Miracle-dz/UniFAR-FTUs huggingface dataset:
Structures of HLA-A*1101 Complexed with Immunodominant Nonamer and Decamer HIV-1 Epitopes Clearly Reveal the Presence of a Middle, Secondary Anchor Residue1

HLA-A*1101 is one of the most common human class I alleles worldwide. An increased frequency of HLA-A*1101 has been observed in cohorts of female sex workers from Northern Thailand who are highly exposed to HIV-1 and yet have remained persistently seronegative. In view of this apparent association of HLA-A*1101 with resistance to acquisition of HIV-1 infection, and given the importance of eliciting strong CTL responses to control and eliminate HIV-1, we have determined the crystal structure of HLA-A*1101 complexed with two immunodominant HIV-1 CTL epitopes: the nonamer reverse transcriptase(313–321) (AIFQSSMTK) and decamer Nef(73–82) (QVPLRPMTYK) peptides. The structures confirm the presence of primary anchor residues P2-Ile/-Val and P9-/P10-Lys, and also clearly reveal the presence of secondary anchor residues P6-Ser for reverse transcriptase and P7-Met for Nef. The overall backbone conformation of both peptides is defined as two bulges that are separated by a more buried middle residue. In this study, we discuss how this topology may offer functional advantages in the selection and presentation of HIV-1 CTL epitopes by HLA-A*1101. Overall, this structural analysis permits a more accurate definition of the peptide-binding motif of HLA-A*1101, the characterization of its antigenic surface, and the correlation of molecular determinants with resistance to HIV-1 infection. These studies are relevant for the rational design of HLA-A*1101-restricted CTL epitopes with improved binding and immunological properties for the development of HIV-1 vaccines.
Neovascularization of the Xenopus embryo

The receptor tyrosine kinase, Flk‐1 or VEGFR‐2, and its ligand, vascular endothelial growth factor (VEGF) are required for the development of the embryonic vasculature. Targeted disruption of either gene in mice results in the failure of vascular system formation. The Xenopushomologues of flk‐1 and VEGF have been cloned and their expression has been examined throughout early embryonic development. These studies indicate that flk‐1 is expressed in groups of endothelial precursor cells which will form the major blood vessels of the embryo, including the posterior cardinal veins, the dorsal aorta, the vitelline veins, and the endocardium. VEGF expression is found in tissues adjacent to the mesenchyme containing the flk‐1‐ expressing endothelial precursors. Expression of both flk‐1 and VEGF is transient, appearing as the primary vascular plexus is forming and declining steadily after the onset of functional embryonic circulation. After establishment of the primary vascular structures, flk‐1 expression is also observed in the intersegmental veins which form by an angiogenic mechanism. Overall, these results support a role for VEGF/flk‐1 signaling in both vasculogenesis and angiogenesis in the Xenopus embryo. When VEGF is expressed ectopically in Xenopus embryos by microinjection of either plasmid DNA or synthetic mRNA, large, disorganized vascular structures are produced. This result indicates that ectopic VEGF is capable of altering the architecture of the developing vascular network. Dev. Dyn. 1997;210:66–77. © 1997 Wiley‐Liss, Inc.
Searching through time in the New York Times HCIR Challenge 2010

In this paper we describe the Time Explorer, an application designed for analyzing how news changes over time. We extend on current time-based systems in several important ways. First, Time Explorer is designed to help users discover how entities such as people and locations associated with a query change over time. Second, by searching on time expressions extracted automatically from text, the application allows the user to explore not only how topics evolved in the past, but also how they will continue to evolve in the future. Finally, Time Explorer is designed around an intuitive interface that allows users to interact with time and entities in a powerful way. While aspects of these features can be found in other systems, they are combined in Time Explorer in a way that allows searching through time in no time at all.
Resposta ovariana de cabras submetidas a implantes de progesterona seguidos de aplicações de gonadotrofina coriônica equina

The objective of the present study was to compare the effect of different dosages of equine chorionic gonadotrophin (eCG) on the follicular dynamics and hormonal concentrations in Alpine goats. During the breeding season, the goats were submitted to estrous and ovulation synchronization with a device containing progesterone for 14 days. Female goats (n=24) were divided at random into four groups of 6 animals each. On the day of dispositive removal, the animals received 0 (Control), 200, 300 and 400 UI of eCG. Follicular development was observed by ultrasonography one day prior to administration of eCG until next ovulation. The plasma estradiol (E2) and progesterone (P4) concentrations were daily determined using RIA. All treated animals showed estrous. Estrous cycle with three and four waves of follicular growth were observed. Size of the largest follicle was smaller in control group animals of the third wave (5.5 ± 0.50 mm) when compared to those treated with 300 UI of eCG (7.17 ± 0.35 mm). Gonadotrophin increased the number of small and medium follicles considering the control group because the average number of corpora lutea were higher in 400 UI (4.27 ± 0.23) females than those treated with 200 UI (1.95 ± 0.19). Plasma concentrations of progesterone and stradiol showed differences among experimental groups. Combinations among progesterones and eCG is an adequate alternative for estrus synchronization and support the development of new protocols for reproduction techniques as superovulation and embryo transfer in goats.
A case study of implementing home appliance middleware on Linux and Java

This paper describes a case study of implementing a home appliance that enables us to control it via HTTP. The appliance been has implemented by using the Java language, and runs on Linux. The combination enables us to build the home appliance very cheaply. We present the implementation of our current prototype of a Web-based home appliance, and show how the combination of Java and Linux has reduced the development cost dramatically.
Influência do Genótipo e do Sexo Sobre o Valor Hematócrito em Galinhas Reprodutoras Pesadas

The objective of this research was to evaluate the effect of the genotype and sex on the value of meat-type chicken hematocrit (percentage packed cells volume). One hundred and eighty breeders of 18 experimental genotypes were used. Individual samples of blood were collected and the percentage packed cells volume was determined. For the factor genotype, it was possible to distinguish two different groups with averages changing from 45,83 to 41,69% and 41,24 to 37,21%. For sex, the values showed significant difference with values of 46,20 ± 4,14% for males and 35,74 ± 3,16% for females. In conclusion the genotype and sex influenced the hematocrit value in meat-type chickens, above to cluster every genotypes in two groups.
Functional properties, developmental regulation, and chromosomal localization of murine connexin36, a gap‐junctional protein expressed preferentially in retina and brain

Retinal neurons of virtually every type are coupled by gap‐junctional channels whose pharmacological and gating properties have been studied extensively. We have begun to identify the molecular composition and functional properties of the connexins that form these ‘electrical synapses,’ and have cloned several that constitute a new subclass (γ) of the connexin family expressed predominantly in retina and brain. In this paper, we present a series of experiments characterizing connexin36 (Cx36), a member of the γ subclass that was cloned from a mouse retinal cDNA library. Cx36 has been localized to mouse chromosome 2, in a region syntenic to human chromosome 5, and immunocytochemistry showed strong labeling in the ganglion cell and inner nuclear layers of the mouse retina. Comparison of the developmental time course of Cx36 expression in mouse retina with the genesis of the various classes of retinal cells suggests that the expression of Cx36 occurs primarily after cellular differentiation is complete. Because photic stimulation can affect the gap‐junctional coupling between retinal neurons, we determined whether lighting conditions might influence the steady state levels of Cx36 transcript in the mouse retina. Steady‐state levels of Cx36 transcript were significantly higher in animals reared under typical cyclic‐light conditions; exposure either to constant darkness or to continuous illumination reduced the steady‐state level of mRNA approximately 40%. Injection of Cx36 cRNA into pairs of Xenopus oocytes induced intercellular conductances that were relatively insensitive to transjunctional voltage, a property shared with other members of the γ subclass of connexins. Like skate Cx35, mouse Cx36 was unable to form heterotypic gap‐junctional channels when paired with two other rodent connexins. In addition, mouse Cx36 failed to form voltage‐activated hemichannels, whereas both skate and perch Cx35 displayed quinine‐sensitive hemichannel activity. The conservation of intercellular channel gating contrasts with the failure of Cx36 to make hemichannels, suggesting that the voltage‐gating mechanisms of hemichannels may be distinct from those of intact intercellular channels. J. Neurosci. Res. 59:813–826, 2000 © 2000 Wiley‐Liss, Inc.
Annotation: an Investigative Survey of Annotation Types and Systems

Annotation plays a important role in our daily life and study. Mostly documents exist in digital format on the web, people spends a large amount of their time on searching the web browsers for looking useful information. This is the unidirectional interaction with user.Annotations grow geometrically because of the reflections on documents shown by different writers and with their writing time. Firstly we have introduced the history of the annotation then some research related work done in the annotation results. Annotation can be done for the Web, java, pdf, text, xps (XML Paper Specification), mobile, image, multimedia etc. We focus on the survey to see the use of annotation in different areas along with the usage in different scenarios. In Information research for decision making and integrating an annotation database can be founded on the parameters such as document, user and time. Website which supports annotation systems, provide user friendly interfaces, easy-to-use structural and layout annotation functions.Web database helps to generate query result pages or search result records based on a user's query. Automatic extraction of the data from such query result pages is very important for different applications, such as data integration, meta querying cooperates with multiple web databases.Researchers have shown the many approaches to develop and implement web annotation systems.Our attention is toanalyse the annotation and need in web databases to improve a search result research.
Signal to interference performance for a TDMA portable radio link

The authors present measurement and simulation results of signal-to-interference ratio performance for a time-division multiple-access (TDMA) portable radio link The radio link transmits short TDMA bursts of only 82 symbols at 450 kb/s using 4-QAM (quadrature amplitude modulation). Demodulation is performed by a low-overhead digital coherent demodulator with two-branch selection diversity. The measured performance of the link is compared with the simulation results using word error ratio as a criterion. The results are also compared with signal-to-noise performance. To simulate the effect of portable movement, the measurements have been performed for several different fading rates. Desired and interfering TDMA burst signals were subjected to independent Rayleigh fading on two diversity branches. <<ETX>>
An approach to sensor fault diagnosis based on fully-decoupled parity equation and parameter estimation

An approach for multiple sensor faults diagnosis is presented. Fully-decoupled parity equations and parameters estimation are combined in this method. The residual generated from a fully-decoupled parity equation is sensitive to a special sensor fault and decoupled from all other sensor faults. The faults in sensors are represented as biases and changes in scale factor. A parameter estimator based on a Kalman filter is designed to identify biases and changes in scale factor from the information contained in the residuals. The fully-decoupled parity vectors, which are designed to detect and isolate sensor faults, are generated in various conditions, and their existence condition is given. A simulation example on a linear airplane model is given for illustration.
Specification and development of an equalizer-demodulator for wideband digital microwave radio signals

The authors describe the specification and implementation of a sophisticated digital signal processor to be used for equalizing and demodulating high-rate, high-order quadrature-amplitude-modulated (QAM) signals used in digital radio systems. The processor uses state-of-the-art algorithms as well as the latest high-speed CMOS VLSI technology to achieve a processing rate in excess of 10 gigamultiply/adds per second. The system exhibits several unique features; in particular, 40 Mband signals can be processed with 64-tap equalizer and the functions of baud and carrier recovery are implemented digitally. The signal processing problems to be solved are described, and from them a set of requirements is developed. A summary of the algorithms needed to recover symbol timing, equalize the incoming signals, and remove carrier offset is provided. A brief discussion of the hardware tradeoffs is followed by a detailed description of the system design. <<ETX>>
THE EFFICACY OF PACKAGING MATERIALS IN REDUCING MICROBIAL CONTAMINATION IN READY-TO-EAT STREET VENDED FRIED FISH AND SUBSEQUENT CONSUMER PERCEPTION

Street vending of ready-to-eat (RTE) food is an important source of livelihood accounting for the employment of millions of people who are poor, unskilled and have limited formal education (Bino, 2006). Despite the susceptibility of fish to microbial infestation, vendors sell the unpackaged RTE products in the open street market thereby exposing consumers to pathogens. This study was purposed to test for Salmonella, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes and Total Viable Counts in vended fried fish namely “Changu”, “Tafi” and “Una” from twelve street vendors in Kilifi, Bamburi and Ukunda. Secondly, to evaluate the efficacies of three packaging materials in suppressing bacterial contamination in RTE street vended fried fish and thirdly, to evaluate consumer perception on packaged street vended fish. Fried fish were sampled from open markets for four successive days and tested alongside packaged control samples from same processed batches. Another set of samples under three different packaging treatments were kept at the open market and tested for bacterial growth. Then a consumer survey was carried out to establish public perception on packaging RTE open market vended fish. TVC recorded up to 7.14x105 CFU/g, total coliforms and faecal coliforms recorded above 2400 MPN/100g while E. coli and S. aureus counts in Ukunda and Bamburi were elevated beyond the microbiological quality limits for RTE food. Packaging pouches arbitrarily coded PK1, PK2 and PK3 extended fish eating quality for two days by suppressing microbial growth. Consumers embraced the need for packaging RTE street vended fried fish and appreciated the financial implications involved. Key Words: Ready-To-Eat fish, Microbial contamination in fish, Fish packaging material.
Risk Identification Method for Cloud Computing Safety based on LSA-GCC and LSA-SAM

This paper proposes a generalized cluster risk evaluation model by applying a data mining method to the cloud computing risk evaluation. The model maps data sets into a semantic space via singular value decomposition (SVD), uses a clustering algorithm to classify them and to extract the prototype vector of a particular category from clustering results, and assigns a definite weight to each category so as to set up an initial prototype vector model. The model is taken as the basis for risk evaluation of information system. After the data to be evaluated were mapped to the same semantic space, they are calculated with the prototype vector of each category, so as to obtain the similarity of the category, and the cumulative sum of the similarity with the weight of the corresponding category comes out. Finally, a mean value is calculated to obtain the risk value of the data to be evaluated, namely, the risk value of the occasion when the data is obtained. In this paper, the safety risk information is obtained from the operating system log and Web application server log of a virtual host; the Latent Semantic Analysis-based Generalized Cluster Classifier (LSA-GCC) is adopted and the MapReduce-based LSA-GCC and LSASAM parallel acceleration experiment is conducted. The experimental results show that in a cloud computing environment of large-scale parallel processing, the method used in this paper can identify the log events of a cloud computing system and conduct risk prompt rapidly.
Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome*

We report the first proteomic analysis of the SLP76 interactome in resting and activated primary mouse mast cells. This was made possible by a novel genetic approach used for the first time here. It consists in generating knock-in mice that express signaling molecules bearing a C-terminal tag that has a high affinity for a streptavidin analog. Tagged molecules can be used as molecular baits to affinity-purify the molecular complex in which they are engaged, which can then be studied by mass spectrometry. We examined first SLP76 because, although this cytosolic adapter is critical for both T cell and mast cell activation, its role is well known in T cells but not in mast cells. Tagged SLP76 was expressed in physiological amounts and fully functional in mast cells. We unexpectedly found that SLP76 is exquisitely sensitive to mast cell granular proteases, that Zn2+-dependent metalloproteases are especially abundant in mast cells and that they were responsible for SLP76 degradation. Adding a Zn2+ chelator fully protected SLP76 in mast cell lysates, thereby enabling an efficient affinity-purification of this adapter with its partners. Label-free quantitative mass spectrometry analysis of affinity-purified SLP76 interactomes uncovered both partners already described in T cells and novel partners seen in mast cells only. Noticeably, molecules inducibly recruited in both cell types primarily concur to activation signals, whereas molecules recruited in activated mast cells only are mostly associated with inhibition signals. The transmembrane adapter LAT2, and the serine/threonine kinase with an exchange factor activity Bcr were the most recruited molecules. Biochemical and functional validations established the unexpected finding that Bcr is recruited by SLP76 and positively regulates antigen-induced mast cell activation. Knock-in mice expressing tagged molecules with a normal tissue distribution and expression therefore provide potent novel tools to investigate signalosomes and to uncover novel signaling molecules in mast cells.
Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale

Abstract Mucorales (Zygomycota) are ubiquitous, morphologically simple terrestrial fungi that are united taxonomically by possession of a coenocytic mycelium upon which nonmotile mitotic spores are produced asexually in uni-to multispored sporangia, and zygospores, where known, are produced following fusion of sexually compatible hyphae. Here we report the first comprehensive phylogenetic analysis of essentially all genera of Mucorales (63 species, 54 genera and 13 families) based on partial nucleotide sequence data of nuclear small subunit (18S) ribosomal RNA and nuclear large subunit (28S) ribosomal RNA genes, translation elongation factor-1α gene exons, and a morphological data set consisting of 1826, 389, 1092 and 11 characters, respectively. Individual and combined data sets were analyzed by unequally weighted maximum parsimony (MP) to investigate evolutionary relationships among and within mucoralean families. A Micromucor—Umbelopsis clade, traditionally included in the Mortierellaceae, was identified as the basal sister-group to all other Mucorales. A major discovery of this study is that traditional family-level classification schemes for this order appear to be highly artificial as evidenced by polyphyly of four of the seven families containing two or more genera. As presently circumscribed, these four families include 83% of the Mucorales. In addition, the largest and best known genera, Mucor and Absidia, were resolved as polyphyletic. The results provide a robust phylogenetic framework for additional evolutionary studies of the Mucorales.
Polarizing activity, Sonic hedgehog, and tooth development in embryonic and postnatal mouse

Tooth development involves reciprocal epithelial‐mesenchymal interactions, polarized growth, mesenchyme condensation, and complex morphogenetic events. Because these processes bear similarities to those occurring in the developing limb, we asked whether morphogenetic signals found in the limb also occur in the developing tooth. We grafted mouse embryo tooth germs to the anterior margin of host chick embryo wing buds and determined whether the dental tissues had polarizing activity. Indeed, the grafts induced supernumerary digits. Activity of both molar and incisor tooth germs increased from bud to cap stages and was maximal at late bell stage in newborn. With further development the polarizing activity began to decrease, became undetectable in adult molar mesenchyme but persisted in incisor mesenchyme, correlating with the fact that incisors grow throughout postnatal life while molars do not. When different portions of neonatal incisors were assayed, a clear proximo‐distal gradient of activity was apparent, with maximal activity restricted to the most proximal portion where undifferentiated mesenchyme and enamel organ reside. In situ hybridizations demonstrated that prior to induction of supernumerary digits, the tooth germ grafts induced expression in host tissue of Hoxd‐12 and Hoxd‐13. In addition, whole‐mount in situ hybridizations and immunohistochemistry showed that developing tooth germs express Sonic hedgehog (Shh). Shh expression was first detected in bud stage tooth germs; at later stages Shh transcripts were prominent in enamel knot and differentiating ameloblasts at the cuspal region. We concluded that tooth germs possess polarizing activity and produce polarizing factors such as Shh. As in the limb, these factor(s) and activity probably play key roles in establishing polarity and regulating morphogenesis during early tooth development. Given its subsequent association with differentiating ameloblasts, Shh probably participates also in cytogenetic events during odontogenesis. © 1996 Wiley‐Liss, Inc.