. One of the products that appeared to be more highly expressed in keratoconus cultures and corneas displayed 100% homology with leukocyte common antigen related protein (LAR), a transmembrane phosphotyrosine phosphatase. Western analyses and immunohistochemistry with monoclonal and/or polyclonal antibodies to LAR were used to examine keratocyte cultures and fresh frozen normal, keratoconus and pseudophakic bullous corneas. We identified a gene product with 100% homology to LAR that is expressed at the RNA level in keratoconus corneas and cell cultures but is found only at low or undetectable levels in normal cultures and normal and pseudophakic bullous keratopathy (PBK) corneas. By Western blotting and immunofluorescence with specific LAR antibodies, the protein was identified in keratoconus stromal cell cultures but not in normal cultures. When fresh frozen tissue was examined, LAR protein was localized to numerous stromal cells throughout central keratoconus corneas, while no central staining was seen in normal or bullous keratopathy corneas. LAR, a transmembrane phosphotyrosine phosphatase, is more highly expressed in keratoconus corneas and stromal cell cultures as demonstrated by differential display, Northern analyses, immunohistochemistry and Western blotting.
Redesign of thresher machine for farmers using rapid upper limb assessment (RULA) method

The use of thresher machines for threshing rice plants helped farmers in improving agricultural productivity. However, thresher machine design that is currently available has not fairly concerned on the working position and posture of the farmers using it. The working position that was modeled by farmers when operating a thresher machine tent to cause injury because of the dimensions of the engine and the body of farmers that did not conform to each other. RULA method was one of the methods that could analyze work postures. From the results of the data collection and the process using RULA method, it was clear that the measures that had to be taken to the thresher machines which used to be available were promptly modified in order to avoid musculoskeletal problem. Improvements that could be undertaken to avoid the musculoskeletal problem on farmers who used the thresher machine were redesigning the thresher machine based on farmers working posture. One of these ways was by adjusting the dimensions of the farmers' body with the dimensions of the machine. In addition, the use of adjustable concept in the design could probably assist the farmers adjust the working position with the machinery they used.
The Interplay of Aesthetics, Usability and Credibility in Mobile Websites and the Moderation by Culture

The relationships between aesthetics, usability and credibility have been widely investigated in human-computer interaction (HCI). However, in the mobile domain, limited empirical evidence exists showing the interplay among these three constructs and the role culture plays. To address this, we carried out a survey on four systematically designed mobile websites among 233 subjects from Canada and Nigeria, which belong to low- and high-context cultures respectively. Using path modeling, we investigated the relationships among the perceptions of these three HCI constructs and the possible differences that exist between the two cultures. Our results show: 1) it is the perception of aesthetics that predominantly drives the judgment of mobile web credibility at the global and subgroup levels, with the effect size being greater for the Canadian group than for the Nigerian group; 2) the direct effect of aesthetics on usability is moderated by culture, with the magnitude being stronger for the Nigerian group than for the Canadian group; and 3) our models explain 29-83% of the variance of credibility.
Modeling and Evaluation of a Twist Drive Actuator for Soft Robotics

Robotic technology is widening its scope into applications where robots coexist with humans and other living beings in a common space, and where cooperative and other physical interactions between the robots and the living beings are anticipated and actually occur. Safety of living beings and of robots in such an environment calls for solutions in robot mechanisms that are different from the recently used ones in industrial robotics. In this paper we present an actuator named a Twist Drive, which uses two strings that by twisting on each other generate a pulling force. The mechanism can be used to replace gear reducers in robot joints with benefits that originate in its muscle-like operation and in its nonlinear characteristics. A mathematical model to describe the kinematic transmission characteristics of the mechanism is presented and compared to experimental data. A passive characteristic of kinematic stiffness is discussed and evaluated in the paper. Experimental results show the adequacy of the proposed models. Durability of commercially available strings was tested and the results reported. Application in a robot's joint is briefly presented by an example.
Influence of Simulation Parameters on the Excitable Media Behaviour – The Case of Turbulent Mixing

© 2012 Ionescu, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Influence of Simulation Parameters on the Excitable Media Behaviour – The Case of Turbulent Mixing
Clinicopathological features of small nonfunctioning pancreatic neuroendocrine tumors.

AIM To present our experiences in studying the clinicopathological features of small nonfunctioning pancreatic neuroendocrine tumors (NF-pNETs). METHODS The subjects included 9 patients with NF-pNETs who underwent pancreatectomy between April 1996 and September 2012. The surgical procedure, histopathological findings, and prognosis were assessed. RESULTS All tumors were incidentally detected by computed tomography. The median diameter was 10 mm (5-32 mm). One patient was diagnosed with von Hippel-Lindau disease, and the others were sporadic cases. For the histopathological findings, 7 patients were G1; 1 patient was G2; and 1 patient, whose tumor was 22 mm, had neuroendocrine carcinoma (NEC). One patient who had a tumor that was 32 mm had direct invasion to a regional lymph node and 1 patient with NEC, had regional lymph node metastases. Six of the 7 patients with sporadic NF-pNETs, excluding the patient with NEC, had tumors that were smaller than 10 mm. Tumors smaller than 10 mm showed no malignancy and lacked lymph node metastasis. CONCLUSION Sporadic NF-pNETs smaller than 10 mm tend to have less malignant potential. These findings suggest that lymphadenectomy may be omitted for small NF-pNETs after further investigation.
Hypoxic Preconditioning and Hypoxic‐Ischemic Brain Damage in the Immature Rat: Pathologic and Metabolic Correlates

Abstract: It has been reported that immature rats subjected to cerebral hypoxia‐ischemia sustain less brain damage if they are previously exposed to systemic hypoxia compared with animals not exposed to prior hypoxia. Accordingly, neuropathologic and metabolic experiments were conducted to confirm and extend the observation that hypoxic preconditioning protects the perinatal brain from subsequent hypoxic‐ischemic brain damage. Six‐day postnatal rats were subjected to systemic hypoxia with 8% oxygen at 37°C for 2.5 h. Twenty‐four hours later, they were exposed to unilateral cerebral hypoxia‐ischemia for 2.5 h, produced by unilateral common carotid artery ligation and systemic hypoxia with 8% oxygen. Neuropathologic analysis, conducted at 30 days of postnatal age, indicated a substantial reduction in the severity of brain damage in the preconditioned rats, such that only 6 of 14 such animals exhibited cystic infarction, but all 13 animals without prior preconditioning exhibited infarction (p < 0.001). Measurement of cerebral glycolytic and tricarboxylic acid intermediates and high‐energy phosphate reserves at the terminus of and at 4 and 24 h following hypoxia‐ischemia showed no differences in the extent of alterations in the preconditioned and nonpreconditioned immature rats. A difference was seen in the restitution of high‐energy stores during the first 24 h of recovery from hypoxia‐ischemia, with a more optimal preservation of these metabolites in the preconditioned animals, reflecting the less severe ultimate brain damage. Accordingly, the neuroprotection afforded to the preconditioned animals was not the result of any differences in the extent of anaerobic glycolysis, tissue acidosis, or depletion in high‐energy reserves during hypoxia‐ischemia but rather the result of other mechanisms that improved the metabolic status of the immature brain during the early hours of reperfusion following hypoxia‐ischemia.
Reduction Strategies and Geochemical Characterization of Lithic Assemblages: A Comparison of Three Case Studies from Western North America

Based on a simple model of lithic procurement, reduction, and use, we generate predictions for patterns in source diversity and average distance-to-source measurements for flaked stone assemblages left behind by small-scale and residentially mobile populations. We apply this model to geochemical data from obsidian artifacts from three regions in western North America. As predicted, results show markedly different patterns in the geochemical composition of small flakes, large flakes, and formal tools. While small flakes and tools tend to have greater source diversity and are on average farther from their original source, the large flake assemblage is composed of fewer and closer sources. These results suggest that a failure to include very late stage reduction (e.g., pressure flakes) and microdebitage in characterization studies may bias interpretations about the extent of residential mobility and/or trade patterns because more distant sources will be underrepresented.
Artifacts in Wiener Kernels Estimated Using Gaussian White Noise

Wiener's nonlinear system identification theory characterizes a system function with a set of kernels of integrals. One method of determining these Wiener kernels is the cross-correlation technique proposed by Lee and Schetzen, which uses Gaussian white noise as the input to the unknown system. Because a test stimulus is only an approximation of infinitely long Gaussian white noise, it is possible that artifacts are generated during the estimation of the kernels. To help identify and characterize these artifacts, Wiener kernel estimates for two simple nonlinear model systems were made using a pseudorandom Gaussian white noise sequence. The results showed that because of the approximation of a Gaussian distribution, artifacts appear in the estimated kernels due to a form of aliasing. These artifacts can be reduced by increasing the sequence length of the input noise.
Nonrandom Distribution of Pseudomonas aeruginosa and Staphylococcus aureus in Chronic Wounds

ABSTRACT The spatial organization of Pseudomonas aeruginosa and Staphylococcus aureus in chronic wounds was investigated in the present study. Wound biopsy specimens were obtained from patients diagnosed as having chronic venous leg ulcers, and bacterial aggregates in these wounds were detected and located by the use of peptide nucleic acid-based fluorescence in situ hybridization and confocal laser scanning microscopy (CLSM). We acquired CLSM images of multiple regions in multiple sections cut from five wounds containing P. aeruginosa and five wounds containing S. aureus and measured the distance of the bacterial aggregates to the wound surface. The distance of the P. aeruginosa aggregates to the wound surface was significantly greater than that of the S. aureus aggregates, suggesting that the distribution of the bacteria in the chronic wounds was nonrandom. The results are discussed in relation to our recent finding that swab culturing techniques may underestimate the presence of P. aeruginosa in chronic wounds and in relation to the hypothesis that P. aeruginosa bacteria located in the deeper regions of chronic wounds may play an important role in keeping the wounds arrested in a stage dominated by inflammatory processes.
[Perforin, granzyme and granulysin association to kill intracellular parasites].

Perforine, granzyme et granulysine : un trio de choc inducteur de la microptose parasitaire Hind Chamkha1*, Xia Li1*, Guillaume Rouvet1,2*, Jerome Thiery3 1 M1 Biologie Sante, Universite Paris-Saclay, 91405 Orsay, France ; 2 Ecole normale superieure de Cachan ; 3 Inserm UMR 1186, immunologie integrative des tumeurs, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94800 Villejuif, France. * Ces trois auteurs ont participe egalement a la redaction de cette Nouvelle. hind.chamkha@u-psud.fr, xia.li@u-psud.fr guillaume.rouvet@ens-cachan.fr jerome.thiery@gustaveroussy.fr
Normal development and effects of neonatal infraorbital nerve damage upon the innervation of the trigeminal brainstem complex by primary afferent fibers containing calcitonin gene‐related peptide

Immunocytochemistry was used to study the normal development and response to infraorbital nerve (ION) damage of the innervation of the trigeminal (V) brainstem complex by axons recognized by an antibody directed against calcitonin gene‐related peptide (CGRP). CGRP‐like immunoreactivity (CGRPLI) was present in axons that occupied the outer V spinal tract (TrV) at all levels of the V brainstem complex. Almost no fibers terminated within V nucleus principalis (PrV), out there was dense CGRPLI in the supratrigeminal nucleus. There was also very little CGRPLI within rostral V subnucleus oralis (SpO). However, in the caudal one‐half of the nucleus, a dense elongated patch of immunoreactivity was consistently present just medial to TrV. Only occasional CGRP‐positive axons could be seen within V subnucleus interpolaris (SpI), but the paratrigeminal nucleus contained dense immunoreactivity. Trigeminal subnucleus caudalis (SpC) also contained CGRPLI that was very dense in lamina I and the outer portion of lamina II. Scattered terminals were also present in layers III and IV and dense terminal clusters were in lamina V. CGRP‐immunoreactive neurons were present in the V ganglion by embryonic (E‐) day 16 and immunoreactive axons could be seen in the V brainstem complex on E–17. At birth, CGRP‐positive axons in the V brainstem complex had achieved a distribution very similar to that in adult rats. The major difference between the patterns of labelling in neonates and adults was the presence of relatively large numbers of CGRP‐positive fibers in ventral PrV and SpO of the former animals. The disappearance of these fibers was completed by the middle of the third postnatal week. Transection of the ION on the day of birth had little effect upon CGRP in SpO, SpI, and SpC, but it did result in an increase in CGRP‐positive fibers in PrV ipsilateral to the damaged nerve. When considered together with previous findings, these results suggest that CGRP‐positive axons express this peptide well after they have entered the V brainstem complex and that the central terminal field of these fibers is not substantially altered by a manipulation which results in the death of nearly 60% of all V primary afferent neurons. © 1992 Wiley‐Liss, Inc.
NLOS Signal detection algorithm for TDOA method in wireless sensor network

In this paper, the iteration localization algorithm that NLOS signal is iteratively removed to get the exact location in the wireless sensor network is proposed. To evaluate the performance of the proposed algorithm, TDOA location estimation method is used, and readers are located on every 150m intervals with rectangular shape in 300m×300m searching field. In that searching field, the error distance is analyzed according to increasing the number of iteration, sub-blink and the estimated sensor node locations which are located in the iteration range. From simulation results, the error distance is diminished according to increasing the number of the sub-blink and iteration with the proposed location estimation algorithm in NLOS environment. Therefore, we confirm that, to get more exact location information in wireless sensor network in NLOS environments, the proposed location estimation algorithm removing NLOS signal effects through iteration scheme is suitable.
Principles in building spiritual assessment tools

Fivebasicprinciplesshouldbeconsideredwhen creatinga spiritual assessment tool to beusedby amultidisciplinaryhospiceteam.Beforediscussing them,however,it is importantto addressthe relationshipbetween spiritual issuesand religious/nonreligious beliefs. The assessment processgetsbadlymuddledwhenthis relationshipis not clear. Somehospiceteammembershave been known to function as though spiritualandreligiousrealitiesweresynonymous.Accordingly, somenonreligiousmembersincludethe concept of a spiritualdimensionto life in their rejectionof religion. Otherswho are religiousrejectthe possibilityof non-
New insight into abnormal prion protein using monoclonal antibodies.

Studies of abnormal prion protein (PrPres) are hindered by the lack of specific monoclonal antibodies (mAbs), and the relationships between PrPres, infectivity, and strain specificity in prion diseases are still subject to debate. We have studied PrPres with new mAbs produced against PrP in mice using various immunization strategies. PrPres was analyzed by Western blot with different prion strains in various hosts. Differences in the electrophoretic pattern of human PrPres revealed by these antibodies provide new insight into PrPres cleavage by proteases and interpretation of strain typing. This study confirms that the N-terminal extremity of PrPres is differentially sensitive to proteases. Conversely, the C-terminal extremity, which resists proteolysis, seems to be abnormally detectable by antibodies in ultrastructural studies. This work confirms the highly complex role of PrPres in prion diseases and provides new tools which will be made available to facilitate progress in qualitative and quantitative studies of PrP.
An evaluation of maternal cell contamination in cultures of chorionic villi for the prenatal diagnosis of chromosome abnormalities

Culture of chorionic villus cells provides a method of obtaining chromosomes of excellent quality for first trimester prenatal diagnosis. Concern exists that maternal cells present in the biopsy may contaminate the culture and lead to misdiagnosis. This study has confirmed that karyotypes obtained from female villus cultures were non‐maternal by establishing the presence of paternal markers using Q‐ and C‐banding. Male cultures were harvested serially to investigate the possibility of maternal cell overgrowth. Of 82 successful cultures investigated, 37 were male and 45 female and of the males 4 contained a mixture of male and female cells. Thorough dissection of the material is essential if maternal cell contamination is to be mininimised. The use of heteromorphic chromosome markers to establish that fetal cells have grown provides valuable reassurance.