Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor necrosis factor receptor II gene polymorphism and severity of rheumatoid arthritis.

OBJECTIVE The gene encoding tumor necrosis factor receptor type II (TNFRII) is a strong candidate in the pathogenesis of rheumatoid arthritis (RA). An association between a single-nucleotide polymorphism (196M/R) in exon 6 of the TNFRII gene and familial RA was recently reported. The present study was undertaken to test the hypothesis that there is an association between this polymorphism and the severity of RA. METHODS One hundred two white patients with early RA were included in this prospective study. The French version of the Health Assessment Questionnaire (F-HAQ) and a radiographic damage score (modified Sharp/van der Heijde method) were used to quantify the functional and structural severity of RA at baseline and after 4 years of followup. TNFRII 196M/R polymorphism genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism analysis. RESULTS Among the 102 patients with RA, 63 (61.8%) were homozygous for the 196M allele, 36 (35.3%) were heterozygous for alleles 196M and 196R, and 3 (2.9%) were homozygous for the 196R allele. At baseline, the median radiographic and F-HAQ scores did not differ between RA patients who carried the 196R allele and those who did not. After 4 years of followup, the F-HAQ score was higher in RA patients carrying the 196R allele (median 1 [interquartile range (IQR) 0.125, 1.375]) than in noncarriers (0.375 [IQR 0, 1]) (P = 0.02), while the median radiographic score did not differ between RA patients who carried the 196R allele and those who did not. CONCLUSION The results of the present study support the hypothesis that there is an association between the TNFRII 196 M/R gene polymorphism and the functional severity of early RA.
A new bandwidth adaptive non-local kernel regression algorithm for image/video restoration and its GPU realization

This paper presents a new bandwidth adaptive nonlocal kernel regression (BA-NLKR) algorithm for image and video restoration. NLKR is a recent approach for improving the performance of conventional steering kernel regression (SKR) and local polynomial regression (LPR) in image/video processing. Its bandwidth, which controls the amount of smoothing, however is chosen empirically. The proposed algorithm incorporates the intersecting confidence intervals (ICI) bandwidth selection method into the framework of NLKR to facilitate automatic bandwidth selection so as to achieve better performance. A parallel implementation of the proposed algorithm is also introduced to reduce significantly its computation time. The effectiveness of the proposed algorithm is illustrated by experimental results on both single image and videos super resolution and denoising.
Investigation of the Bed and Structural Slopes on Bed Shear Stress and Flow Characteristics around an Impermeable Groyne

In this paper, effects of the cross shore and groyne wall slopes on flow parameters around an impermeable groyne were considered using a three-dimensional numerical CFD model (i.e., FLUENT). The k-e turbulence model was used to evaluate the Reynolds stresses. The model was first applied to a vertical groyne on a flat bed and the model results were compared with the relevant experimental data. The results of this numerical test showed good agreements with the corresponding experimental measurements, in terms of water elevation, velocity magnitudes and reattachment length. The model was then applied to a series of structures with different lateral wall slopes on various cross sectional bed slopes. The numerical model results revealed that by increasing the cross shore bed slope in any case of the structural slopes, the magnitude of the maximum velocity and bed shear stresses decreased. These values decreased further as the structural slope reduced.
Probabilistic λ-calculus and Quantitative Program Analysis

We show how the framework of probabilistic abstract interpretation can be applied to statically analyse a probabilistic version of the λ-calculus. The resulting analysis allows for a more speculative use of its outcomes based on the consideration of statistically defined quantities. After introducing a linear operator based semantics for our probabilistic λ-calculus ΛP , and reviewing the framework of abstract interpretation and strictness analysis, we demonstrate our technique by constructing a probabilistic (first-order) strictness analysis for ΛP .
DySANA: dynamic speech and noise adaptation for voice activity detection

We describe a method of simultaneusly tracking noise and speech levels for signal-to-noise ratio adaptive speech endpoint detection. The method is based on the Kalman filter framework with switching observations and uses a dynamic distribution that 1) limits the rate of change of these levels 2) enforces a range on the values for the two levels and 3) enforces a ratio between the noise and the signal levels. We call this a Lombard dynamic distribution since it encodes the expectation that a speaker will increase his or her vocal intensity in noise. The method also employs a state transition matrix which encodes a prior on the states and provides a continuity constraint. The new method provides 46.1% relative improvement in WER over a baseline GMM based endpointer at 20 dB SNR.
Mechanistic Processes Controlling Persistent Changes of Forest Canopy Structure After 2005 Amazon Drought

The long‐term impact of Amazonian drought on canopy structure has been observed in ground and remote sensing measurements. However, it is still unclear whether it is caused by biotic (e.g., plant structure damage) or environmental (e.g., water deficiency) factors. We used the Community Land Model version 4.5 (CLM4.5) and radar backscatter observations from SeaWinds Scatterometer on board QuikSCAT (QSCAT) satellite to investigate the relative role of biotic and environmental factors in controlling the forest canopy disturbance and recovery processes after the 2005 Amazonian drought. We validated the CLM4.5 simulation of the drought impact and the recovery of leaf carbon (C) pool, an indicator of canopy structure, over southwestern Amazonia with QSCAT backscatter observations, which are sensitive to canopy structure change. We found that the leaf C pool simulated by CLM4.5 recovered to the 2000–2009 mean level (343 g C m−2) in 3 years after a sharp decrease in 2005, consistent with the QSCAT observed slow recovery. Through sensitivity experiments, we found that the slow C recovery was primarily due to biotic factors represented by the canopy damage and reduction of plant C pools. The recovery of soil water and the coupling between water and C pools, which is an environmental factor, only contributes ~24% to the leaf C recovery. The results showed (1) the strength of scatterometer backscatter measurements in capturing canopy damage over tropical forests and in validating C cycle models and (2) the biotic factors play the dominant role in regulating the drought induced disturbance and persistent canopy changes in CLM4.5.
Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a Species in the Genus Tumebacillus

ABSTRACT We present here the first genome sequence of a species in the genus Tumebacillus. The draft genome sequence of Tumebacillus flagellatus GST4 provides a genetic basis for future studies addressing the origins, evolution, and ecological role of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding genes for further studies.
Evaluation of Plasmodium vivax Cell-Traversal Protein for Ookinetes and Sporozoites as a Preerythrocytic P. vivax Vaccine

ABSTRACT Four different vaccine platforms, each targeting the human malaria parasite Plasmodium vivax cell-traversal protein for ookinetes and sporozoites (PvCelTOS), were generated and assessed for protective efficacy. These platforms consisted of a recombinant chimpanzee adenoviral vector 63 (ChAd63) expressing PvCelTOS (Ad), a recombinant modified vaccinia virus Ankara expressing PvCelTOS (MVA), PvCelTOS conjugated to bacteriophage Qβ virus-like particles (VLPs), and a recombinant PvCelTOS protein expressed in eukaryotic HEK293T cells (protein). Inbred BALB/c mice and outbred CD-1 mice were immunized using the following prime-boost regimens: Ad-MVA, Ad-VLPs, and Ad-protein. Protective efficacy against sporozoite challenge was assessed after immunization using a novel chimeric rodent Plasmodium berghei parasite (Pb-PvCelTOS). This chimeric parasite expresses P. vivax CelTOS in place of the endogenous P. berghei CelTOS and produces fully infectious sporozoites. A single Ad immunization in BALB/c and CD-1 mice induced anti-PvCelTOS antibodies which were boosted efficiently using MVA, VLP, or protein immunization. PvCelTOS-specific gamma interferon- and tumor necrosis factor alpha-producing CD8+ T cells were induced at high frequencies by all prime-boost regimens in BALB/c mice but not in CD-1 mice; in CD-1 mice, they were only marginally increased after boosting with MVA. Despite the induction of anti-PvCelTOS antibodies and PvCelTOS-specific CD8+ T-cell responses, only low levels of protective efficacy against challenge with Pb-PvCelTOS sporozoites were obtained using any immunization strategy. In BALB/c mice, no immunization regimens provided significant protection against a Pb-PvCelTOS chimeric sporozoite challenge. In CD-1 mice, modest protective efficacy against challenge with chimeric P. berghei sporozoites expressing either PvCelTOS or P. falciparum CelTOS was observed using the Ad-protein vaccination regimen.
A multimodal person-following system for telepresence applications

This paper presents the design and implementation of a multimodal person-following system for a mobile telepresence robot. A color histogram matching and position matching algorithm was developed for a person-recognition function using Kinect sensors. Robot motion was controlled by adjusting its velocity according to the humans position in relation to the robot. The robot was able to follow the targeted person in various person-following modes, such as the back-following mode, the side-by-side accompaniment mode as well as the front-guiding mode. An obstacle avoidance function was also implemented using the virtual potential field algorithm.
Experimental Evaluation of a Branch-and-Bound Algorithm for Computing Pathwidth and Directed Pathwidth

Path decompositions of graphs are an important ingredient of dynamic programming algorithms for solving efficiently many NP-hard problems. Therefore, computing the pathwidth and associated path decomposition of graphs has both a theoretical and practical interest. In this article, we design a branch-and-bound algorithm that computes the exact pathwidth of graphs and a corresponding path decomposition. Our main contribution consists of several nontrivial techniques to reduce the size of the input graph (preprocessing) and to cut the exploration space during the search phase of the algorithm. We evaluate experimentally our algorithm by comparing it to existing algorithms of the literature. It appears from the simulations that our algorithm offers a significant gain with respect to previous work. In particular, it is able to compute the exact pathwidth of any graph with less than 60 nodes in a reasonable running time (≤ 10min on a standard laptop). Moreover, our algorithm achieves good performance when used as a heuristic (i.e., when returning best result found within bounded time limit). Our algorithm is not restricted to undirected graphs since it actually computes the directed pathwidth that generalizes the notion of pathwidth to digraphs.
3D Human Face Modelling: Soft Tissues Landmarking

Method: Working in the Differential Geometry domain, through the Coefficients of the Fundamental Forms, the Principal Curvatures, Mean and Gaussian Curvatures and also with the derivatives and the Shape and Curvedness Indexes, a Matlab® algorithm for extracting nine landmarks is built. Each landmark is unique for the behaviour of these geometrical descriptors in correspondence of its zone of interest. This particular behaviour of the descriptor is used to localize each landmark and for extracting it.
Arq Gastroenterol 35 ARQGA / 1054 STAPLED HEMORRHOIDECTOMY FOR THE TREATMENT OF HEMORRHOIDS

Background – The use of circular staplers in the treatment of hemorrhoidal disease is known as a simple procedure, with low morbidity, less post-treatment pain and with the same efficacy when compared to the classical hemorrhoidectomy. Aim – Analyze the operative technique, intra-operative and immediate postoperative complications and late results in 100 patients treated for hemorrhoid disease by stapling technique. Patients and Methods – The group included 53 males and 47 females with mean age of 49.8 years, operated during the period June 2000 to June 2002 in the “Hospital Universitário” (São Paulo University Hospital) and “Hospital Sírio Libanês”, in São Paulo, SP, Brazil. Results – The majority of patients (78%) were discharged on the first post-operative day. Eight patients required supplementary analgesia and were given intramuscular diclofenac sodium and four of them received intramuscular tramadol. One intraoperative complication was bleeding which was difficult to control and required a blood transfusion. One patient was reoperated on the first postoperative day due to intermittent and persistent bleeding, however without hemodynamic changes or a drop in hematocrit. Two patients presented hemorrhoidal thrombosis in the early postoperative stage. The postoperative follow-up displayed: recurrence of prolapse, five cases (5%); anal sub-stenosis, two cases (2%); anal fissure, one case (1%); persistent pain, two cases (2%). Seven reoperations were performed: one due to bleeding, one due to sub-stenosis and five due to recurrence of hemorrhoidal prolapse and persistence of symptoms. Conclusion – Stapling is simple to accomplish, has low postoperative pain and rate of complications, however, the incidence of late reoperations is rather high and therefore major follow-up for better analysis is required. HEADINGS – Hemorrhoids, surgery. Surgical staplers. Suture techniques. Pain, postoperative. 1 Hospital Sírio Libanês; 2 Hospital Universitário, of University of São Paulo; 3 Department of Gastroenterology and 4 Department of Surgery of São Paulo University Medical School, São Paulo, SP, Brazil. Endereço para correspondência: Dr. Sergio Carlos Nahas – Rua Jabebira, 136 – 05602-020 – São Paulo, SP, Brazil. e-mail: sergionahas@uol.com. br ART IGO OR IGIN AL / OR IGIN AL ART ICLE
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I

Significance Using large-scale classical and quantum simulations, we elucidate key aspects of the molecular function of complex I, a protein central to biological energy conversion. Complex I serves as the primary electron entry point into the mitochondrial and bacterial respiratory chains and operates as a redox-coupled proton pump. Our simulations suggest that transient water chains establish highly efficient pathways for proton transfer. Our findings form a basis for understanding long-range energy conversion in complex I, and mechanistic similarities to other redox-driven proton-pumps, such as cytochrome c oxidase and bacteriorhodopsin. Complex I serves as the primary electron entry point into the mitochondrial and bacterial respiratory chains. It catalyzes the reduction of quinones by electron transfer from NADH, and couples this exergonic reaction to the translocation of protons against an electrochemical proton gradient. The membrane domain of the enzyme extends ∼180 Å from the site of quinone reduction to the most distant proton pathway. To elucidate possible mechanisms of the long-range proton-coupled electron transfer process, we perform large-scale atomistic molecular dynamics simulations of the membrane domain of complex I from Escherichia coli. We observe spontaneous hydration of a putative proton entry channel at the NuoN/K interface, which is sensitive to the protonation state of buried glutamic acid residues. In hybrid quantum mechanics/classical mechanics simulations, we find that the observed water wires support rapid proton transfer from the protein surface to the center of the membrane domain. To explore the functional relevance of the pseudosymmetric inverted-repeat structures of the antiporter-like subunits NuoL/M/N, we constructed a symmetry-related structure of a possible alternate-access state. In molecular dynamics simulations, we find the resulting structural changes to be metastable and reversible at the protein backbone level. However, the increased hydration induced by the conformational change persists, with water molecules establishing enhanced lateral connectivity and pathways for proton transfer between conserved ionizable residues along the center of the membrane domain. Overall, the observed water-gated transitions establish conduits for the unidirectional proton translocation processes, and provide a possible coupling mechanism for the energy transduction in complex I.
Large-Scale Multi-Label Learning with Incomplete Label Assignments

Multi-label learning deals with the classification problems where each instance can be assigned with multiple labels simultaneously. Conventional multi-label learning approaches mainly focus on exploiting label correlations. It is usually assumed, explicitly or implicitly, that the label sets for training instances are fully labeled without any missing labels. However, in many real-world multi-label datasets, the label assignments for training instances can be incomplete. Some groundtruth labels can be missed by the labeler from the label set. This problem is especially typical when the number instances is very large, and the labeling cost is very high, which makes it almost impossible to get a fully labeled training set. In this paper, we study the problem of large-scale multi-label learning with incomplete label assignments. We propose an approach, called Mpu, based upon positive and unlabeled stochastic gradient descent and stacked models. Unlike prior works, our method can effectively and efficiently consider missing labels and label correlations simultaneously, and is very scalable, that has linear time complexities over the size of the data. Extensive experiments on two real-world multi-label datasets show that our Mpu model consistently outperform other commonly-used baselines.
The Schoenlein-Henoch Syndrome in Childhood with Particular Reference to the Occurrence of Nephritis

The full syndrome of a purpuric skin eruption, intestinal bleeding and swollen joints was first described by Henoch (1874). Since that date there have been numerous papers about the syndrome. Gairdner (1948) reviewed the literature and grouped the condition with acute rheumatism, acute nephritis and polyarteritis nodosa. The name ' Schoenlein-Henoch Syndrome' used by Gairdner is adhered to in the present communication. Attention to the association of the syndrome with nephritis was drawn by Henoch (1899), and this was amplified by other authors (Macalister, 1906; Osler, 1914). Nephritis is now recognized as being the most serious complication of the disease. Gairdner (1948) found evidence of renal involvement in all but one of his 12 cases. Haematuria was reported in four of 44 cases described by Davis (1948) and in 10 of 20 cases described by Balf (1951). In neither of these papers was it made clear in all cases whether the haematuria was macroscopic only or whether microscopic haematuria was also included, and neither author mentioned whether complete and repeated urine analyses were made in their cases. The 44 cases reported by Davis included adults as well as children, the ages ranging from 4 to 71 years. Unfortunately he did not state the proportion of children in his series. No paper has been found which sets out specifically to determine the incidence of nephritis in a large series of cases. This paper describes the relapse rate in 40 cases of the Schoenlein-Henoch syndrome in children, with the incidence and progress of complicating nephritis. Material Only cases in which there was no doubt as to diagnosis, each exhibiting at least the typical rash of maculo-papules and petechiae and either abdominal or joint symptoms and having normal platelet counts, have been admitted to this study. All the patients attended either the Children's Hospital, Sheffield, or the paediatric department of the City General Hospital, Sheffield, during the five-year period of January, 1947, to December, 1951. The urine was examined microscopically and chemically regularly for at least two months after the start of the disease and one month after clinical recovery. Twenty-seven cases were followed-up for periods ranging from six months to five years after the onset of the disease. Of the remaining patients, in eight the disease was of too recent onset to include them in the group followed-up, and five could not be traced. In children whose urine contained more than 10 mg. % of protein and red blood cells and casts in the centrifuged deposit, 12-hour Addis counts were made, using the criteria of Giles (1947) for normality.
Theory of true-amplitude one-way wave equations and true-amplitude common-shot migration

One-way wave operators are powerful tools for forward modeling and migration. Here, we describe a recently developed true-amplitude implementation of modified one-way operators and present some numerical examples. By “true-amplitude” one-way forward modeling we mean that the solutions are dynamically correct as well as kinematically correct. That is, ray theory applied to these equations yields the upward- and downward-traveling eikonal equations of the full wave equation, and the amplitude satisfies the transport equation of the full wave equation. The solutions of these equations are used in the standard wave-equation migration imaging condition. The boundary data for the downgoing wave is also modified from the one used in the classic theory because the latter data is not consistent with a point source for the full wave equation. When the full wave-form solutions are replaced by their ray-theoretic approximations, the imaging formula reduces to the common-shot Kirchhoff inversion formula. In this sense.
Covert channel detection using Information Theory

This paper presents an information theory based detection framework for covert channels. We first show that the usual notion of interference does not characterize the notion of deliberate information flow of covert channels. We then show that even an enhanced notion of “iterated multivalued interference” can not capture flows with capacity lower than one bit of information per channel use. We then characterize and compute the capacity of covert channels that use control flows for a class of systems.
Off-Grid Solar Power Bank

: In this paper, a single-switch two-stage DC-DC conversion circuit is proposed for an off-grid solar power application. A photovoltaic (PV) panel powers the load and a storage unit (battery) via the proposed circuit. The battery is designed to balance the supply and the demand of power under different irradiation situations. Based on conventional cascaded DC-DC converters, the proposed design is developed with the single switch technique reducing size, cost and power loss. The control scheme in this design is pulse width modulation (PWM) with pulse frequency modulation (PFM). The PWM module is similar to conventional design except its ramp signal with a variable frequency is provided by a resettable integrator. As a result, the PWM and PFM modules regulate the two stages of the proposed circuit separately with the same switching control signal. In this paper, the modes of operation of the circuit are discussed as well as the control schemes. The design process is described along with the circuit analysis and comparisons with conventional design are made as well. A prototype has been built to verify the proposed circuit with simulation and experimental results.