Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis

Intricate signal networks and transcriptional regulators translate the recognition of pathogens into defense responses. In this study, we carried out a gene co-expression analysis of all currently publicly available microarray data, which were generated in experiments that studied the interaction of the model plant Arabidopsis thaliana with microbial pathogens. This work was conducted to identify (i) modules of functionally related co-expressed genes that are differentially expressed in response to multiple biotic stresses, and (ii) hub genes that may function as core regulators of disease responses. Using Weighted Gene Co-expression Network Analysis (WGCNA) we constructed an undirected network leveraging a rich curated expression dataset comprising 272 microarrays that involved microbial infections of Arabidopsis plants with a wide array of fungal and bacterial pathogens with biotrophic, hemibiotrophic, and necrotrophic lifestyles. WGCNA produced a network with scale-free and small-world properties composed of 205 distinct clusters of co-expressed genes. Modules of functionally related co-expressed genes that are differentially regulated in response to multiple pathogens were identified by integrating differential gene expression testing with functional enrichment analyses of gene ontology terms, known disease associated genes, transcriptional regulators, and cis-regulatory elements. The significance of functional enrichments was validated by comparisons with randomly generated networks. Network topology was then analyzed to identify intra- and inter-modular gene hubs. Based on high connectivity, and centrality in meta-modules that are clearly enriched in defense responses, we propose a list of 66 target genes for reverse genetic experiments to further dissect the Arabidopsis immune system. Our results show that statistical-based data trimming prior to network analysis allows the integration of expression datasets generated by different groups, under different experimental conditions and biological systems, into a functionally meaningful co-expression network.
Improving Xen security through disaggregation

Virtual machine monitors (VMMs) have been hailed as the basis for an increasing number of reliable or trusted computing systems. The Xen VMM is a relatively small piece of software -- a hypervisor -- that runs at a lower level than a conventional operating system in order to provide isolation between virtual machines: its size is offered as an argument for its trustworthiness. However, the management of a Xen-based system requires a privileged, full-blown operating system to be included in the trusted computing base (TCB). In this paper, we introduce our work to disaggregate the management virtual machine in a Xen-based system. We begin by analysing the Xen architecture and explaining why the status quo results in a large TCB. We then describe our implementation, which moves the domain builder, the most important privileged component, into a minimal trusted compartment. We illustrate how this approach may be used to implement "trusted virtualisation" and improve the security of virtual TPM implementations. Finally, we evaluate our approach in terms of the reduction in TCB size, and by performing a security analysis of the disaggregated system.
The Effect of Digital Games and Game Strategies on Young Adolescents' Aggression

Violence is a major element in many of the present-day's digital games. Despite the extensive research on this subject, the effect of violent digital games on the aggression level among children has not been satisfactorily clarified. The study examines the combined effect of collaborative/competitive game strategy and the presence or absence of violence in the game on the aggression of young adolescents. Fifty-six young adolescents (28 girls, 28 boys) aged 10–13 years old participated in this study. They played digital games and answered questionnaires designed to check the influence of the game on their aggression level immediately after the game. Findings indicate that game strategy may have a significant effect on aggression level: collaborative game strategy was found to repress aggression, whereas competitive strategy was found to raise aggression levels among all subjects. The very existence of violence in the game was not found to be responsible for the aggression level of players. No differences in player aggression levels were found between genders.
A Tangible 3D Desktop Environment with Force Feedback

In recent yeas various 3D desktop environments have been developed. They don't, however, become a popular interaction method in HCI (human computer interface) research field. Restrictions in 3D operations using a mouse are the major reason. The mouse is inappropriate for manipulating objects in a 3D task space. Users have difficulties for adequately managing the mouse in 3D object manipulations. In this paper, we propose to replace the mouse by a haptic device, an interaction device enabling easy object manipulations in the 3D task space. The haptic device also allows the users to touch the objects with depth perceptions and feel some tactile sensations. It can present some special effects like shocks, vibrations, and weights when they touch the object. We designed and developed a 3D operational environment where the desktop can be treated as a real world property by using the haptic device. We describe the implementation method and operational interface of the proposed new 3D desktop environment empowered by the haptic device and an experiment conducted for verifying the effectiveness of the proposed system.
targeted gene knockout by direct delivery of zinc-finger nuclease proteins

nature methods | ADVANCE ONLINE PUBLICATION | purify in quantities sufficient for analysis in cell culture (data not shown). Following these results, and based on the observation that ZFP DNA-binding domains carry a net positive charge (Fig. 1a), we hypothesized that ZFNs might penetrate the cell in the absence of additional modification. We expressed in Escherichia coli ZFNs designed to target the CCR5 gene and lacking any transduction domain and then purified them to homogeneity from either the soluble or the insoluble fractions (Supplementary Fig. 1). In vitro analysis confirmed that functional ZFN proteins with similar DNA cleavage profiles could be obtained by either method (Supplementary Fig. 2 and Supplementary Note). To determine the ability of ZFN proteins to penetrate cells and stimulate mutagenesis, we generated a fluorescence-based reporter system to measure ZFN-induced DSBs (Fig. 1b). This system uses an integrated EGFP gene whose expression has been interrupted by a frameshift mutation introduced by a strategically placed ZFN cleavage site. ZFN proteins that penetrate reporter cells can induce DSBs at this target site and drive the introduction of small insertions and deletions in the EGFP locus by NHEJ. Because NHEJ is a stochastic process, approximately one-third of these mutational events (+2, +5, +8,. bp or −1, −4, −7,. bp) will restore the frame and EGFP function. Direct application of ZFN proteins to reporter cells resulted in a dose-dependent increase in EGFP fluorescence, with maximum activity (6% EGFP-positive cells) achieved after treatment with 2 μM ZFN proteins (Fig. 1c). By comparison, transient transfection of ZFN expression plasmids under saturating conditions resulted in ~7% EGFP-positive cells (Supplementary Fig. 3). We observed no difference in activity between ZFN proteins purified from the soluble fraction or inclusion bodies (Supplementary Fig. 4). At all ZFN concentrations evaluated, the use of transient hypothermic culture conditions9 enhanced the efficiency of mutagenesis nearly twofold (Fig. 1c,d). Extended periods of incubation (>60 min) did not increase the frequency of genome editing (Supplementary Fig. 5). Consecutive protein treatments, however, did increase the percentage of EGFP-positive cells (Fig. 1d,e). Notably, repeated treatment with ZFN proteins over 3 d using transient hypothermic conditions yielded ~12% EGFP-positive cells (Fig. 1e). Sequence analysis of isolated EGFPpositive cells verified targeted mutagenesis, confirming the presence of the anticipated ZFN-induced insertions and deletions in the EGFP locus (Fig. 1f). To determine the contribution of each ZFN component to cellular penetration, we incubated cells with fluorescently labeled ZFN or FokI cleavage domain proteins (Supplementary Fig. 6). We observed fluorescence in cell lysate following treatment with ZFN—in the presence or absence of a nuclear localization targeted gene knockout by direct delivery of zincfinger nuclease proteins
The Representation of Foreign Cultures in English Textbooks

A case study of the foreign cultures represented in two English language textbooks used by Hong Kong secondary schools was conducted. Its aim was to investigate whether the representation of foreign cultures in these textbooks reflected the status of English as an international language. In order to do this, references to foreign cultures were categorized into four aspects: products, practices, perspectives, and persons. It was found overall that the representation favoured the cultures of English-speaking countries, while the cultures of Africa were under-represented. The selection of English language textbooks and the implications for redressing the imbalance in cultural content are discussed.
Implementing Conceptual Change Teaching in Primary Science

A study was made of the extent to which 8 teachers in grades K-3 were able to implement a 2-week conceptual change science unit in their classrooms following a 4-week summer institute. The effects of the institute program, which was designed to help teachers develop the subject-matter and pedagogical knowledge needed to teach a unit on light and shadows, were assessed by analyzing (1) videotapes of lessons taught before and after the program, (2) interviews that measured students' understanding of light and shadows pehnomena before and after the unit was taught, and (3) teachers' written evaluations of their units. 1 year later, teachers were interviewed about their continuing use of the unit and conceptual change teaching strategies generally. Results, which indicated that the 8 teachers were generally successful in implementing a conceptual change unit of their own on light and shadows and in changing students' conceptions, are discussed in relation to case methods and cognitive-apprenticeship models of training.
ABA and Students with Autism Spectrum Disorders

Applied behavior analysis (ABA) is recognized as an essential and scientifically valid method of educating and managing children and youth with autism spectrum disorders. At the same time, ABA is at the center of a number of strident debates regarding methodological preferences for educating students with autism-related disabilities. This article discusses issues related to the ABA debate: implementation forms, outcome expectations, exclusive versus selective use of applied behavior analysis, time-related considerations, and personnel requirements for effective ABA implementation, evaluation, and communication.
Invited review: Activation of G proteins by GTP and the mechanism of Gα‐catalyzed GTP hydrolysis

This review addresses the regulatory consequences of the binding of GTP to the alpha subunits (Gα) of heterotrimeric G proteins, the reaction mechanism of GTP hydrolysis catalyzed by Gα and the means by which GTPase activating proteins (GAPs) stimulate the GTPase activity of Gα. The high energy of GTP binding is used to restrain and stabilize the conformation of the Gα switch segments, particularly switch II, to afford stable complementary to the surfaces of Gα effectors, while excluding interaction with Gβγ, the regulatory binding partner of GDP‐bound Gα. Upon GTP hydrolysis, the energy of these conformational restraints is dissipated and the two switch segments, particularly switch II, become flexible and are able to adopt a conformation suitable for tight binding to Gβγ. Catalytic site pre‐organization presents a significant activation energy barrier to Gα GTPase activity. The glutamine residue near the N‐terminus of switch II (Glncat) must adopt a conformation in which it orients and stabilizes the γ phosphate and the water nucleophile for an in‐line attack. The transition state is probably loose with dissociative character; phosphoryl transfer may be concerted. The catalytic arginine in switch I (Argcat), together with amide hydrogen bonds from the phosphate binding loop, stabilize charge at the β‐γ bridge oxygen of the leaving group. GAPs that harbor “regulator of protein signaling” (RGS) domains, or structurally unrelated domains within G protein effectors that function as GAPs, accelerate catalysis by stabilizing the pre‐transition state for Gα‐catalyzed GTP hydrolysis, primarily by restraining Argcat and Glncat to their catalytic conformations. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 449–462, 2016.
Four-phase re-speaker training system

Since the re-speaker approach to the automatic captioning of TV broadcastings using large vocabulary continuous speech recognition (LVCSR) is on the increase, there is also a growing demand for training systems that would allow new speakers to learn the procedure. This paper describes a specially designed re-speaker training system that provides gradual four-phase tutoring process with quantitative indicators of a trainee progress to enable faster (and thus cheaper) training of the re-speakers. The performance evaluation of three re-speakers who were trained on the proposed system is also reported.
Evaluation of Infection Control Measures in Preventing the Nosocomial Transmission of Multidrug-Resistant Mycobacterium tuberculosis in a New York City Hospital

Abstract Objective: To evaluate the efficacy of Centers for Disease Control and Prevention (CDC)-recommended infection control measures implemented in response to an outbreak of multidrug-resistant (MDR) tuberculosis (TB). Design: Retrospective cohort studies of acquired immunodeficiency syndrome (AIDS) patients and healthcare workers. The study period (January 1989 through September 1992) was divided into period I, before changes in infection control; period II, after aggressive use of administrative controls (eg, rapid placement of TB patients or suspected TB patients in single-patient rooms); and period III, while engineering changes were made (eg, improving ventilation in TB isolation rooms). Setting: A New York City hospital that was the site of one of the first reported outbreaks of MDR-TB among AIDS patients in the United States. Participants: All AIDS patients admitted during periods I and II. Healthcare workers on nine inpatient units with TB patients and six without TB patients. Results: The epidemic (38 patients) waned during period II and only one MDR-TB patient presented during period III. The MDR-TB attack rate among AIDS patients hospitalized on the same ward on the same days as an infectious MDR-TB patient was 8.8% (19 of 216) during period I, decreasing to 2.6% (5 of 193; P= 0.01) during period II. In a small group of healthcare workers with tuberculin skin test data, conversions during periods II through III were higher on wards with than without TB patients (5 of 29 versus 0 of 15; P= 0.15), although the difference was not statistically significant. Conclusions: Transmission of MDR-TB among AIDS patients decreased markedly after enforcement of readily implementable administrative measures, ending the outbreak. However, tuberculin skin-test conversions among healthcare workers may not have been prevented by these measures. CDC guidelines for prevention of nosocomial transmission of TB should be implemented fully at all US hospitals.
Impact of child summertime obesity interventions on body mass index, and weight-related behaviours: a systematic review and meta-analysis protocol

Introduction In previous studies, it has been found that on average, children consistently gained weight during the summer months at an increased rate compared with the 9-month school year. This contributed to an increased prevalence of overweight and obesity in children. Several obesity-related interventions have occurred during or targeting the summer months. We propose to conduct a systematic review and meta-analysis of the impact of obesity prevention and treatment interventions for school-age children conducted during the summer or targeting the summer months when children are not in school on their body mass index (BMI), or weight-related behaviours. Methods and analyses A literature search will be conducted by the first author (JPM) using MEDLINE/PubMed, Cochrane Library, Scopus, CINAHL, PsycINFO, EMBASE and Proquest Dissertations and Theses databases from the date of inception to present. Studies must examine interventions that address the modification or promotion of weight-related behaviours (eg, dietary patterns, eating behaviours, physical activity (PA), sedentary behaviour or sleep) and target school-age children (ages 5–18). The primary outcomes will be changes from baseline to postintervention and/or the last available follow-up measurement in weight, BMI, BMI percentile, standardised BMI or per cent body fat. Secondary outcomes will include changes in dietary intake, PA, sedentary behaviour or sleep. Risk of bias will be assessed using the Cochrane risk of bias tool for randomised and non-randomised studies, as appropriate. Ethics and dissemination Because this is a protocol for a systematic review, ethics approval will not be required. The findings will be disseminated via presentations at scientific conferences and published in a peer-reviewed journal. All amendments to the protocol will be documented and dated and reported in the PROSPERO trial registry. PROSPERO registration number CRD42016041750
Developing Overhand Throwing Skills for a Child With Autism With a Collaborative Approach in School-Based Therapy

Purpose: This case report presents an interdisciplinary approach in school-based therapy, combining physical therapy and applied behavior analysis to improve the motor skills and the participation in recreational activities of a child with autism spectrum disorder. Methods: A 9-year-old child with autism spectrum disorder participated in a 20-week gross motor intervention designed to improve the child's overhand throwing ability, which included weekly physical therapy instruction and daily throwing trials using applied behavior analysis approaches. Results: The child demonstrated gains in throwing accuracy, significant gains on measures of the Bruininks-Oseretsky Test of Motor Proficiency-2, the Test of Gross Motor Development-2, and the School Function Assessment. Conclusion: This unique approach in school-based therapy demonstrates effective strategies for a multidisciplinary intervention to improve motor learning skills and participation in recreational activities in the school setting.
Bone loss during simulated weightlessness: a biomechanical and mineralization study in the rat model.

BACKGROUND Astronauts exposed to weightlessness for extended periods experience significant decreases in bone mineral density. The clinical implications of this demineralization are not entirely clear, and the biomechanics involved are not completely understood. HYPOTHESIS Local (rather than global) measurements of geometry and calcium concentration effectively predict femur strength in adult rats exposed to a hind-limb suspension model of weightlessness. METHODS Female Fischer rats (6-mo-old) were divided into groups of control and hind-limb-suspended animals. Animals were sacrificed after 2 or 4 wk of hind-limb suspension, and both femurs removed from each animal. The 3-point bending strength and total bone mineralization were determined for one femur from each animal, and the mid-shaft cross-sectional geometrical properties and distribution of calcium were determined for the contralateral femur. RESULTS Although suspension led to significant decreases in total bone mineralization, the concentration of calcium at the anterior periosteal surface was unaffected. Total bone percent mineralization was not well correlated with structural properties, but bone geometrical properties (particularly cross-sectional moment of inertia and length) correlated strongly with ultimate bending strength (r2 = 0.81). Differences in bone geometry due to suspension were consistent with a distribution of bone material closer to the axis of the femur. CONCLUSIONS Structural properties of bone are predicted well by bone geometry and poorly by total bone percent mineralization. Decreased bone mechanical strength in this model of weightlessness is primarily due to a distribution of bone material nearer the axis of the bone.
Bus-clamping-based switch vector table of DTC

This paper proposes a new type of switch vector table based on bus-clamping of DTC for induction motor drives. This strategy will combine look-up table method of Takahashi DTC with bus-clamping technology, then, a new bus-clamping DTC (BCDTC) switch vector table will be gained. BCDTC is consistent with the traditional DTC strategy, depends on monitoring and control the stator flux vector Φ̅s, tracking its trajectory for a circular to achieve direct torque control requirement. As introduced bus-clamping technology, BCDTC strategy leads to keep each inverter phase conduction on or off during 60° interval in every half cycle of the stator flux vector. As BCDTC strategy is not based on fixed modulation time, so a quick response system is obtained, and bus-clamping technique makes the inverter switch frequency reduced, resulting to the torque ripple reduced.
Basal Ornithine Decarboxylase Activity Modifies Apoptotic and Hypertrophic Marker Expression in Post-Ischemic Hearts

Polyamines play a role in ischemia-reperfusion injury of brain, kidney and probably heart. Primary data on car- diac myoblasts suggested that the induction of polyamine metabolism induces a hypertrophy like effect in normoxic hearts but apoptosis in reperfused hearts. The aim of this study was to investigate the relevance of these findings for post- ischemic hearts. Rat hearts were exposed to 45 min global normothermic flow arrest followed by 120 min of reperfusion. Controls were constitutively perfused for 165 min under normoxic conditions. Ornithine decarboxylase (ODC) activity was inhibited by administration of difluoromethylornithine (DFMO, 100 � M) starting 30 min after the onset of reperfu- sion and lasting for 10 min. Calcium receptor activation was induced by administration of putrescine (100 � M) and its in- hibition by administration of NPS (10 � M). Left ventricular mRNA expression of bcl-2, bax, and BNP were determined by real time RT-PCR. Results: BNP was induced by putrescine via activation of calcium receptors in normoxic and post- ischemic hearts. Inhibition of ODC had a strong effect on bcl-2 expression whereby putrescine induced bax in post- ischemic but not normoxic hearts. Inhibition of ODC increased the bcl-2/bax ratio but putrescine worsened it. In conclu- sion, induction of polyamine metabolism induced a pro-apoptotic profile in left ventricles via calcium receptor activation in post-ischemic hearts but not in normoxic hearts and induced BNP expression under both conditions.
Concurrent Dissections of the Ascending Aorta and Right Coronary Artery During Percutaneous Coronary Intervention : A Case Report

Iatrogenic aortic dissection caused by coronary angiography or angioplasty is a rare but potentially life-threatening complication. Awareness of the complication and its prompt recognition are important. We describe a 78-year-old woman who underwent coronary angioplasty for acute non-ST elevation myocardial infarction. An ostial dissection of the right coronary artery (RCA) with extension into the entire ascending aorta occurred during the an attempt to recanalize an occluded RCA. The literature recommends surgical intervention or stenting of the coronary dissection under these circumstances. However, the patient was managed conservatively. Serial evaluation with noninvasive imaging studies showed resolution of the ascending aortic dissection.