Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of a Flagellar Export Locus of Helicobacter pylori

ABSTRACT Motility of Helicobacter species has been shown to be essential for successful colonization of the host. We have investigated the organization of a flagellar export locus in Helicobacter pylori. A 7-kb fragment of the H. pylori CCUG 17874 genome was cloned and sequenced, revealing an operon comprising an open reading frame of unknown function (ORF03), essential housekeeping genes (ileS and murB), flagellar export genes (fliI and fliQ), and a homolog to a gene implicated in virulence factor transport in other pathogens (virB11). A promoter for this operon, showing similarity to the Escherichia coli ς70 consensus, was identified by primer extension. Cotranscription of the genes in the operon was demonstrated by reverse transcription-PCR, and transcription of virB11, fliI, fliQ, andmurB was detected in human or mouse biopsies obtained from infected hosts. The genetic organization of this locus was conserved in a panel of H. pylori clinical isolates. EngineeredfliI and fliQ mutant strains were completely aflagellate and nonmotile, whereas a virB11 mutant still produced flagella. The fliI and fliQ mutant strains produced reduced levels of flagellin and the hook protein FlgE. Production of OMP4, a member of the outer membrane protein family identified in H. pylori 26695, was reduced in both thevirB11 mutant and the fliI mutant, suggesting related functions of the virulence factor export protein (VirB11) and the flagellar export component (FliI).
Improving Dependency Parsers with Supertags

Transition-based dependency parsing systems can utilize rich feature representations. However, in practice, features are generally limited to combinations of lexical tokens and part-of-speech tags. In this paper, we investigate richer features based on supertags, which represent lexical templates extracted from dependency structure annotated corpus. First, we develop two types of supertags that encode information about head position and dependency relations in different levels of granularity. Then, we propose a transition-based dependency parser that incorporates the predictions from a CRF-based supertagger as new features. On standard English Penn Treebank corpus, we show that our supertag features achieve parsing improvements of 1.3% in unlabeled attachment, 2.07% root attachment, and 3.94% in complete tree accuracy.
GENETIC‐ENVIRONMENTAL INTERACTIONS IN PHYSICAL GROWTH

Abstract. Variability in stature among young children is often ascribed to health and nutrition differences in malnourished populations and to genetic differences in well‐nourished populations. Hence, it was hypothesized that parent‐child correlations in malnourished Guatemalan populations would be markedly lower than those reported for European samples. Instead, it was found that parent‐child and sibling correlations were similar in both kinds of populations. The simplest interpretation of these results is that variability in stature among malnourished children is as much a reflection of genetic differences as in developed nations. However, explanations can also be advanced which would attribute the higher than expected correlations to the environment. For instance, it could be that socioeconomic and nutritional status is correlated across generations. In other words, parents who had relatively better conditions as children are more likely to provide a better environment for their children. Consequently, the relative contribution of genetics and environment to variability in height is still unsettled. Nonetheless, it appears that variability in body size in malnourished populations, regardless of the relative importance of its causes, is a useful indicator of health and nutrition.
Root lifting techniques and applications to list decoding

Motivatived by Guruswami and Rudra's construction of folded Reed-Solomon codes, we give algorithms to solve functional equations of the form Q(x, f(x), f(x)) = 0, where Q is a trivariate polynomial. We compare two approaches, one based on Newton's iteration and the second using relaxed series techniques.
Cross layer multi QoS metric routing for multimedia traffic in 802.11E over MANETs

To support QoS for a multimedia traffic, IEEE 802.11e standard Enhanced distributed channel access (EDCA) has been proposed. However, the EDCA is more focused on providing quality of service(QoS) solution at the MAC layer, which is necessary, but perhaps not sufficient as the layered TCP stack architecture does not satisfy the QoS demands in ad hoc network. This is due to the fact that routing protocol is responsible for the successful packet delivery and QoS Support. The conventional single scalar routing protocols are not suitable for high traffic QoS sensitive multimedia traffic load on Mobile ad Hoc Networks (MANETs). The paper proposes a Cross layer Multimetric link disjoint Multipath Routing (CMMR) protocol based on distinct QoS constraints. The paper uses cross-layer communications to consider multiple layer metrics like MAC queue utilization, node density degree, and mobility factor to achieve channel state awareness and keep the up to date status of the route in terms of QOS proficiency at each intermediate node. The proposed algorithm is validated with an extensive simulation with high real time traffic using NS3. The results show significant improvement of CMMR in terms of packet delivery, and end-to-end delay.
Endogenous sex hormones and endometrial cancer risk in women in the European Prospective Investigation into Cancer and Nutrition (EPIC)

Epidemiological data show that reproductive and hormonal factors are involved in the etiology of endometrial cancer, but there is little data on the association with endogenous sex hormone levels. We analyzed the association between prediagnostic serum concentrations of sex steroids and endometrial cancer risk in the European Prospective Investigation into Cancer and Nutrition using a nested case–control design of 247 incident endometrial cancer cases and 481 controls, matched on center, menopausal status, age, variables relating to blood collection, and, for premenopausal women, phase of menstrual cycle. Using conditional regression analysis, endometrial cancer risk among postmenopausal women was positively associated with increasing levels of total testosterone, free testosterone, estrone, total estradiol, and free estradiol. The odds ratios (ORs) for the highest versus lowest tertile were 2.66 (95% confidence interval (CI) 1.50–4.72; P=0.002 for a continuous linear trend) for estrone, 2.07 (95% CI 1.20–3.60; P=0.001) for estradiol, and 1.66 (95% CI 0.98–2.82; P=0.001) for free estradiol. For total and free testosterone, ORs for the highest versus lowest tertile were 1.44 (95% CI 0.88–2.36; P=0.05) and 2.05 (95% CI 1.23–3.42; P=0.005) respectively. Androstenedione and dehydroepiandrosterone sulfate were not associated with risk. Sex hormone-binding globulin was significantly inversely associated with risk (OR for the highest versus lowest tertile was 0.57, 95% CI 0.34–0.95; P=0.004). In premenopausal women, serum sex hormone concentrations were not clearly associated with endometrial cancer risk, but numbers were too small to draw firm conclusions. In conclusion, relatively high blood concentrations of estrogens and free testosterone are associated with an increased endometrial cancer risk in postmenopausal women.
An American founder mutation in MLH1

Mutations in the mismatch repair genes cause Lynch syndrome (LS), conferring high risk of colorectal, endometrial and some other cancers. After the same splice site mutation in the MLH1 gene (c.589‐2A>G) had been observed in four ostensibly unrelated American families with typical LS cancers, its occurrence in comprehensive series of LS cases (Mayo Clinic, Germany and Italy) was determined. It occurred in 10 out of 995 LS mutation carriers (1.0%) diagnosed in the Mayo Clinic diagnostic laboratory. It did not occur among 1,803 cases tested for MLH1 mutations by the German HNPCC consortium, while it occurred in three probands and an additional five family members diagnosed in Italy. In the U.S., the splice site mutation occurs on a large (∼4.8 Mb) shared haplotype that also harbors the variant c.2146G>A, which predicts a missense change in codon 716 referred to here as V716M. In Italy, it occurs on a different, shorter shared haplotype (∼2.2 Mb) that does not carry V716M. The V716M variant was found to be present by itself in the U.S., German and Italian populations with individuals sharing a common haplotype of 280 kb, allowing us to calculate that the variant arose around 5,600 years ago (225 generations; 95% confidence interval 183–272). The splice site mutation in America arose or was introduced some 450 years ago (18 generations; 95% confidence interval 14–23); it accounts for 1.0% all LS in the Unites States and can be readily screened for.
Sp3/REST/HDAC1/HDAC2 Complex Represses and Sp1/HIF-1/p300 Complex Activates ncx1 Gene Transcription, in Brain Ischemia and in Ischemic Brain Preconditioning, by Epigenetic Mechanism

The Na+-Ca2+ exchanger 1 (NCX1) is reduced in stroke by the RE1-silencing transcription factor (REST), whereas it is increased in ischemic brain preconditioning (PC) by hypoxia-inducible factor 1 (HIF-1). Because ncx1 brain promoter (ncx1-Br) has five putative consensus sequences, named Sp1A–E, for the specificity protein (Sp) family of transcription factors (Sp1–4), we investigated the role of this family in regulating ncx1 transcription in rat cortical neurons. Here we found that Sp1 is a transcriptional activator, whereas Sp3 is a transcriptional repressor of ncx1, and that both bind ncx1-Br in a sequence-specific manner, modulating ncx1 transcription through the Sp1 sites C–E. Furthermore, by transient middle cerebral artery occlusion (tMCAO) in rats, the transcriptional repressors Sp3 and REST colocalized with the two histone-deacetylases (HDACs) HDAC1 and HDAC2 on the ncx1-Br, with a consequent hypoacetylation. Contrarily, in PC+tMCAO the transcriptional activators Sp1 and HIF-1 colocalized with histone acetyltransferase p300 on ncx1-Br with a consequent hyperacetylation. In addition, in neurons silenced with siRNA of NCX1 and subjected to oxygen and glucose deprivation (OGD) (3 h) plus reoxygenation (RX) (24 h), the neuroprotection of Class I HDAC inhibitor MS-275 was counteracted, whereas in neurons overexpressing NCX1 and subjected to ischemic preconditioning (PC+OGD/RX), the neurotoxic effect of p300 inhibitor C646 was prevented. Collectively, these results demonstrate that NCX1 expression is regulated by the Sp3/REST/HDAC1/HDAC2 complex in tMCAO and by the Sp1/HIF-1/p300 complex in PC+tMCAO and that epigenetic intervention, by modulating the acetylation of ncx1-Br, may be a strategy for the development of innovative therapeutic intervention in stroke.
User population and user contributions to virtual publics: a systems model

This paper provides a comprehensive review of empirical research into user contributions to computer-mediated discourse in public cyber-spaces, referred to here as virtual publics. This review is used to build a systems model of such discourse. The major components of the model are i) critical mass, ii) social loafing, and iii) the collective impact of individual cognitive constraints on the processing of group messages. By drawing these three components into a single model it becomes possible to describe the shape of a “user-contributions/user-population function” after controlling for context. Virtual publics can be created with the support of various technologies including email, newsgroups, webbased bulletin boards etc. Traditionally the choice of technology platform and the way it is used has largely depended on arbitrary factors. This paper suggests that choices of this nature can be based on knowledge about required segmentation points for discourse as they relate to a particular type of technology. This is because the “user-contributions/user-population function” will map differently to different classes of technology. Similarly the different classes of technologies used to enable virtual publics will each have different stress zones at which users will experience information overload resulting from computer mediated discourse.
All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.
A Novel Image Signature Method for Content Authentication

We proposed an image signature method for content authentication, which applies a hierarchical approach to construct an image signature. In the first level, DWT and DCT are used to extract image features; then these features are encrypted by using sub-keys that are generated by a cryptographically hash function. In the second level, Karhunen–Loeve transformation is used to reduce the signature length. The main features of the proposed method are as follows: (i) It achieves a trade-off between robustness and tampering sensitivity. (ii) It provides a tool for image tampering detection and tampering localization. (iii) It can be used to detect the thumbnail of the large image to improve detection efficiency. (iv) It provides the compact signature, and the signature length is independent of the image size. Experimental results show that proposed method is robust for content-preserving manipulations such as JPEG compression, adding noise, filtering and Gamma correction, etc.
Antimicrobial and Barrier Properties of Bovine Gelatin Films Reinforced by Nano TiO2

The effects of nano titanium dioxide incorporation were investigated on the water vapor permeability, oxygen permeability, and antimicrobial properties of bovine gelatin films. The nano TiO 2 (TiO2- N) was homogenized by sonication and incorporated into bovine gelatin solutions at different concentrations (e.g. 1, 2, 3, and 5% w/w of dried gelatin). The permeability of the films to water vapor and oxygen was significantly decreased by incorporating of low concentration TiO2-N to gelatin solutions. TiO2-N gelatin films showed an excellent antimicrobial activity against Staphylococcus aureus and Escherichia coli. These properties suggest that TiO2-N has the potential as filler in gelatin-based films for using as an active packaging materials in pharmaceutical and food packaging industries.
Robust Fusion of Multiband Images With Different Spatial and Spectral Resolutions for Change Detection

Archetypal scenarios for change detection generally consider two images acquired through sensors of the same modality. However, in some specific cases such as emergency situations, the only images available may be those acquired through different kinds of sensors. More precisely, this paper addresses the problem of detecting changes between two multiband optical images characterized by different spatial and spectral resolutions. This sensor dissimilarity introduces additional issues in the context of operational change detection. To alleviate these issues, classical change detection methods are applied after independent preprocessing steps (e.g., resampling) used to get the same spatial and spectral resolutions for the pair of observed images. Nevertheless, these preprocessing steps tend to throw away relevant information. Conversely, in this paper, we propose a method that more effectively uses the available information by modeling the two observed images as spatial and spectral versions of two (unobserved) latent images characterized by the same high spatial and high spectral resolutions. As they cover the same scene, these latent images are expected to be globally similar except for possible changes in sparse spatial locations. Thus, the change detection task is envisioned through a robust multiband image fusion method, which enforces the differences between the estimated latent images to be spatially sparse. This robust fusion problem is formulated as an inverse problem, which is iteratively solved using an efficient block-coordinate descent algorithm. The proposed method is applied to real panchromatic, multispectral, and hyperspectral images with simulated realistic and real changes. A comparison with state-of-the-art change detection methods evidences the accuracy of the proposed strategy.
A voting stereo matching method for real-time obstacle detection

Depth from stereo is one of the most active research areas in the computer vision field. The heavily investigated problem in stereo approaches is the matching between two or more images of a scene observed, by two or more video cameras, from different viewpoints. It consists of identifying features in the left and right images that are projections of the same physical feature in the three-dimensional world. This paper presents a real-time stereo matching method using a voting schema. The correspondence problem is first mapped onto a two-dimensional matrix, called matching matrix, where each element represents a possible match between two features extracted from the left and right images. Local and global constraints are then used to search the true elements of the matching matrix, which represent compatible matches. The valid elements are determined by applying the local constraints. Global constraints are used to define the voting rules between the valid elements. The voting based-method is evaluated for real-time obstacle detection in front of a moving car using linear stereo vision.
Privacy-Preserving Mechanisms for Crowdsensing: Survey and Research Challenges

Crowdsensing (CS) is a new data collection paradigm based on the willingness of people to utilize their mobile devices to sense and transmit data of interest. Given the large amount of cellular users, mobile sensor networks will be able to collect enough data to address large-scale societal problems in a fast, easy, and cost-effective manner. One important issue in CS is that of privacy; without appropriate privacy-preserving mechanisms, many users will not be willing to participate in the data collection process. This paper presents the state-of-the-art in privacy-preserving mechanisms for CS systems. After a general description of CS systems and their main components, this paper addresses the most important issues to consider in the design, implementation, and evaluation of privacy-preserving mechanisms. Then, following a new taxonomy, the most important mechanisms available in the literature are described and qualitatively evaluated. Finally, this paper presents research challenges that should be addressed in order to improve the performance of future privacy-preserving mechanisms for CS systems.
Thermal conversion of solid wastes and biomass.

This 49 chapter book contains papers presented at a symposium on energy recovery from thermal conversion of solid wastes and agricultural and forestry residues. There are 9 sections which cover the worldwide status of pyrolysis, gasification, and liquefaction processes. Separate abstracts of each chapter have been prepared for inclusion in the Energy Data Base.
Neighborhood Social Cohesion and Disorder in Relation to Walking in Community-Dwelling Older Adults

Objectives: To examine the role of neighborhood social conditions and walking in community-dwelling older adults. Methods: A multi-level analysis of data from 4,317 older adults (mean age = 74.5; 73% black) from a geographically-defined urban community. Participants completed structured interviews including 14 questions on neighborhood conditions and self-reported walking. The neighborhood questions were summarized into individual-level measures of perceived neighborhood social cohesion and disorder. These measures were aggregated by neighborhood to construct neighborhood-level measures of social cohesion and disorder. Results: Neighborhood-level disorder, but not social cohesion, was significantly associated with walking, independent individual-level neighborhood perceptions and other correlates of walking. Further adjustment for race weakened this association to a marginally significant level. Discussion: Neighborhood conditions may shape walking behavior in older adults, especially conditions that reflect physical neglect or social threat. Promotion of walking behavior in older adults may require improvement of the safety and upkeep of the neighborhood environment.
Community-level micronutrient fortification of a food supplement in India: a controlled trial in preschool children aged 36-66 mo.

BACKGROUND Children participating in the Integrated Child Development Service (ICDS) in India have high rates of iron and vitamin A deficiency. OBJECTIVE The objective was to assess the efficacy of a premix fortified with iron and vitamin A and added at the community level to prepared khichdi, a rice and dal mixture, in increasing iron and vitamin A stores and decreasing the prevalence of iron deficiency, anemia, and vitamin A deficiency. DESIGN This cluster, randomized, double-blind, controlled trial was initiated in 30 Anganwadi centers (daycare centers) in West Bengal state, India. Children aged 36-66 mo (n = 516) attending village-based ICDS centers were randomly assigned to receive either a fortified or a nonfortified premix for 24 wk. Blood was drawn at 0 and 24 wk by venipuncture for the measurement of hemoglobin, serum ferritin, and serum retinol. RESULTS The change in the hemoglobin concentration of anemic children was significantly different between fortified and nonfortified khichdi groups (P < 0.001). Prevalence rates of anemia, iron deficiency, and iron deficiency anemia were significantly lower after 24 wk in the fortified-khichdi group than in the nonfortified-khichdi group (P < 0.001). There were no significant differences in serum retinol concentrations or in the prevalence of vitamin A deficiency between the fortified- and nonfortified-khichdi groups. CONCLUSION A premix fortified with iron, vitamin A, and folic acid and added to supplementary food at the community level can be effective at increasing iron stores and reducing the prevalence of iron deficiency and anemia.
Stress-Induced Characteristics of Silicon-on-Insulator Rib Waveguides

In this paper the influence of stress induced effect in the most popular Silicon-on-Insulator (SOI) small rib waveguide is analysed. Birefringence-free condition and the influence of the top oxide cladding are investigated and appropriate design rules for this type of SOI waveguides are presented.