Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate Binding Protein SBP2 of a Putative ABC Transporter as a Novel Vaccine Antigen of Moraxella catarrhalis

ABSTRACT Moraxella catarrhalis is a common respiratory tract pathogen that causes otitis media in children and infections in adults with chronic obstructive pulmonary disease. Since the introduction of the pneumococcal conjugate vaccines with/without protein D of nontypeable Haemophilus influenzae, M. catarrhalis has become a high-priority pathogen in otitis media. For the development of antibacterial vaccines and therapies, substrate binding proteins of ATP-binding cassette transporters are important targets. In this study, we identified and characterized a substrate binding protein, SBP2, of M. catarrhalis. Among 30 clinical isolates tested, the sbp2 gene sequence was highly conserved. In 2 different analyses (whole-cell enzyme-linked immunosorbent assay and flow cytometry), polyclonal antibodies raised to recombinant SBP2 demonstrated that SBP2 expresses epitopes on the bacterial surface of the wild type but not the sbp2 mutant. Mice immunized with recombinant SBP2 showed significantly enhanced clearance of M. catarrhalis from the lung compared to that in the control group at both 25-μg and 50-μg doses (P < 0.001). We conclude that SBP2 is a novel, attractive candidate as a vaccine antigen against M. catarrhalis.
A tool for construction of stochastic spatio-temporal models assimilated with observational data

A framework and a software tool has been developed to execute two important steps in the model development cycle of temporal numerical models simulating geographic change using rules of cause and effect. The first step supported by the tool is the software implementation of spatio- temporal models. This can be done with the tool by combining generic operations on 2D map and 3D block data in an iterative script structure included in the standard Python programming language. The second step supported by the tool is the optimisation of models using the methods of genetic algorithms and particle filters. A number of case study models is presented to illustrate how the tool works.
Population Structure of the Relapsing Fever Spirochete Borrelia hermsii as Indicated by Polymorphism of Two Multigene Families That Encode Immunogenic Outer Surface Lipoproteins

ABSTRACT The tick-borne relapsing fever spirochete Borrelia hermsii evades the mammalian immune system by periodically switching expression among members of two multigene families that encode immunogenic, antigenically distinct outer surface proteins. The type strain, B. hermsii HS1, has at least 40 complete genes and pseudogenes that participate in this multiphasic antigenic variation. Originally termed vmp (for variable major protein) genes, they have been reclassified as vsp(for variable small protein) and vlp (for variable large protein) genes, based on size and amino acid sequence similarities. To date, antigenic variation in B. hermsiihas been studied only in the type strain, HS1. Nucleotide sequence comparisons of 23 B. hermsii HS1 genes revealed five distinct groups, the vsp gene family and four subfamilies of vlp genes. We used PCR with family- and subfamily-specific primers, followed by restriction fragment length polymorphism analysis, to compare the vspand vlp repertoires of HS1 and seven other B. hermsii isolates from Washington, Idaho, and California. This analysis, together with pulsed-field gel electrophoresis genome profiles, revealed that the eight isolates formed three distinct groups, which likely represent clonal lineages. Members of the three groups coexisted in the same geographic area, but they could also be isolated across large geographical distances. This population structure may result from immune selection by the host, as has been proposed for other pathogens with polymorphic antigens.
On the multiple unicast capacity of 3-source, 3-terminal directed acyclic networks

We consider a directed acyclic network with unit-capacity edges and n source-terminal (s<sub>i</sub> - t<sub>i</sub>) pairs that wish to communicate at unit rate via network coding. The connectivity between the s<sub>i</sub>-t<sub>i</sub> pairs is quantified by means of a connectivity level vector, [k<sub>1</sub> k<sub>2</sub> . k<sub>n</sub>] such that there exist k<sub>i</sub> edge-disjoint paths between s<sub>i</sub> and t<sub>i</sub>. In this work we attempt to classify networks based on the connectivity level. Specifically, for case of n = 3, and a given connectivity level vector [k<sub>1</sub> k<sub>2</sub> k<sub>3</sub>], we aim to either present a constructive network coding scheme or an instance of a network that cannot support the desired rate. Certain generalizations for the case of higher n have also been found.
Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease

Hirschsprung disease (HSCR) is a congenital malformation of the hindgut resulting from a disruption of neural crest cell migration during embryonic development. It has a complex genetic aetiology with several genes involved in its pathogenesis. PHOX2B plays a key function in the development of neural crest derivatives, and heterozygous mutations cause a complex dysautonomia associating HSCR, Congenital Central Hypoventilation Syndrome (CCHS) and neuroblastoma (NB) in various combinations. In order to determine the role of PHOX2B in isolated HSCR, we performed a mutational screening in a cohort of 207 Spanish HSCR patients. Our most relevant finding has been the identification of a de novo and novel deletion (c.393_410del18) in a patient with HSCR. Results of in silico and functional assays support its pathogenic effect related to HSCR. Therefore our results support that PHOX2B loss-of-function is a rare cause of HSCR phenotype.
Somatic INK4a‐ARF locus mutations: A significant mechanism of gene inactivation in squamous cell carcinomas of the head and neck

The INK4a‐ARF locus is located on human chromosome 9p21 and is known to encode two functionally distinct tumor‐suppressor genes. The p16INK4a (p16) tumor‐suppressor gene product is a negative regulator of cyclin‐dependent kinases 4 and 6, which in turn positively regulate progression of mammalian cells through the cell cycle. The p14ARF tumor‐suppressor gene product specifically interacts with human double minute 2, leading to the subsequent stabilization of p53 and G1 arrest. Previous investigations analyzing the p16 gene in squamous cell carcinomas of the head and neck (SCCHNs) have suggested the predominate inactivating events to be homozygous gene deletions and hypermethylation of the p16 promoter. Somatic mutational inactivation of p16 has been reported to be low (0–10%, with a combined incidence of 25 of 279, or 9%) and to play only a minor role in the development of SCCHN. The present study examined whether this particular mechanism of INK4a/ARF inactivation, specifically somatic mutation, has been underestimated in SCCHN by determining the mutational status of the p16 and p14ARF genes in 100 primary SCCHNs with the use of polymerase chain reaction technology and a highly sensitive, nonradioactive modification of single‐stranded conformational polymorphism (SSCP) analysis termed “cold” SSCP. Exons 1α, 1β, and 2 of INK4a/ARF were amplified using intron‐based primers or a combination of intron‐ and exon‐based primers. A total of 27 SCCHNs (27%) exhibited sequence alterations in this locus, 22 (22%) of which were somatic sequence alterations and five (5%) of which were a single polymorphism in codon 148. Of the 22 somatic alterations, 20 (91%) directly or indirectly involved exon 2, and two (9%) were located within exon 1α. No mutations were found in exon 1β. All 22 somatic mutations would be expected to yield altered p16 proteins, but only 15 of them should affect p14ARF proteins. Specific somatic alterations included microdeletions or insertions (nine of 22, 41%), a microrearrangement (one of 22, 5%), and single nucleotide substitutions (12 of 22, 56%). In addition, we analyzed the functional characteristics of seven unique mutant p16 proteins identified in this study by assessing their ability to inhibit cyclin‐dependent kinase 4 activity. Six of the seven mutant proteins tested exhibited reduced function compared with wild‐type p16, ranging from minor decreases of function (twofold to eightfold) in four samples to total loss of function (29‐ to 38‐fold decrease) in two other samples. Overall, somatic mutation of the INK4a/ARF tumor suppressor locus, resulting in functionally deficient p16 and possibly p14ARF proteins, seems to be a prevalent event in the development of SCCHN. Mol. Carcinog. 30:26–36, 2001. © 2001 Wiley‐Liss, Inc.
A Comparative Study of Parallel Prefix Adders in FPGA Implementation of EAC

Several regular parallel trees have been proposed over the years to optimize logic depth, area, fan-out and in- terconnect count for logic circuits. In this paper, we propose a comparative study of different parallel prefix trees used in the design of a new end-around carry (EAC) adder targeting FPGA technology. This new adder is based on the fast 128-bit binary floating-point EAC adder which has been implemented in the IBM POWER6 microprocessor's fused multiply-add unit. The parallel prefix tree implemented on the IBM's EAC adder is a Kogge-Stone tree which has been chosen for its high performance and its low power consumption. Our comparative study highlights the main performance differences among fourteen different architecture configurations when targeting an FPGA EAC adder design. We focus on the area requirements and the critical path delay of these designs. Our experimental results show that there is one architecture configuration with the lower area requirement and the higher performance.
Treedy: A Heuristic for Counting and Sampling Subsets

Consider a collection of weighted subsets of a ground set N. Given a query subset Q of N, how fast can one (1) find the weighted sum over all subsets of Q, and (2) sample a subset of Q proportionally to the weights? We present a tree-based greedy heuristic, Treedy, that for a given positive tolerance d answers such counting and sampling queries to within a guaranteed relative error d and total variation distance d, respectively. Experimental results on artificial instances and in application to Bayesian structure discovery in Bayesian networks show that approximations yield dramatic savings in running time compared to exact computation, and that Treedy typically outperforms a previously proposed sorting-based heuristic.
Noise injection into inputs in sparsely connected Hopfield and winner-take-all neural networks

In this paper, we show that noise injection into inputs in unsupervised learning neural networks does not improve their performance as it does in supervised learning neural networks. Specifically, we show that training noise degrades the classification ability of a sparsely connected version of the Hopfield neural network, whereas the performance of a sparsely connected winner-take-all neural network does not depend on the injected training noise.
Modeling surfaces of arbitrary topology using manifolds

Manifolds describe complicated objects that are locally $\Re\sp{n}$ by defining a set of overlapping maps from the object to $\Re\sp{n}$. In this thesis we present a general technique for inverting that process: we define a complicated object from a set of overlapping subsets of $\Re\sp{n}$. We first present a constructive definition that describes how to perform such a construction in general. We then apply this construction to the particular problem of defining surfaces of arbitrary topology. The surface is built in two steps: we build a manifold with the correct topology then embed the manifold into $\Re\sp3$ using traditional spline techniques. The surface inherits many of the properties of B-splines: local control, a compact representation, and guaranteed continuity of arbitrary degree. The surface is specified using a polyhedral control mesh instead of a rectangular one; the resulting surface approximates the polyhedral mesh much as a B-spline approximates its rectangular control mesh. Like a B-spline, the surface is a single, continuous object.
Understanding the Physiological Demands of Netball: a time-motion investigation

The purpose of the present time-motion analysis study was to gain greater understanding of physiological demands placed on netball players during competition. Six players for 3 positional groups were analysed; Centre (C), Goal Shooter (GS) and Goal Keeper (GK). Players were individually filmed throughout three 60 minute English Superleague matches. Game footage was replayed and coded into six different movement activities using a computerised analysis system (Sportscode, Australia). The frequency, duration and percentage match time spent performing each activity, as well as work to rest (W:R) ratios were calculated. Electronic timing gates (Newtest Powertimer, Finland) were used to calculate players speed in each activity and subsequently the distances travelled were estimated. C (7984 ± 767m) travelled significantly further than GS and GK (4210 ± 477m and 4283 ± 261m, respectively; p<0.01 and p<0.01). C also had significantly higher W:R ratios (1:1.9) than GS and GK (1: 4.5 and 1: 2.9, respectively; p<0.01, and p=0.01, respectively). The intermittent nature of netball was highlighted with players changing activity every 4.1s. Collectively the results have implications for designing position specific training programmes with regard to aerobic and anaerobic conditioning, agility and speed development.
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor

The dynamics of α‐amylase inhibitors has been investigated using molecular dynamics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based on a coarse‐grained single‐site‐per‐residue model with a single‐parameter harmonic potential between sufficiently close (r ≤ 7 Å) residue pairs. The major difference between the GNM and the ANM is that no directional preferences can be obtained in the GNM, all residue fluctuations being theoretically isotropic, while ANM does incorporate directional preferences. The dominant modes of motions are identified by (i) the singular value decomposition (SVD) of the MD trajectory matrices, and (ii) the similarity transformation of the Kirchhoff matrices of inter‐residue contacts in the GNM or ANM. The mean‐square fluctuations of individual residues and the cross‐correlations between domain movements retain the same characteristics, in all approaches—although the dispersion of modes and detailed amplitudes of motion obtained in the ANM conform more closely with MD results. The major weakness of the analytical approaches appears, on the other hand, to be their inadequacy to account for the anharmonic motions or multimeric transitions driven by the slowest collective mode observed in MD. Such motions usually suffer, however, from MD sampling inefficiencies, and multiple independent runs should be tested before making conclusions about their validity and detailed mechanisms. Overall this study invites attention to (i) the robustness of the average properties (mean‐square fluctuations, cross‐correlations) controlled by the low frequency motions, which are invariably reproduced in all approaches, and (ii) the utility and efficiency of the ANM, the computational time cost of which is of the order of “minutes” (real time), as opposed to “days” for MD simulations. Proteins 2000;40:512–524. © 2000 Wiley‐Liss, Inc.
Under Consideration for Publication in J. Functional Programming Higher-order Functions for Parsing *

In combinator parsing, the text of parsers resembles BNF notation. We present the basic method, and a number of extensions. We address the special problems presented by white– space, and parsers with separate lexical and syntactic phases. In particular, a combining form for handling the " offside rule " is given. Other extensions to the basic method include an " into " combining form with many useful applications, and a simple means by which combinator parsers can produce more informative error messages.
On the number of cycles in a graph

Abstract There is a sizable literature on investigating the minimum and maximum numbers of cycles in a class of graphs. However, the answer is known only for special classes. This paper presents a result on the smallest number of cycles in Hamiltonian 3-connected cubic graphs. Further, it describes a proof technique that could improve an upper bound of the largest number of cycles in a Hamiltonian graph.
American surgery: an illustrated history

by the horrors Dean so lavishly catalogues, and overkill and compassion fatigue soon set in. The account of the psychological sequelae of the war and their clinical treatment is absorbing, but sheds little light on modem problems. It is unclear whether Dean commends or deplores the harshness with which so many of these cases were handled; unclear, too, as the book progresses, whether comparison between two disparate eras serves any real purpose. A full-length study of the American Civil War in its own psychological terms, rather than through the "lens of Vietnam", might have been more valuable. In a field as slippery as military psychiatry, comparisons across time have always been hazardous; yet something about Vietnam-the long tradition of rhetorical excess, perhapsdrives scholars to make them. Jonathan Shay's much mocked invocation of the Trojan war in his Achilles in Vietnam (1992) did at least shed light on the importance of rites of absolution in re-integrating warriors into society; whereas Dean's seemingly more sensible excursion back to the 1860s pays smaller dividends. Simpler comparisons-say, with Australian soldiers' adjustment after Vietnam-are presumably too obvious to attract publishers.
Expression Invariant Face Recognition using a 3D Morphable Model

c) Normalized Expression normalisation for two scans of the same individual. The robust fitting gives a good estimate (b) of the true face surface given the noisy mea- surement (a). It fills in holes and removes artifacts using prior knowledge from the face model. The pose and expression normalized faces (c) are used for face recognition.
Gang-GC: Locality-aware Parallel Data Placement Optimizations for Key-Value Storages

Many cloud applications rely on fast and non-relational storage to aid in the processing of large amounts of data. Managed runtimes are now widely used to support the execution of several storage solutions of the NoSQL movement, particularly when dealing with big data key-value store-driven applications. The benefits of these runtimes can however be limited by modern parallel throughput-oriented GC algorithms, where related objects have the potential to be dispersed in memory, either in the same or different generations. In the long run this causes more page faults and degradation of locality on system-level memory caches. We propose, Gang-CG, an extension to modern heap layouts and to a parallel GC algorithm to promote locality between groups of related objects. This is done without extensive profiling of the applications and in a way that is transparent to the programmer, without the need to use specialized data structures. The heap layout and algorithmic extensions were implemented over the Parallel Scavenge garbage collector of the HotSpot JVM\@. Using microbenchmarks that capture the architecture of several key-value stores databases, we show negligible overhead in frequent operations such as the allocation of new objects and improvements to the access speed of data, supported by lower misses in system-level memory caches. Overall, we show a 6\% improvement in the average time of read and update operations and an average decrease of 12.4\% in page faults.
Methods of recommender system: A review

There are number of users and items in any type of recommender system. There are numerous information on internet and so many visitors on websites which add some challenges for generating recommender system. A recommender system extracts the user preferences or interests from the related data sets so there is low information overload. Therefore, new recommendation system is required which will provide more quality recommendations for huge data sets. So, for these types of issues we have discovered several techniques of recommendation techniques which are three types such as: Content-based filtering, Collaborative filtering and Hybrid filtering. This paper also analyzes different algorithms in each type of recommender system.
Low Power 8 x 8 Bit CMOS Multiplier Using 65 nm Technology

This paper presents low power 8x8 bit multipliers which are implemented with Tanner Tool v13.0 at 500MHz frequency with 65nm technology which is having a supply voltage 1.0v. There are different CMOS multiplier circuits are analyzed names as Braun multiplier, Wallace tree multiplier, Row bypass Braun multiplier, Column bypass Braun multiplier, Row and Column bypass Braun multiplier and these multiplier are realized using bridge style full adder with semi domino logic . All these multipliers are compared in terms of delay, power dissipation and power delay product. Simulation results show that the Braun multiplier with using bridge style adder with semi domino logic has minimum power delay product and is faster as compared to other CMOS multipliers.
Cryosectioning distortion reduction using tape support

Distortion due to tissue sectioning is a major hurdle in 3D reconstruction; tape support (Ullberg, 1977) offers a possible solution. With this approach a transparent tape is placed on the exposed block-face prior to collecting each section. The tape supports the tissue during the cutting process. To evaluate the efficacy of tape support, we measured the cutting-induced distortion when collecting sections using two such products, 3M tape and Instrumedics Tape Windows, and compared the results to the traditional method employing an antiroll device.
Transdermal testosterone may improve ovarian response to gonadotrophins in low-responder IVF patients: a randomized, clinical trial.

BACKGROUND Studies in macaques have indicated that androgens have some synergistic effects with FSH on folliculogenesis. This study investigated the usefulness of pretreatment with transdermal testosterone in low-responder IVF patients. METHODS Randomized clinical trial including 62 infertile women who had a background of the first IVF treatment cycle cancelled because of poor follicular response. Patients were randomized in two treatment groups in their second IVF attempt. In patients in Group 1 (n = 31), transdermal application of testosterone preceding standard gonadotrophin ovarian stimulation under pituitary suppression was used. In Group 2 (n = 31 patients), ovarian stimulation was carried out with high-dose gonadotrophin in association with a minidose GnRH agonist protocol. The primary end-point was the incidence of low-responder patients. The main secondary outcome was the incidence of patients reaching ovum retrieval. RESULTS The percentage of cycles with low response was significantly lower in Group 1 than in Group 2 (32.2 versus 71% 95% confidence interval for the difference, 15.7-61.6; P < 0.05). The number of patients with ovum retrieval tended to be higher in Group 1 than in Group 2 (80.6 versus 58.1% P = 0.09), the difference reaching statistical significance (81.2 versus 41.1%; P < 0.05) when only patients having normal basal FSH levels (16 and 17 patients in Groups 1 and 2, respectively) were considered. CONCLUSIONS Pretreatment with transdermal testosterone may improve the ovarian sensitivity to FSH and follicular response to gonadotrophin treatment in previous low-responder IVF patients. This approach leads to an increased follicular response compared with a high-dose gonadotrophin and minidose GnRH agonist protocol.