Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy*

HemAT from Bacillus subtilis (HemAT-Bs) is a heme-based O2 sensor protein that acts as a signal transducer responsible for aerotaxis. HemAT-Bs discriminates its physiological effector (O2) from other gas molecules (CO and NO), although all of them bind to a heme. To monitor the conformational changes in the protein moiety upon binding of different ligands, we have investigated ultraviolet resonance Raman (UVRR) spectra of the ligand-free and O2-, CO-, and NO-bound forms of full-length HemAT-Bs and several mutants (Y70F, H86A, T95A, and Y133F) and found that Tyr70 in the heme distal side and Tyr133 and Trp132 from the G-helix in the heme proximal side undergo environmental changes upon ligand binding. In addition, the UVRR results confirmed our previous model, which suggested that Thr95 forms a hydrogen bond with heme-bound O2, but Tyr70 does not. It is deduced from this study that hydrogen bonds between Thr95 and heme-bound O2 and between His86 and heme 6-propionate communicate the heme structural changes to the protein moiety upon O2 binding but not upon CO and NO binding. Accordingly, the present UVRR results suggest that O2 binding to heme causes displacement of the G-helix, which would be important for transduction of the conformational changes from the sensor domain to the signaling domain.
From structure-from-motion point clouds to fast location recognition

Efficient view registration with respect to a given 3D reconstruction has many applications like inside-out tracking in indoor and outdoor environments, and geo-locating images from large photo collections. We present a fast location recognition technique based on structure from motion point clouds. Vocabulary tree-based indexing of features directly returns relevant fragments of 3D models instead of documents from the images database. Additionally, we propose a compressed 3D scene representation which improves recognition rates while simultaneously reducing the computation time and the memory consumption. The design of our method is based on algorithms that efficiently utilize modern graphics processing units to deliver real-time performance for view registration. We demonstrate the approach by matching hand-held outdoor videos to known 3D urban models, and by registering images from online photo collections to the corresponding landmarks.
A flexible transaction model for software engineering

It is generally recognized that the classical transaction model, providing atomicity and serializability, is too strong for certain application areas since it unnecessarily restricts concurrency. The author is concerned with supporting cooperative work in multiuser design environments, particularly teams of programmers cooperating to develop and maintain software systems. An extended transaction model that meets the special requirements of software engineering projects is presented, possible implementation techniques are described, and a number of issues regarding the incorporation of such a model into multiuser software development environments are discussed. <<ETX>>
Extracellular Matrix–Bound Angiopoietin-Like 4 Inhibits Endothelial Cell Adhesion, Migration, and Sprouting and Alters Actin Cytoskeleton

Angiopoietin-like 4 (ANGPTL4) is a secreted protein that belongs to the angiopoietin family and is involved in angiogenesis and metabolism regulation. We previously reported the induction of angptl4 by hypoxia in endothelial cells and in human ischemic tissues from peripheral artery disease. We here observed in a mouse model of hindlimb ischemia that the mRNA upregulation in the vessels correlates with the accumulation of the full-length protein in ischemic tissues. We then investigated its functions in endothelial cells. In response to hypoxia, endogenous ANGPTL4 accumulates in the subendothelial extracellular matrix (ECM). Although the secreted protein undergoes proteolysis leading to truncated fragments present in the medium, only full-length ANGPTL4 interacts with the ECM. Competition and direct binding assays indicate that the strong interaction of ANGPTL4 with the ECM is heparin/heparan sulfate proteoglycan dependent. The balance between matrix-associated and soluble forms of ANGPTL4 points to the role of the ECM in the regulation of its bioavailability. The angiogenic function of the ECM-bound full-length protein was investigated using either the form associated with the conditioned ECM from ANGPTL4-transfected HEK293 cells or the purified immobilized protein. We show that matrix-associated and immobilized ANGPTL4 limit the formation of actin stress fibers and focal contacts in the adhering endothelial cells and inhibit their adhesion. Immobilized ANGPTL4 also decreases motility of endothelial cells and inhibits the sprouting and tube formation. Altogether, these findings show that hypoxic endothelial cells accumulate ANGPTL4 in the ECM, which in turn negatively regulates their angiogenic capacities through an autocrine pathway.
Clinical and pathological characteristics of male patients with systemic lupus erythematosus from northeast China : a ten-year retrospective study

This study was designed to specifically compare the clinical and pathological characteristics of male patients from northeast China, who were diagnosed with systemic lupus erythematosus (SLE). The data from 777 SLE patients were retrospectively analyzed. Among these, 85 patients were male, while 692 were female. Our retrospective analysis of the clinical and pathological data indicated that the male-to-female ratio for SLE was 1 to 8.14, and male SLE patients typically displayed lower frequency of photosensitivity and arthritis, but a higher Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score. Male patients also had a high frequency of proteinuria and a low frequency of anti-Ro/Anti-Sjögren’s-syndrome-related antigen A (SSA). The 73 male lupus nephritis (LN) patients displayed a high incidence of renal dysfunction in all clinical types, and 42 among these with type IV pathological type, underwent renal biopsies. In addition, type V was observed to be the most common pathological type in male patients with occult nephritis (60.0%), whereas type IV and III appeared to be the common pathological types in male patients with nephritis syndrome. In addition, male patients with nephrotic syndrome displayed type V pathological type, while those with renal dysfunction had type IV and type IV+V pathological types. Moreover, male patients with LN also displayed a lower frequency of complete response (CR). Thus, it is recommended to consider gender differences early, in order to aid accurate diagnosis and necessary treatment. Overall, renal biopsy should be ideally considered for better outcomes, especially in male patients with LN.
Human Pose Estimation with Regression by Fusing MultiView Visual Information

We consider the problem of estimating 3D human body pose from visual signals within a discriminative framework. It is challenging because there is a wide gap between complex 3D human motion and planar visual observation, which makes this a severally ill-conditioned problem. In this paper, we focus on three critical factors to tackle human body pose estimation, namely, feature extraction, learning algorithm and camera utilization. On the feature level, we describe images using the salient interest points represented by SIFT-like descriptors, in which the position, appearance, and local structural information are encoded simultaneously. On the learning algorithm level, we propose to use Gaussian processes and multiple linear regression to model the mapping between poses and features. Fusing image information from multiple cameras in different views is of great interest to us on the camera level. We make a comprehensive evaluation on the HumanEva database and get two new insights into the three crucial issues for human pose estimation: (1) Although the choice of feature is very important to the problem, once the learning algorithm becomes efficient, the choice of feature is no longer critical; (2) The impact of information combination from multiple cameras on pose estimation is closely related to not only the quantity of image information, but also its quality. In most cases it’s true that the more information is involved, the better results can be achieved. But when the information quantity is the same, the differences in quality will lead to totally different performance. Furthermore, dense evaluations demonstrate that our approaches are an accurate and robust solution to the human body pose estimation problem.
Association between HIV/AIDS and Multi-Drug Resistance Tuberculosis: A Systematic Review and Meta-Analysis

Background Human immunodeficiency virus (HIV), multi-drug resistant tuberculosis (MDR) is emerging as major challenge facing tuberculosis control programs worldwide particularly in Asia and Africa. Findings from different studies on associations of HIV co-infection and drug resistance among patients with TB have been contradictory (discordant). Some institution based studies found strongly increased risks for multi-drug resistant TB (MDR TB) among patients co-infected with TB and HIV, whereas other studies found no increased risk (it remains less clear in community based studies. The aim was to conduct a systematic review and meta-analysis of the association between multi-drug resistant tuberculosis and HIV infection. Methods and findings Systematic review of the published literature of observational studies was conducted. Original studies were identified using databases of Medline/Pubmed, Google Scholar and HINARI. The descriptions of original studies were made using frequency and forest plot. Publication bias was assessed using Funnel plot graphically and Egger weighted and Begg rank regression tests statistically. Heterogeneity across studies was checked using Cochrane Q test statistic and I2. Pool risk estimates of MDR-TB and sub-grouping analysis were computed to analyze associations with HIV. Random effects of the meta-analysis of all 24 observational studies showed that HIV is associated with a marginal increased risk of multi-drug resistant tuberculosis (estimated Pooled OR 1.24; 95%, 1.04–1.43). Subgroup analyses showed that effect estimates were higher (Pooled OR 2.28; 95%, 1.52–3.04) for primary multi-drug resistance tuberculosis and moderate association between HIV/AIDS and MDR-TB among population based studies and no significant association in institution settings. Conclusions This study demonstrated that there is association between MDR-TB and HIV. Capacity for diagnosis of MDR-TB and initiating and scale up of antiretroviral treatment, and collaborations between HIV and TB control programs need to be considered and strengthened.
Towards Efficient Anonymous Communications in Sensor Networks

Anonymous communication is a challenging task in resource constrained wireless sensor networks (WSN). However, anonymity is important for many sensor networks, in which we want to conceal the location and identify of important nodes (such as source nodes and base stations) from attackers. Existing WSN anonymous protocols either cannot achieve complete anonymity, or have large computation and/or storage overheads. In this paper, we present an efficient anonymous communication protocol for sensor networks. Our protocol can achieve sender/source anonymity, communication -relationship anonymity, and the base station anonymity simultaneously, while having small overheads on computation, storage and communication.
UDP identification and error mitigation in toa-based indoor localization systems using neural network architecture

Time-of-Arrival (ToA) based localization has attracted considerable attention for solving the very complex and challenging problem of indoor localization, mainly due to its fine range estimation process. However, ToA-based localization systems are very vulnerable to the blockage of the direct path (DP) and occurrence of undetected direct path (UDP) conditions. Erroneous detection of other multipath components as DP, which corresponds to the true distance between transmitter and receiver, introduces substantial ranging and localization error into ToA-based systems. Therefore, in order to enable robust and accurate ToA-based indoor localization, it is important to identify and mitigate occurrence of DP blockage. In this paper we present two methodologies to identify and mitigate the UDP conditions in indoor environments. We first introduce our identification technique which utilizes the statistics of radio propagation channel metrics along with binary hypothesis testing and then we introduce our novel identification technique which integrates the same statistics into a neural network architecture. We analyze each approach and the effects of neural network parameters on the accuracy of the localization system. We also compare the results of the two approaches in a sample indoor environment using both real-time measurement and ray tracing simulation. The identification metrics are extracted from wideband frequency-domain measurements conducted in a typical office building with a system bandwidth of 500 MHz, centered around 1 GHz. Then we show that with the knowledge of the channel condition, it is possible to improve the localization performance by mitigating those UDP-induced ranging errors. Finally, we compare the standard deviation of localization error of traditional localization system and UDP identification-enhanced localization system with their respective lower bound.
Use of Objective Psychomotor Tests in Health Professionals

Evaluation of psychomotor skills is undertaken in a number of broad contexts. This includes testing of health professional populations as a measure of innate ability, to evaluate skill acquisition, or to compare professions. However, the use of psychomotor tests is frequently confounded by a lack of understanding of a particular tool's psychometric properties, strengths, and weaknesses. To identify and appraise the most commonly used tests on health professional populations, 86 articles were reviewed and the top nine tests identified. Few tests have had sufficient validity or reliability testing on health professionals. Based on the evidence available, use of the Grooved Pegboard Test, the Purdue Pegboard Test, or the Finger Tapping Test is recommended for the evaluation of dexterity in a health professional population; however, this choice may be dependent on the task(s) to which findings are generalised. More rigorous evaluation of validity and other psychometric properties is required.
No evidence for accumulation of insulin glargine (LANTUS®): a multiple injection study in patients with Type 1 diabetes

Aims Insulin glargine is a long‐acting insulin analogue that is metabolically active for at least 24 h. We investigated the multiple‐dose pharmacokinetic properties of insulin glargine to determine whether daily injections lead to the accumulation of circulating insulin levels and a corresponding decrease in blood glucose levels in patients with Type 1 diabetes.
Has the U.S. Finance Industry Become Less Efficient? on the Theory and Measurement of Financial Intermediation

I use the neoclassical growth model to study financial intermediation in the U.S. over the past 140 years. I measure the cost of intermediation on the one hand, and the production of assets and liquidity services on the other. Surprisingly, the model suggests that the finance industry has become less efficient: the unit cost of intermediation is higher today than it was a century ago. Improvements in information technology seem to have been cancelled out by increases in trading activities whose social value is difficult to assess.
Galaxy evolution in clusters up to z= 1.0

We present a combined study of the colour-magnitude relation, colour distribution and luminosity function (LF) of a sample of 24 clusters at redshifts 0.3 < z < 1. The sample is largely composed of X-ray selected/detected clusters. Most of the clusters at redshifts z < 0.6 display X-ray luminosity or richness typical of poor clusters or groups, rather than the more typical, massive clusters studied in literature at redshifts z? 0.3. All our clusters, including groups, display a colour-magnitude relation consistent with a passively evolving stellar population formed at a redshift z f ? 2, in accordance with observed galaxy populations in more massive clusters studied at comparable redshifts. Colours and luminosity functions (LFs) show that the cluster galaxy population is consistent with the presence of at least two components: old systems formed at high redshift that have evolved passively from that epoch, together with a galaxy population displaying more recent star formation. The former population forms at 2? z f ? 5, the latter at redshifts z < 1. A model in which stars do not evolve is clearly rejected both by the colour of reddest galaxies and by the characteristic luminosity m* measures. All clusters (with one possible exception) are detected independently by an almost three-dimensional optical search employing sky position and colour - this despite the primary X-ray selection and low X-ray flux/optical richness displayed by most of the sample.
A Response Surface Analysis of Propofol–Remifentanil Pharmacodynamic Interaction in Volunteers

Background: Characterizing drug interactions using a response surface allows for the determination of the interaction over a complete range of clinically relevant concentrations. Gathering the data necessary to create this surface is difficult to do in a clinical setting and requires the use of volunteer experiments with surrogate noxious stimuli to adequately control the process for data collection. The pharmacodynamic synergy of opioids and hypnotics was investigated using a volunteer study paradigm. Methods: Twenty-four volunteer subjects (12 male, 12 female) were studied using computer-controlled infusions of propofol and remifentanil to create an increasing staircase drug concentration profile in each subject. Three different drug delivery profiles were administered to subjects, one with a single agent and two with combinations of propofol and remifentanil. At each plateau of the staircase profile, drug effect was assessed using four surrogate measures: Observer Assessment of Alertness/Sedation score, tibial pressure algometry, electrical tetany, and response to laryngoscopy. Response surfaces were developed that mapped the interaction of propofol and remifentanil to these surrogate effect measures in all subjects. An interaction parameter was used to assess whether these two drugs behave synergistically to blunt response to noxious stimuli. Results: The response surfaces showed considerable synergy between remifentanil and propofol for blunting response to the noxious stimuli. The interaction index, a measure of synergy, was 8.2 and 14.7 for response to algometry and tetany, respectively (P < 0.001), and 5.1 and 33.2 for sedation and laryngoscopy, respectively (P < 0.001), using the Greco interaction model. The surrogate stimuli mapped to clinically relevant concentrations for these agents in combination. Conclusions: The response surface models reveal the tremendous synergy between remifentanil and propofol. The surface morphologic features give some indication of the relative contribution of sedation and analgesia to blunting subject response. Further, the results of this investigation validate the volunteer study paradigm and use of surrogate effect measures for its clinical relevance.
General trajectory prior for Non-Rigid reconstruction

Trajectory basis Non-Rigid Structure From Motion (NRSFM) currently faces two problems: the limit of reconstructability and the need to tune the basis size for different sequences. This paper provides a novel theoretical bound on 3D reconstruction error, arguing that the existing definition of reconstructability is fundamentally flawed in that it fails to consider system condition. This insight motivates a novel strategy whereby the trajectory's response to a set of high-pass filters is minimised. The new approach eliminates the need to tune the basis size and is more efficient for long sequences. Additionally, the truncated DCT basis is shown to have a dual interpretation as a high-pass filter. The success of trajectory filter reconstruction is demonstrated quantitatively on synthetic projections of real motion capture sequences and qualitatively on real image sequences.
Paediatric HIV and elimination of mother-to-child transmission of HIV in the ASEAN region: a call to action

Abstract Recent achievements in scaling up paediatric antiretroviral therapy (ART) have changed the life of children living with HIV, who now stay healthy and live longer lives. However, as it becomes more of a chronic infection, a range of new problems have begun to arise. These include the disclosure of HIV serostatus to children, adherence to ART, long-term toxicities of antiretroviral drugs and their sexual and reproductive health, which are posing significant challenges to the existing health systems caring for children with HIV with limited resources, experiences and capacities. While intensified efforts and actions to improve care and treatment for these children are needed, it is crucial to accelerate the prevention of mother-to-child transmission (PMTCT) of HIV, which is the main cause of paediatric HIV in the ASEAN region so as to eliminate the fundamental cause of the problem. This report argues that given over 70% of women have access to at least one antenatal care visit in the region and acceptance of HIV testing after receiving counselling on PMTCT could be as high as 90%, there is an opportunity to strengthen PMTCT services and eventually eliminate new paediatric HIV infections in the ASEAN countries.
Modelling Genetic Variations using Fragmentation-Coagulation Processes

We propose a novel class of Bayesian nonparametric models for sequential data called fragmentation-coagulation processes (FCPs). FCPs model a set of sequences using a partition-valued Markov process which evolves by splitting and merging clusters. An FCP is exchangeable, projective, stationary and reversible, and its equilibrium distributions are given by the Chinese restaurant process. As opposed to hidden Markov models, FCPs allow for flexible modelling of the number of clusters, and they avoid label switching non-identifiability problems. We develop an efficient Gibbs sampler for FCPs which uses uniformization and the forward-backward algorithm. Our development of FCPs is motivated by applications in population genetics, and we demonstrate the utility of FCPs on problems of genotype imputation with phased and unphased SNP data.
Psychometric properties of the Czech version of the Beck Anxiety Inventory - comparison between diagnostic groups.

OBJECTIVE Beck anxiety inventory (BAI) is widely used self-rating questionnaire evaluating the severity of anxiety symptoms. The aim of our study was to confirm validity and reliability of Czech version of BAI, identify cut-off points and prove sensitivity to measure improvement after therapy. METHODS The patients selected for the study were treated in the department of psychiatry, University Hospital Olomouc between January 2008 and 2014. Patients meeting criteria for anxiety, or depressive disorder were involved. RESULTS 789 patients and 284 healthy controls agreed to participate in the study. Czech version of Beck anxiety inventory proved high internal consistency (α=0.92) and good test-retest reliability over one week (BAI seems to be independent of other used scales - Beck depression inventory and the Clinical Global Impression. BAI is also sensitive to measure change after therapy. CONCLUSION Czech version of BAI was found to have enough internal stability and test-retest reliability same as the original version. It may also be useful to detect improvement after therapy.