Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities

ABSTRACT Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequencies, especially those representing yet-uncultured taxa, which include the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms isolated directly from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community's metabolic potential.
University of Huddersfield Repository Extracting Spatio-temporal Texture Signatures for Crowd Abnormality Detection

—In order to achieve automatic prediction and warning of hazardous crowd behaviors, a Spatio-Temporal Volume (STV) analysis method is proposed in this research to detect crowd abnormality recorded in CCTV streams. The method starts from building STV models using video data. STV slices – called Spatio-Temporal Textures (STT) - can then be analyzed to detect crowded regions. After calculating the Gray Level Co-occurrence Matrix (GLCM) among those regions, abnormal crowd behavior can be identified, including panic behaviors and other behavioral patterns. In this research, the proposed STT signatures have been defined and experimented on benchmarking video databases. The proposed algorithm has shown a promising accuracy and efficiency for detecting crowd-based abnormal behaviors. It has been proved that the STT signatures are suitable descriptors for detecting certain crowd events, which provide an encouraging direction for real-time surveillance and video retrieval applications.
Efficient Probabilistic Classification Vector Machine With Incremental Basis Function Selection

Probabilistic classification vector machine (PCVM) is a sparse learning approach aiming to address the stability problems of relevance vector machine for classification problems. Because PCVM is based on the expectation maximization algorithm, it suffers from sensitivity to initialization, convergence to local minima, and the limitation of Bayesian estimation making only point estimates. Another disadvantage is that PCVM was not efficient for large data sets. To address these problems, this paper proposes an efficient PCVM (EPCVM) by sequentially adding or deleting basis functions according to the marginal likelihood maximization for efficient training. Because of the truncated prior used in EPCVM, two approximation techniques, i.e., Laplace approximation and expectation propagation (EP), have been used to implement EPCVM to obtain full Bayesian solutions. We have verified Laplace approximation and EP with a hybrid Monte Carlo approach. The generalization performance and computational effectiveness of EPCVM are extensively evaluated. Theoretical discussions using Rademacher complexity reveal the relationship between the sparsity and the generalization bound of EPCVM.
High rates of acute stress disorder impact quality-of-life outcomes in injured adolescents: mechanism and gender predict acute stress disorder risk.

BACKGROUND Injury is the leading cause of death and functional disability in adolescent children. Little is known about quality of life and psychological outcomes after trauma in adolescents. The Trauma Recovery Project in Adolescents is a prospective epidemiologic study designed to examine multiple outcomes after major trauma in adolescents aged 12 to 19 years, including quality of life (QoL) and psychological sequelae such as acute stress disorder (ASD) and posttraumatic stress disorder (PTSD). The specific objectives of the present report are to examine ASD rates and the association of ASD with QoL outcomes in injured adolescents. METHODS Between April 26, 1999, and November 13, 2002, 401 eligible trauma patients aged 12 to 19 years triaged to five participating trauma center hospitals in a regionalized trauma system were enrolled in the study. The admission criteria for patients were as follows: (1) age 12 to 19 years and (2) injury diagnoses excluding severe traumatic brain injury (TBI) or spinal cord injury. QoL after trauma was measured using the Quality of Well-being (QWB) scale, a sensitive and well-validated functional index (range, 0 = death to 1.000 = optimum functioning). ASD (before discharge) was diagnosed with the Impact of Events Scale-Revised. Scores of 24+ were used to diagnose ASD. Patient outcomes were assessed at discharge and at 3, 6, 12, 18, and 24 months after discharge. RESULTS ASD before discharge was diagnosed in 40% of adolescent trauma survivors. ASD status was associated with large QoL deficits during follow-up, as follows: 3-month, ASD-positive QWB score = 0.667 vs. ASD-negative QWB score = 0.710, p < 0.01; 6-month, ASD-positive QWB score = 0.704 vs. ASD-negative QWB score = 0.742, p < 0.001; 12-month: ASD-positive QWB score = 0.718 vs. ASD-negative QWB score = 0.757, p < 0.01; 24-month, ASD-positive QWB score = 0.725 vs. ASD-negative QWB score = 0.769, p < 0.01. Female sex and violent mechanism predicted ASD risk (47% female vs. 36% male; odds ratio, 1.6; p < 0.05; violence 54% vs. 38%; odds ratio, 1.9; p < 0.01). CONCLUSIONS Adolescent trauma survivors have high rates of ASD. ASD severely impacts QoL outcomes and is associated with female sex and mechanism of injury in adolescents. Early recognition and treatment of ASD in seriously injured adolescents will improve QoL outcomes.
Vat, an Amazing Gene Conferring Resistance to Aphids and Viruses They Carry: From Molecular Structure to Field Effects

We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster. The role of these polymorphisms in plant/aphid interactions remains unclear. The Vat gene structure suggests a functioning with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced during cell puncture by the aphid. A few hours later, several miRNAs are upregulated in Vat plants. Peroxidase activity increases, and callose and lignin are deposited in the walls of the cells adjacent to the stylet path, disturbing aphid behavior. In aphids feeding on Vat plants, Piwi-interacting RNA-like sequences are abundant and the levels of other miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). Resistance to viruses is qualitative and local. Durability of NLR genes is highly variable. A. gossypii clones are adapted to Vat resistance, either by introducing a new effector that interferes with the deployment of plant defenses, or by adapting to the defenses it triggered. Viruses transmitted in a non-persistent manner cannot adapt to Vat resistance. At population level, Vat reduces aphid density and genetic diversity. The durability of Vat resistance to A. gossypii populations depends strongly on the agro-ecosystem, including, in particular, the presence of other cucurbit crops serving as alternative hosts for adapted clones in fall and winter. At the crop level, Vat resistance decreases the intensity of virus epidemics when A. gossypii is the main aphid vector in the crop environment.
Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis[OPEN]

ETTIN translates changes in auxin levels into diverse transcriptional outcomes to control specific processes during Arabidopsis plant development. The phytohormone auxin governs crucial developmental decisions throughout the plant life cycle. Auxin signaling is effectuated by auxin response factors (ARFs) whose activity is repressed by Aux/IAA proteins under low auxin levels, but relieved from repression when cellular auxin concentrations increase. ARF3/ETTIN (ETT) is a conserved noncanonical Arabidopsis thaliana ARF that adopts an alternative auxin-sensing mode of translating auxin levels into multiple transcriptional outcomes. However, a mechanistic model for how this auxin-dependent modulation of ETT activity regulates gene expression has not yet been elucidated. Here, we take a genome-wide approach to show how ETT controls developmental processes in the Arabidopsis shoot through its auxin-sensing property. Moreover, analysis of direct ETT targets suggests that ETT functions as a central node in coordinating auxin dynamics and plant development and reveals tight feedback regulation at both the transcriptional and protein-interaction levels. Finally, we present an example to demonstrate how auxin sensitivity of ETT-protein interactions can shape the composition of downstream transcriptomes to ensure specific developmental outcomes. These results show that direct effects of auxin on protein factors, such as ETT-TF complexes, comprise an important part of auxin biology and likely contribute to the vast number of biological processes affected by this simple molecule.
Coverage of diarrhoea-associated Escherichia coli isolates from different origins with two types of phage cocktails

Eighty‐nine T4‐like phages from our phage collection were tested against four collections of childhood diarrhoea‐associated Escherichia coli isolates representing different geographical origins (Mexico versus Bangladesh), serotypes (69 O, 27 H serotypes), pathotypes (ETEC, EPEC, EIEC, EAEC, VTEC, Shigella), epidemiological settings (community and hospitalized diarrhoea) and years of isolation. With a cocktail consisting of 3 to 14 T4‐like phages, we achieved 54% to 69% coverage against predominantly EPEC isolates from Mexico, 30% to 53% against mostly ETEC isolates from a prospective survey in Bangladesh, 24% to 61% against a mixture of pathotypes isolated from hospitalized children in Bangladesh, and 60% coverage against Shigella isolates. In comparison a commercial Russian phage cocktail containing a complex mixture of many different genera of coliphages showed 19%, 33%, 50% and 90% coverage, respectively, against the four above‐mentioned collections. Few O serotype‐specific phages and no broad‐host range phages were detected in our T4‐like phage collection. Interference phenomena between the phage isolates were observed when constituting larger phage cocktails. Since the coverage of a given T4‐like phage cocktail differed with geographical area and epidemiological setting, a phage composition adapted to a local situation is needed for phage therapy approaches against E. coli pathogens.
The effects of "neighborhood size" in reading and lexical decision.

The effects of neighborhood size ("N")--the number of words differing from a target word by exactly 1 letter (i.e., "neighbors")--on word identification was assessed in 3 experiments. In Experiments 1 and 2, the frequency of the highest frequency neighbor was equated, and N had opposite effects in lexical decision and reading. In Experiment 1, a larger N facilitated lexical decision judgments, whereas in Experiment 2, a larger N had an inhibitory effect on reading sentences that contained the words of Experiment 1. Moreover, a significant inhibitory effect in Experiment 2 that was due to a larger N appeared on gaze duration on the target word, and there was no hint of facilitation on the measures of reading that tap the earliest processing of a word. In Experiment 3, the number of higher frequency neighbors was equated for the high-N and low-N words, and a larger N caused target words to be skipped significantly more and produced inhibitory effects later in reading, some of which were plausibly due to misidentification of the target word when skipped. Regression analyses indicated that, in reading, increasing the number of higher frequency neighbors had a clear inhibitory effect on word identification and that increasing the number of lower frequency neighbors may have a weak facilitative effect on word identification.
Preface - The Universal Paradigm and the Islamic World-System: Economy, Society, Ethics and Science

Written by a contemporary pioneer in the area of the universal paradigm and Islamic world-systems, this book offers a fresh post-modernist outlook on new epistemological investigations in the universal paradigm. It addresses the problems of the unity of knowledge in learning systems, thereby invoking the foundations of Islamic epistemology. The author presents a phenomenological model of unity of knowledge in economics, ethics, science and society. Some critical areas where this model can be applied are also explored. As a foundational study on Islamic theory of knowledge covering the fields of Islamic economics, finance, science and society, the book will be valuable to researchers, practitioners and global academic institutions.
Exposing software security and availability risks for commercial mobile devices

The advent of smaller, faster, and always connected handheld devices along with the ever-increasing reliance on technology for our everyday activities have introduced novel threats and risks. Beyond hardware security another primary factor that affects the reliability of the device is mobile applications. Indeed, the shift to smart commercially available mobile devices has created a pressing need for understanding the risks in using third-party mobile code running on the mobile devices. This new generation of smart devices and systems, including iPhone and Google Android, are powerful enough to accomplish most of the user tasks previously requiring a personal computer. In our paper, we discuss the cyber threats that stem from these new smart device capabilities and the on-line application markets for mobile devices. These threats include malware, data exfiltration, exploitation through USB, and user and data tracking. In this manuscript, we present our efforts towards a framework for exposing the functionality of a mobile application through a combination of static and dynamic program analysis that attempts to explore all available execution paths including libraries. We verified our approach by testing a large number of Android applications with our dynamic analysis framework to exhibit its functionality and viability. The framework allows complete automation of the execution process so that no user input is required. We also discuss how our static analysis output can be used to inform the execution of the dynamic analysis. Our approach can serve as an extensible basis to fulfill other useful purposes such as symbolic execution, program verification, interactive debugger, and other approaches that require deep inspection of an Android application. In summary, we believe that our efforts are the beginning of a long journey to asserting and exposing the risks of commercially available mobile devices. Our future work will include non-Android platforms.
The jet model for Sgr A*: radio and X-ray spectrum

The preliminary detection of the Galactic Center black hole Sgr A* in X-rays by the Chandra mission, as well as recent mm-VLBI measurements, impose strict constraints on this source. Using a relativistic jet model for Sgr A*, we calculate the synchrotron and synchrotron self-Compton emission. The predicted spectrum provides an excellent fit to the radio spectrum and the the X-ray observations. Limits on the infrared flux and the low X-ray flux require a high-energy cut-off in the electron spectrum at gamma_e ~< 100. The implied lack of a significant power-law tail of high-energy electrons also suppresses the appearance of the extended, optically thin radio emission usually seen in astrophysical jets. The jet therefore appears rather compact and naturally satisfies current VLBI limits. The initial parameters of the model are tightly constrained by the radio spectrum and the "submm-bump" in particular. While the jet most likely is coupled to some kind of accretion flow, we suggest that the most visible signatures can be produced by this outflow. If SSC emission from the jet contributes to the Sgr A* spectrum, significant variability in X-rays would be expected. The model could be generic for other low-luminosity AGN or even X-ray binaries.
Exogenous superantigens acutely trigger distinct levels of peripheral T cell tolerance/immunosuppression: Dose‐response relationship

Ligand‐specific immunosuppression requires an understanding of the parameters that control peripheral T cell tolerance. T cell receptor (TcR) transgenic mice offer a clear advantage for studying post‐thymic tolerance mechanisms in vivo that are operational in a monoclonal T cell population with preselected antigen specificity. Yet it is unclear whether the rules defined in monoclonal T cells of genetically manipulated mice reflect those operative in clonally diverse peripheral T cells of normal mice. To analyze acute tolerance mechanisms in unselected peripheral T cells, we challenged normal mice with the superantigen staphylococcal enterotoxin B (SEB) and analyzed ligand‐reactive Vβ8+ T cells for TcR‐triggered tolerance mechanisms such as anergy, TcR down‐regulation, or apoptosis. Upon challenge with graded doses of SEB (0.001–10 μg) Vβ8− T cells become anergic within 6–16 h. Importantly, a dosage effect of SEB in regard to the level of anergy induced was observed. Anergy induced by low concentrations of SEB (0.001–0.1 μg) is transient and is overcome by clonal growth, while higher concentrations of SEB (0.1–10 μg) cause long‐lasting anergy resistant to cell cycle progression. At high SEB concentrations (1–10 mg) about 50% of the anergic Vβ8+ T cells additionally down‐regulate their TcR‐CD3 complex, followed by a loss of CD2, CD4, CD8 accessory molecules. In parallel, T cell phenotypenegative but genotypically Vβ8+ T cells are generated. The T cell phenotypenegative cells reacquire their Vβ8+ T cell phenotype upon culture in vitro. In vivo, a subset of Vβ8+ cells, defined by an intermediate stage of TcR down‐regulation, i.e. Vβ8lowCD3+ cells, but not T cell phenotype‐negative cells are selectively programmed for apoptosis, which occurs within 1 h. These data suggest that SEB triggers distinct tolerance pathways which operate in a hierarchical fashion in clonally diverse ligand‐reactive T cells. Specifically, the results illustrate the power of exogenous superantigens to exploit these distinct tolerance pathways, thereby achieving distinct levels of immunosuppression.
Packet Sampling (PSAMP) Protocol Specifications

This document specifies the export of packet information from a Packet SAMPling (PSAMP) Exporting Process to a PSAMP Collecting Process. For export of packet information, the IP Flow Information eXport (IPFIX) protocol is used, as both the IPFIX and PSAMP architecture match very well, and the means provided by the IPFIX protocol are sufficient. The document specifies in detail how the IPFIX protocol is used for PSAMP export of packet information. [STANDARDS-TRACK]
A simple design rule for 1st order form-closure of underactuated hands

Abstract. The property of form-closure of a grasp, as generally defined in the literature, is based on the assumption that contact points between the hand and the object are fixed in space. However, this assumption is false when considering a grasp exerted by an underactuated hand, since in this case, it is not possible to control the position of each phalanx independently. In spite of researchers' interest in studying form-closure, none of the available published work on this subject takes into consideration the particular kinematics of underactuated hands. Actually, there are few available tools to qualify or quantify the stability of a grasp exerted by an underactuated hand, thus the design of underactuated hands mostly results from an intuitive approach. This paper aims to reduce this gap. A classification of underactuated hands is proposed, based on the expression of contact forces. This highlights the influence of non-backdrivable mechanisms introduced in the transmission of the closing motion of the hand on the stability of the grasp. The way to extend the original definition of form-closure to underactuated grasps is illustrated. A more general definition is formulated, which checks the stability of the set "object + hand". Using this new definition, a simple rule is proposed for designing a hand capable of achieving 1st order form-closed grasps. This paper was presented at the IFToMM/ASME International Workshop on Underactuated Grasping (UG2010), 19 August 2010, Montreal, Canada.
A method for recognition and localization of generic objects for indoor navigation

We introduce an efficient method for recognition and localization of generic objects for robot navigation, which works on real scenes. The generic objects used in our experiments are desks and doors as they are suitable landmarks for navigation. The recognition method uses significant surfaces and accompanying functional evidence for recognition of such objects. Currently, our system works with planar surfaces only and assumes that the objects are in a "standard" pose. The localization and orientation of an object are represented with the most significant surface in an "s-map". Some results for laboratory scenes are given. <<ETX>>
Family use of health care: United States, 1980.

Information on families' use of health care in 1980 is presented in this report. The data discussed here were gathered in the national household sample of the National Medical Care Utilization and Expenditure Survey. In this sample, information was collected on health problems, health care received, expenditures for care, health insurance, and related topics throughout calendar year 1980 from approximately 6,800 families in the U.S. civilian noninstitutionalized population. (The report entirely excludes families with military heads, even if they have civilian members.) For this report, a family was initially defined as (1) two or more persons living together who were related by either blood, marriage, adoption, or a formal foster care relationship or (2) a single person living outside such relationships. But because these data were collected across an entire year, the important concept of "longitudinal family" was developed. This concept was necessary to deal with the fact that the composition of a family could change over time and that families could come into existence and go out of existence over time. As the data are based on this dynamic concept of families, all measures of the use of health services are calculated in annual rates. Family data are important for understanding the health care system because decisions to seek and use health care are usually family decisions, health care is usually paid for out of family resources, and family distributions for health-related variables differ from the distributions found for individuals. Data on both multiple-person families (families that averaged 1.5 persons or more during the year) and one-person families (families that averaged less than 1.5 persons during the year) are presented in this report. Only findings for multiple-person families, however, are addressed in this section. It is multiple-person families that are usually referred to in discussions of families by both the general public and professional social scientists.