Miracle-dz/UniFAR-FTUs huggingface dataset:
Prioritizing hypothesis tests for high throughput data

MOTIVATION The advent of high throughput data has led to a massive increase in the number of hypothesis tests conducted in many types of biological studies and a concomitant increase in stringency of significance thresholds. Filtering methods, which use independent information to eliminate less promising tests and thus reduce multiple testing, have been widely and successfully applied. However, key questions remain about how to best apply them: When is filtering beneficial and when is it detrimental? How good does the independent information need to be in order for filtering to be effective? How should one choose the filter cutoff that separates tests that pass the filter from those that don't? RESULT We quantify the effect of the quality of the filter information, the filter cutoff and other factors on the effectiveness of the filter and show a number of results: If the filter has a high probability (e.g. 70%) of ranking true positive features highly (e.g. top 10%), then filtering can lead to dramatic increase (e.g. 10-fold) in discovery probability when there is high redundancy in information between hypothesis tests. Filtering is less effective when there is low redundancy between hypothesis tests and its benefit decreases rapidly as the quality of the filter information decreases. Furthermore, the outcome is highly dependent on the choice of filter cutoff. Choosing the cutoff without reference to the data will often lead to a large loss in discovery probability. However, naïve optimization of the cutoff using the data will lead to inflated type I error. We introduce a data-based method for choosing the cutoff that maintains control of the family-wise error rate via a correction factor to the significance threshold. Application of this approach offers as much as a several-fold advantage in discovery probability relative to no filtering, while maintaining type I error control. We also introduce a closely related method of P-value weighting that further improves performance. AVAILABILITY AND IMPLEMENTATION R code for calculating the correction factor is available at http://www.stat.uga.edu/people/faculty/paul-schliekelman CONTACT pdschlie@stat.uga.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Handling Change in Normative Specifications (Extended Abstract)

Normative frameworks provide a means to address the governance of open systems, by oering a mechanism to express responsibilities and permissions of the individual participants with respect to the entire system without compromising their autonomy. Careful design is crucial if it is to meet its requirements. Tools that support the design process can be of great benet. In this paper, we describe a method for choosing the appropriate change in the normative specication, using impact analysis of the critical consequences being preserved or rejected by the change.
Fluorescent Modification of Adenosine 3',5'-Monophosphate: Spectroscopic Properties and Activity in Enzyme Systems

The synthesis of a highly fluorescent analog of adenosine 3',5'-monophosphate, namely, 1,N6-ethenoadenosine 3',5'-monophosphate, has provided a powerful probe for systems involving adenosine 3',5'-monophosphate. The potential utility of this analog is indicated by its long fluorescent lifetime, detectability at low concentration, and relatively long wavelength of excitation (300 nanometers). In protein kinase systems it is a highly acceptable substitute for adenosine 3',5'-monophosphate.
Blood–brain barrier damage and brain penetration of antiepileptic drugs: Role of serum proteins and brain edema

Purpose: Increased blood–brain barrier (BBB) permeability is radiologically detectable in regions affected by drug‐resistant epileptogenic lesions. Brain penetration of antiepileptic drugs (AEDs) may be affected by BBB damage. We studied the effects of BBB damage on brain distribution of hydrophilic [deoxy‐glucose (DOG) and sucrose] and lipophilic (phenytoin and diazepam) molecules. We tested the hypothesis that lipophilic and hydrophilic drug distribution is differentially affected by BBB damage.
Effects of pulmonary rehabilitation in bronchiectasis: A retrospective study

There is limited information about the benefits of pulmonary rehabilitation (PR) in patients with bronchiectasis. This study aimed to evaluate the effects of an out-patient PR program in patients with a primary diagnosis of bronchiectasis and to compare them with a matched COPD group who completed the same PR program. A retrospective review was conducted of patients with bronchiectasis or COPD who completed 6 to 8 weeks of PR at two tertiary institutions. The outcome measures were the 6-minute walk distance (6MWD) and Chronic Respiratory Disease Questionnaire (CRQ). Ninety-five patients with bronchiectasis completed the PR (48 male; FEV1 63 [24] % predicted; age 67 [10] years). Significant improvements in 6MWD (mean change 53.4 m, 95% CI 45.0 to 61.7) and CRQ total score (mean change 14.0 units, 95% CI 11.3 to 16.7) were observed immediately following PR. In patients with complete follow-up (n = 37), these improvements remained significantly higher than baseline at 12 months (20.5 m, 95% CI 1.4 to 39.5 for 6MWD; 12.1 points, 95% CI 5.7 to 18.4 for CRQ total score). The time trend and changes in the 6MWD and CRQ scores were not significantly different between the bronchiectasis and the COPD groups (all p > 0.05). This study supports the inclusion of patients with bronchiectasis in existing PR programs. Further prospective RCTs are warranted to substantiate these findings.
Prognostic value of ebv markers in the clinical management of nasopharyngeal carcinoma (NPC): A multicenter follow‐up study

Between December 1979 and April 1982, 373 patients with untreated, undifferentiated carcinoma of the nasopharynx (NPC), 99 in Hong Kong, 120 in Tunis and 154 in Villejuif, entered a longitudinal study aimed at determining the clinical prognostic value of EBV serology after radiotherapy. A minimum of 3 years' follow‐up was achieved for 319 patients (83 in Tunis, 95 in Hong Kong and 141 in Villejuif) who had regular clinical and serological testing at intervals of 6–8 months. No significant difference in initial serology (i. e., before any treatment) or variations of antibody titers at time of first followup was observed between patients who achieved complete remission after radiotherapy and those who did not. This included IgG and IgA antibodies to VCA, EA or EBNA. However, when patients with confirmed clinical remission I year after completion of radiotherapy were studied, the value of IgG/EA and mainly of IgA/EA increasing titers became highly significant for prediction of relapse, regardless of the initial titers. This demonstrated the clinical usefulness of EBV serology for NPC patients who have confirmed clinical remission after radiotherapy.
Abbott’s ‘budget crisis’, CALD women’s loss? Service providers explore the impact of funding cuts

ABSTRACT Women have been disproportionately affected by funding cuts to services following the 2008 global financial crisis. Using a feminist intersectional analysis of austerity measures applied to family violence (FV) services in Victoria, Australia, including 11 service provider interviews, we find that: the Australian government drew on global narratives of austerity in constructing a ‘budget crisis’, with subsequent cuts to funds addressing FV; budget cuts negatively impacted services’ abilities to address the needs of culturally and linguistically diverse (CALD) women; there is a lack of qualified interpreters and multilingual services, and; there are missed opportunities to engage and support young CALD people in FV services. Policy recommendations to support FV services and their abilities to help CALD women and young people are provided.
Learning class- and location-specific priors for urban semantic labeling with CNNs

This paper addresses the problem of semantic image labeling of urban remote sensing images into land cover maps. We exploit the prior knowledge that cities are composed of comparable spatial arrangements of urban objects, such as buildings. To do so, we cluster OpenStreetMap (OSM) building footprints into groups with similar local statistics, corresponding to different types of urban zones. We use the per-cluster expected building fraction to correct for over- and underrepresentations of classes predicted by a Convolutional Neural Network (CNN), using a Conditional Random Field (CRF). Results indicate a substantial improvement in both numerical and visual accuracy of the labeled maps.
Visualizing hyperbolic Voronoi diagrams

We present an interactive software, HVD, that represents internally the k-order hyperbolic Voronoi diagram of a finite set of sites as an equivalent clipped power diagram. HVD allows users to interactively browse the hyperbolic Voronoi diagrams and renders simultaneously the diagram in the five standard models of hyperbolic geometry: Namely, the Poincaré disk, the Poincaré upper plane, the Klein disk, the Beltrami hemisphere and the Weierstrass hyperboloid.
In Vitro and In Vivo Antibacterial Activities of S-4661, a New Carbapenem

ABSTRACT The in vitro and in vivo antibacterial activities of S-4661, a new 1β-methylcarbapenem, were compared with those of imipenem, meropenem, biapenem, cefpirome, and ceftazidime. The activity of S-4661 against methicillin-susceptible staphylococci and streptococci was comparable to that of imipenem, with an MIC at which 90% of the strains tested were inhibited (MIC90) equal to 0.5 μg/ml or less. S-4661 was highly active against members of the familyEnterobacteriaceae, Haemophilus influenzae, andMoraxella catarrhalis, with MIC90s ranging from 0.032 to 0.5 μg/ml. Against imipenem-resistant Pseudomonas aeruginosa, S-4661 was the most active among test agents (MIC90, 8 μg/ml). Furthermore, S-4661 displayed a high degree of activity against many ceftazidime-, ciprofloxacin-, and gentamicin-resistant isolates of P. aeruginosa. The in vivo efficacy of S-4661 against experimentally induced infections in mice caused by gram-positive and gram-negative bacteria, including penicillin-resistant Streptococcus pneumoniae and drug-resistant P. aeruginosa, reflected its potent in vitro activity and high levels in plasma in mice. We conclude that S-4661 is a promising new carbapenem for the treatment of infections caused by gram-positive and -negative bacteria, including penicillin-resistantS. pneumoniae and drug-resistant P. aeruginosa.
Simulating the impacts of chronic ozone exposure on plant conductance and photosynthesis, and on the regional hydroclimate using WRF/Chem

The Noah-Multiparameterization land surface model in the Weather Research and Forecasting (WRF) with Chemistry (WRF/Chem) is modified to include the effects of chronic ozone exposure (COE) on plant conductance and photosynthesis (PCP) found from field experiments. Based on the modified WRF/Chem, the effects of COE on regional hydroclimate have been investigated over the continental United States. Our results indicate that the model with/without modification in its current configuration can reproduce the rainfall and temperature patterns of the observations and reanalysis data, although it underestimates rainfall in the central Great Plains and overestimates it in the eastern coast states. The experimental tests on the effects of COE include setting different thresholds of ambient ozone concentrations ([O3]) and using different linear regressions to quantify PCP against the COE. Compared with the WRF/Chem control run (i.e., without considering the effects of COE), the modified model at different experiment setups improves the simulated estimates of rainfall and temperatures in Texas and regions to the immediate north. The simulations in June, July and August of 2007–2012 show that surface [O3] decrease latent heat fluxes (LH) by 10–27 W m−2, increase surface air temperatures (T2) by 0.6 °C–2.0 °C, decrease rainfall by 0.9–1.4 mm d−1, and decrease runoff by 0.1–0.17 mm d−1 in Texas and surrounding areas, all of which highly depends on the precise experiment setup, especially the [O3] threshold. The mechanism producing these results is that COE decreases the LH and increases sensible heat fluxes, which in turn increases the Bowen ratios and air temperatures. This lowering of the LH also results in the decrease of convective potential and finally decreases convective rainfall. Employing this modified WRF/Chem model in any high [O3] region can improve the understanding of the interactions of vegetation, meteorology, chemistry/emissions, and crop productivity.
Variable opacity (Opa) outer membrane proteins account for the cell tropisms displayed by Neisseria gonorrhoeae for human leukocytes and epithelial cells.

Opacity proteins (Opa) of Neisseria gonorrhoeae, a family of variant outer membrane proteins implicated in pathogenesis, are subject to phase variation. In strain MS11, 11 different opa gene alleles have been identified, the expression of which can be turned on and off independently. Using a reverse genetic approach, we demonstrate that a single Opa protein variant of strain MS11, Opa50, enables gonococci to invade epithelial cells. The remaining variant Opa proteins show no, or very little, specificity for epithelial cells but instead confer interaction with human polymorphonuclear neutrophils (PMNs). Thus, depending on the opa allele expressed, gonococci are capable of invading epithelial cells or of interacting with human leukocytes. The respective properties of Opa proteins are maintained independent of the gonococcal strain; thus, the specificity for epithelial cells or leukocytes is intrinsic to Opa proteins. Significant homology exists in the surface exposed variable regions of two invasion supporting Opa proteins from independent strains. Efficient epithelial cell invasion is favoured by high level Opa production, however, a 10‐fold reduction still allows significant invasion by gonococci. In contrast, recombinant Escherichia coli expressing Opa proteins adhered or invaded poorly under similar experimental conditions, thus indicating that additional factors besides Opa are required in the Opa‐mediated interaction with human cells.
Comparison of a CFD Analysis and a Thermal Equivalent Circuit Model of a TEFC Induction Machine With Measurements

For a totally enclosed fan-cooled induction machine, two methods of numerical analysis are compared with measurements. The first numerical method is based on computational fluid dynamics (CFDs) and the second one uses a thermal equivalent circuit (TEC). For the analysis based on CFD, a 3-D induction machine including housing is modeled. The numeric solution of the flow equations is determined for stationary temperature distributions. For the TEC, a discretized one-and-a-half-dimensional model of the induction machine is considered. With the TEC model, stationary and transient operating conditions can be simulated. Measurement results are determined by iron-copper-nickel sensors embedded in the stator winding and the housing, as well as by an IR sensor for measuring the rotor temperature. With these measurement signals, stationary and transient operating conditions can be analyzed. For stationary operating conditions, additionally, the housing temperatures are determined by an IR camera. The investigated simulation and measurement methods reveal different local and global temperatures, and thus, only certain aspects and characteristics of the obtained temperatures can be compared. Nevertheless, certain conclusions can be drawn from comparing these aspects considering the actual restrictions of each of the applied methods.
Robust and Randomized Control Design of Mini-UAVs: The MH1000 Platform

Mini-UAVs (Unmanned Aerial Vehicles) have been the subject of a large number of successful designs aimed to research, commercial and military purposes. Although a Mini-UAV platform can be considered as a miniaturized aircraft, due the presence of plant uncertainties, flight dynamic analysis and control system design are critical, and suitable robustness techniques need to be elaborated. In this paper, within the frame of the design of a Mini-UAV platform for environmental monitoring, fire detection and prevention, we present an innovative strategy based on powerful methods provided by the theory of randomized algorithms.
Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A

Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A (Xoo PXO99A), which is the causal agent of bacterial blight on rice. Based on the parameters of 28 nucleotide frequencies and support vector machine algorithm, 41 originally annotated hypothetical genes were recognized as noncoding sequences, which were further supported by principal component analysis and other evidence. Ten of them were tested with reverse transcription-polymerase chain reaction experiments (RT-PCR), and all of them were confirmed to be noncoding sequences. Furthermore, 197 potential new genes not annotated in RefSeq were both recognized by two ab initio gene finding programs. Most of them only have sequence similarities with part of the known genes in other species, so they are unlikely to be protein-coding genes. Twelve potential new genes have high full-length sequence similarities with function-known genes, which are very likely to be true protein-coding genes. All the 12 potential genes were tested with RT-PCR, and 11 of them (92%) were successfully amplified in cDNA template. The RT-PCR experiments confirm that our theoretical prediction has high accuracy. The improvement of Xoo PXO99A annotation is helpful for the research of lifestyle, metabolism, and pathogenicity of this important plant pathogen. The improved annotation can be obtained from http://211.69. 128.148/Xoo.
Involvement of the IκB Kinase (IKK)-Related Kinases Tank-Binding Kinase 1/IKKi and Cullin-Based Ubiquitin Ligases in IFN Regulatory Factor-3 Degradation1

Activation of the innate arm of the immune system following pathogen infection relies on the recruitment of latent transcription factors involved in the induction of a subset of genes responsible for viral clearance. One of these transcription factors, IFN regulatory factor 3 (IRF-3), is targeted for proteosomal degradation following virus infection. However, the molecular mechanisms involved in this process are still unknown. In this study, we show that polyubiquitination of IRF-3 increases in response to Sendai virus infection. Using an E1 temperature-sensitive cell line, we demonstrate that polyubiquitination is required for the observed degradation of IRF-3. Inactivation of NEDD8-activating E1 enzyme also results in stabilization of IRF-3 suggesting the NEDDylation also plays a role in IRF-3 degradation following Sendai virus infection. In agreement with this observation, IRF-3 is recruited to Cullin1 following virus infection and overexpression of a dominant-negative mutant of Cullin1 significantly inhibits the degradation of IRF-3 observed in infected cells. We also asked whether the C-terminal cluster of phosphoacceptor sites of IRF-3 could serve as a destabilization signal and we therefore measured the half-life of C-terminal phosphomimetic IRF-3 mutants. Interestingly, we found them to be short-lived in contrast to wild-type IRF-3. In addition, no degradation of IRF-3 was observed in TBK1−/− mouse embryonic fibroblasts. All together, these data demonstrate that virus infection stimulates a host cell signaling pathway that modulates the expression level of IRF-3 through its C-terminal phosphorylation by the IκB kinase-related kinases followed by its polyubiquitination, which is mediated in part by a Cullin-based ubiquitin ligase.
Radio frequency spoofing system to take over law-breaking drones

Drones have been used by criminals to smuggle cell phones and drugs into prisons. They also may cause accidents in airports and other heavy flight traffic zones, so it is clear that it is interesting to take control of drones in some specific situations. This work is part of a project intended to develop a system (hardware and software) to take control of the law-breaking drones. This system uses an embedded Linux board communicating via SPI with a radio IC to emulate controllers signal, admitting several flight control parameters: raw, pitch, yaw and roll. In addition, this design must follow technical requirements such as power and speed to overcome primary controllers signal. Therefore, we have shown that a system composed by a Beaglebone Black and a GFSK RF transceiver can be used to take control of radio controlled drones.
Improving physical layer security for wireless ad hoc networks via full-duplex receiver jamming

This paper studies physical layer security in a wireless ad hoc network with numerous legitimate transmitter-receiver pairs and passive eavesdroppers. A hybrid full-/half-duplex receiver deployment strategy is proposed to secure legitimate transmissions, by letting a fraction of legitimate receivers work in the full-duplex (FD) mode sending jamming signals to confuse eavesdroppers upon their own information receptions, and other receivers work in the half-duplex mode just receiving desired signals. This paper aims to properly choose the fraction of the FD receivers to enhance network security. Tractable expressions for the connection outage probability and the secrecy outage probability of a typical legitimate link are first derived, based on which the network-wide secrecy throughput is maximized. Some insights into the optimal fraction are further developed. It is concluded that the fraction of the FD receivers triggers a non-trivial trade-off between reliability and secrecy, and the optimal fraction significantly improves the network security performance.
Managing Uncertainty: Harnessing the Power of Scenario Planning

The competitive dynamics for many firms are rapidly changing, with industry after industry being reshaped and resized by numerous disruptive forces in the form of new digital technologies, deregulation, new business models and the threat of new competitive entrants. A dynamic competitive environment represents a daunting challenge to senior executives and strategic planning teams who have responsibility for the strategic development of the firm, particularly in terms of the future direction, scope and the strategy required to deliver on corporate objectives. With rapid change and uncertainty, there is increased scrutiny on the strategic planning tools that are used to undertake a rational and comprehensive analysis of the competitive dynamics that inform strategy formulation. As such, firms need to consider a critical question when developing their Corporate Level Strategy, that is, ‘how can some long-term certainty in their strategic approach be gained in an uncertain future environment? ’ An underpinning principle in attempting to answer this question lies in the fact that some strategic planning tools are better equipped to deliver strategic insight than others.