Miracle-dz/UniFAR-FTUs huggingface dataset:
Conductance in Eosinophils : Unique Characteristics and Absence in Chronic Granulomatous Disease

Efficient mechanisms of H 1 ion extrusion are crucial for normal NADPH oxidase function. However, whether the NADPH oxidase—in analogy with mitochondrial cytochromes—has an inherent H 1 channel activity remains uncertain: electrophysiological studies did not find altered H 1 currents in cells from patients with chronic granulomatous disease (CGD), challenging earlier reports in intact cells. In this study, we describe the presence of two different types of H 1 currents in human eosinophils. The “classical” H 1 current had properties similar to previously described H 1 conductances and was present in CGD cells. In contrast, the “novel” type of H 1 current had not been described previously and displayed unique properties: (a) it was absent in cells from gp91or p47-deficient CGD patients; (b) it was only observed under experimental conditions that allowed NADPH oxidase activation; (c) because of its low threshold of voltage activation, it allowed proton influx and cytosolic acidification; (d) it activated faster and deactivated with slower and distinct kinetics than the classical H 1 currents; and (e) it was z 20-fold more sensitive to Zn 2 1 and was blocked by the histidine-reactive agent, diethylpyrocarbonate (DEPC). In summary, our results demonstrate that the NADPH oxidase or a closely associated protein provides a novel type of H 1 conductance during phagocyte activation. The unique properties of this conductance suggest that its physiological function is not restricted to H 1 extrusion and repolarization, but might include depolarization, pH-dependent signal termination, and determination of the phagosomal pH set point.
A 0.2V energy-harvesting BLE transmitter with a micropower manager achieving 25% system efficiency at 0dBm output and 5.2nW sleep power in 28nm CMOS

Massive deployment of wireless sensor tags (e.g. iBeacon) will only happen if batteries and their replacement effort are avoided. Self-powering by harvesting the ambient energies like indoor solar and thermal gradient is prospective [1], but their inconstant sub-0.5V output hinders their utility. Adding boost converters and regulators inevitably worsens the system efficiency and integration level. This paper reports an energy-harvesting Bluetooth Low-Energy (BLE) transmitter (TX) (Fig. 28.5.1). It features a fully integrated micropower manager (μPM) to limit the sleep power and tolerate variation of the energy-source voltage (VDD, EH) down to 0.2V. U=An ultra-low-voltage (ULV) VCO and Pa, and a passive-intensive type-I PLL are proposed. Fabricated in 28nm CMOS, the TX exhibits a 25% system efficiency at 0dBm output (Pout).
Dental Environmental Noise Evaluation and Health Risk Model Construction to Dental Professionals

Occupational noise is unavoidably produced from dental equipment, building facilities, and human voices in the dental environment. The purpose of this study was to investigate the effect of occupational noise exposure on the dental professionals’ health condition. The psychoacoustics approach noise exposure assessment followed by the health risk assessment was carried on at the paediatric dentistry clinic and the dental laboratory in the Prince Philip Dental Hospital of Hong Kong. The A-weighted equivalent sound level, total loudness, and sharpness values were statistically significantly higher for the noise at the laboratory than that at the clinic. The degree of perceived influences and sharpness of noise were found to have the impacts on the dental professionals’ working performance and health. Moreover, the risk of having a bad hearing state would a have 26% and 31% higher chance for a unit increment of the short-term and long-term impact scores, respectively. The dental professionals with the service length more than 10 years and the daily working hours of more than eight showed the highest risk to their hearing state. The worse the hearing state was, the worse the health state was found for the dental professionals. Also, the risk of dissatisfaction would be increased by 4.41 and 1.22 times for those who worked at the laboratory and a unit increment of the long-term impact score. The constructed health risk mode with the scientific and statistical evidence is hence important for the future noise management of environmental improvement.
The transcription factor PstSTE12 is required for virulence of Puccinia striiformis f. sp. tritici.

Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus that causes extensive damage in wheat. The pathogen is now known to be a heteroecious fungus with an intricate life cycle containing sexual and asexual stages. Orthologues of the STE12 transcription factor that regulate mating and filamentation in Saccharomyces cerevisiae, as well as virulence in other fungi, have been extensively described. Because reliable transformation and gene disruption methods are lacking for Pst, knowledge about the function of its STE12 orthologue is limited. In this study, we identified a putative orthologue of STE12 from Pst in haustoria-enriched transcripts and designated it as PstSTE12. The gene encodes a protein of 879 amino acids containing three helices in the homeodomain, conserved phenylalanine and tryptophan sites, and two C2 /H2 -Zn2+ finger domains. Real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses revealed that the expression of PstSTE12 was highly induced during the early infection stages and peaked during haustorium formation and the pycniospore stage in the aecial host barberry. Subcellular localization assays indicated that PstSTE12 is localized in the nucleus and functions as a transcriptional activator. Yeast one-hybrid assays revealed that PstSTE12 exhibits transcriptional activity, and that its C-terminus is necessary for the activation of transcription. PstSTE12 complemented the mating defect in an α ste12 mutant of S. cerevisiae. In addition, it partially complemented the defects of the Magnaporthe oryzae mst12 mutant in plant infection. Knocking down PstSTE12 via host-induced gene silencing (HIGS) mediated by Barley stripe mosaic virus (BSMV) resulted in a substantial reduction in the growth and spread of hyphae in Pst and weakened the virulence of Pst on wheat. Our results suggest that PstSTE12 probably acts at an intersection participating in the invasion and mating processes of Pst, and provide new insights into the comprehension of the variation of virulence in cereal rust fungi.
A 125GOPS 583mW Network-on-Chip Based Parallel Processor with Bio-inspired Visual-Attention Engine

A network-on-chip (NoC) is applied to achieve extensive communication bandwidth required for parallel computing. A 125 GOPS NoC-based parallel processor with a bio-inspired visual attention engine (VAE) exploits both data and object-level parallelism while dissipating 583 mW by packet-based power management. The use of more PEs, VAE, and low latency NoC enables higher performance and power efficiency over the previous design. NoC-based parallel processor consisting of 12 IPs: a main processor, 8 PE clusters (PECs), VAE, a matching accelerator (MA), and an external interface. The ARMlO-compatible 32b main processor controls the overall system operations. The VAE detects the feature points on the entire image by neural network algorithms like contour extraction. The 8 PECs perform data-intensive image processing applications such as filtering and histogram calculations. The MA accelerates nearest neighbor search to obtain a final recognition result in real-time. The DMA-like external interface distributes automatically the corresponding image data to each PEC to reduce system overhead. Each core is connected to the NoC via a network interface.
Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

Background The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. Methodology/Principal Findings We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general “3 clade” structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. Conclusions/Significance This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.
Lysine11-Linked Polyubiquitination of the AnkB F-Box Effector of Legionella pneumophila

ABSTRACT The fate of the polyubiquitinated protein is determined by the lysine linkages involved in the polymerization of the ubiquitin monomers, which has seven lysine residues (K6, K11, K27, K29, K33, K48, and K63). The translocated AnkB effector of the intravacuolar pathogen Legionella pneumophila is a bona fide F-box protein, which is localized to the cytosolic side of the Legionella-containing vacuole (LCV) and is essential for intravacuolar proliferation within macrophages and amoebae. The F-box domain of AnkB interacts with the host SCF1 E3 ubiquitin ligase that triggers the decoration of the LCV with K48-linked polyubiquitinated proteins that are targeted for proteasomal degradation. Here we report that AnkB becomes rapidly polyubiquitinated within the host cell, and this modification is independent of the F-box domain of AnkB, indicating host-mediated polyubiquitination. We show that the AnkB effector interacts specifically with the host E3 ubiquitin ligase Trim21. Mass spectrometry analyses have shown that AnkB is modified by K11-linked polyubiquitination, which has no effect on its stability. This work shows the first example of K11-linked polyubiquitination of a bacterial effector and its interaction with the host Trim21 ubiquitin ligase.
Polymorphic time systems for estimating program complexity

We present a new approach to static program analysis that permits each expression in a program to be assigned an execution time estimate. Our approach uses a time system in conjunction with a conventional type system to compute both the type and the time of an expression. The time of an expression is either an integer upper bound on the number of ticks the expression will execute, or the distinguished element long that indicates that the expression contains a loop, and thus may run for an arbitrary length of time. Every function type includes a latent time that is used to communicate its expected execution time from the point of its definition to the points of its use. Unlike previous approaches, a time system works in the presence of first-class functions and separate compilation. In addition, time polymorphism allows the time of a function to depend on the times of any functions that it takes as arguments. Time estimates are useful when compiling programs for multiprocessors in order to balance the overhead of initiating a concurrent computation against the expected execution time of the computation. The correctness of our time system is proven with respect to a dynamic semantics.
Characterization of the frameshift signal of Edr, a mammalian example of programmed −1 ribosomal frameshifting

The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed −1 frameshifting in mammalian cellular genes [Shigemoto,K. , Brennan,J., Walls,E,. Watson,C.J., Stott,D. , Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29, 4079–4088]. Here, we have employed site-directed mutagenesis and RNA structure probing to characterize the Edr signal. We began by confirming the functionality and magnitude of the signal and the role of a GGGAAAC motif as the slippery sequence. Subsequently, we derived a model of the Edr stimulatory RNA and assessed its similarity to those stimulatory RNAs found at viral frameshift sites. We found that the structure is an RNA pseudoknot possessing features typical of retroviral frameshifter pseudoknots. From these experiments, we conclude that the Edr signal and by inference, the human orthologue PEG10, do not represent a novel ‘cellular class’ of programmed −1 ribosomal frameshift signal, but rather are similar to viral examples, albeit with some interesting features. The similarity to viral frameshift signals may complicate the design of antiviral therapies that target the frameshift process.
Data Science Methodology for Cybersecurity Projects

Cyber-security solutions are traditionally static and signature-based. The traditional solutions along with the use of analytic models, machine learning and big data could be improved by automatically trigger mitigation or provide relevant awareness to control or limit consequences of threats. This kind of intelligent solutions is covered in the context of Data Science for Cyber-security. Data Science provides a significant role in cyber-security by utilising the power of data (and big data), high-performance computing and data mining (and machine learning) to protect users against cyber-crimes. For this purpose, a successful data science project requires an effective methodology to cover all issues and provide adequate resources. In this paper, we are introducing popular data science methodologies and will compare them in accordance with cyber-security challenges. A comparison discussion has also delivered to explain methodologies strengths and weaknesses in case of cyber-security projects.
There Is No Evidence for a Temporal Link between Pathogen Arrival and Frog Extinctions in North-Eastern Australia

Pathogen spread can cause population declines and even species extinctions. Nonetheless, in the absence of tailored monitoring schemes, documenting pathogen spread can be difficult. In the case of worldwide amphibian declines the best present understanding is that the chytrid fungus Batrachochytrium dendrobatidis (Bd) has recently spread, causing amphibian declines and extinction in the process. However, good evidence demonstrating pathogen arrival followed by amphibian decline is rare, and analysis of putative evidence is often inadequate. Here we attempt to examine the relationship between Bd arrival and amphibian decline across north-eastern Australia, using sites where a wave-like pattern of amphibian decline was first noticed and at which intensive research has since been conducted. We develop an analytical framework that allows rigorous estimation of pathogen arrival date, which can then be used to test for a correlation between the time of pathogen arrival and amphibian decline across sites. Our results show that, with the current dataset, the earliest possible arrival date of Bd in north-eastern Australia is completely unresolved; Bd could have arrived immediately before sampling commenced or may have arrived thousands of years earlier, the present data simply cannot say. The currently available data are thus insufficient to assess the link between timing of pathogen arrival and population decline in this part of the world. This data insufficiency is surprising given that there have been decades of research on chytridiomycosis in Australia and that there is a general belief that the link between Bd arrival and population decline is well resolved in this region. The lack of data on Bd arrival currently acts as a major impediment to determining the role of environmental factors in driving the global amphibian declines, and should be a major focus of future research.
Hybrid SOM-SVM Algorithm for Real Time Series Forecasting

In this paper we show a new on-line parametric model for time series forecasting based on VapnikChervonenkis (VC) theory. Using the strong connection between support vector machines (SVM) and Regularization theory (RT), we propose a regularization operator in order to obtain a suitable expansion of radial basis functions (RBFs) with the corresponding expressions for updating neural parameters. This operator seeks for the “flattest” function in a feature space, minimizing the risk functional. Finally we mention some modifications and extensions that can be applied to control neural resources and select relevant input space.
Impact of the 2015 CMS Inpatient Psychiatric Facility Quality Reporting Rule on Tobacco Treatment

Introduction In its fiscal year 2015 final rule, the Centers for Medicare & Medicaid Services (CMS) required reporting of tobacco treatment quality measures as part of the Inpatient Psychiatric Facilities Prospective Payment System (IPF PPS). This pre-intervention, post-intervention policy analysis evaluates the impact of that policy at a large academic medical center that opted to improve performance as it implemented reporting measures. Methods Electronic medical record data were collected retrospectively for all adult (≥18 years) inpatient psychiatric admissions from January 1, 2014 to December 31, 2015. Data from admissions were analyzed to determine changes in the provision of tobacco treatment including the proportions of patients screened for tobacco use, receiving tobacco cessation counseling, and receiving tobacco cessation medication(s) using a chi-square test. Covariate analysis of treatment differences based on psychiatric diagnosis was analyzed using Cochran-Mantel-Haenszel and Breslow-Day test. Results Post-policy screening for admissions increased significantly (85% vs. 97%; p < .001). Referral to cessation counseling increased 18-fold (4% vs. 74%; p < .001). Receipt of Counselling (8% vs. 67%; p < .001) and referral for cessation medication (32% vs. 68%; p < .001) also increased dramatically. Though statistically non-significant, the number of tobacco users who actually received medications increased markedly between 2014 and 2015, 24% versus 35%. Gains in screening, referral, and treatment did not differ by psychiatric diagnosis. Conclusions The Inpatient Psychiatric Facilities Quality Reporting (IPFQR) Program resulted in a 10-fold increase in the number of smokers who received inpatient tobacco treatment. Should CMS link prospective payment to performance, it could have a major impact on quality of care for tobacco dependence. Implications This is the first study to examine the implementation and impact of new 2015 IPFQR program tobacco measures. This study may illustrate the potential effect that performance based penalties can have should facilities be required to do more than simply report on these tobacco measures. This study exemplifies the impact these new reporting measures can have when psychiatric facilities move beyond letter of the policy, to continually assess organizational performance and implement changes to improve treatment delivery.
Solar Energy Potential Assessment on Rooftops and Facades in Large Built Environments Based on LiDAR Data, Image Processing, and Cloud Computing. Methodological Background, Application, and Validation in Geneva (Solar Cadaster)

The paper presents the core methodology for assessing solar radiation and energy production on building rooftops and vertical facades (still rarely considered) of the inner-city. This integrated tool is based on the use of LiDAR, 2D and 3D cadastral data. Together with solar radiation and astronomical models it calculates the global irradiance for a set of points located on roofs, ground and facades. Although the tool takes simultaneously roofs, ground and facades, different methods of shadow casting are applied. Shadow casting on rooftops is based on image processing techniques. On the other hand, the assessment on facade involves first to create and interpolate points along the facades and then to implement a point-by-point shadow casting routine. The paper is structured in five parts: (i) state of the art on the use of 3D GIS and automated processes in assessing solar radiation in the built environment, (ii) overview on the methodological framework used in the paper, (iii) detailed presentation of the method proposed for solar modelling and shadow casting, in particular by introducing an innovative approach for modelling the Sky View Factor (SVF), (iv) demonstration of the solar model introduced in this paper through applications in Geneva’s building roofs (solar cadaster) and facades, (v) validation of the solar model in some Geneva’s spots, focusing especially on two distinct comparisons: solar model versus fisheye catchments on partially inclined surfaces (roof component); solar model versus photovoltaic simulation tool PVSyst on vertical surfaces (facades). Concerning the roof component, validation results emphasize global sensitivity related to the density of light sources on the sky vault to model the SVF. The low dense sky model with 145 light sources gives satisfying results, especially when processing solar cadasters in large urban areas, thus allowing to save computation time. In the case of building facades, introducing weighting factor in SVF calculation leads to outputs close to those obtained by PVSyst. Such good validation results make the proposed model a reliable tool to: (i) automatically process solar cadaster on building rooftops and facades at large urban scales, (ii) support solar energy planning and energy transition policies.
Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches

ABSTRACT The gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroach Shelfordella lateralis as a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such as Dysgonomonas and Parabacteroides spp. , were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.