Miracle-dz/UniFAR-FTUs huggingface dataset:
Pain rating schema: three distinct subgroups of individuals emerge when rating mild, moderate, and severe pain

Background While the validity of pain assessment has been well documented, the underlying schema (ie, organized, preconceived ideas) of how individuals interpret numerical pain ratings is not well understood. This study’s objectives were to examine numerical pain intensity ratings, from (0 to 10 cm on the visual analog scale [VAS]) across multiple severities of commonly experienced acute pain conditions to determine whether the ratings differed between these pain conditions and/or between individuals. Methods A community sample (N=365, 66% female) rated their anticipated pain intensity (VAS) for threshold, mild, moderate, severe, and tolerance level, using several common pain conditions: headache, toothache, joint injury, delayed-onset muscle soreness, burns, and “general pain. ” Results Cluster analysis revealed three subgroups of individuals, suggesting three types of underlying pain rating schema: 1) Low Rating subgroup (low VAS pain intensity ratings across all the pain severity categories); 2) Low/High Rating subgroup (low VAS pain intensity rating for mild, but high VAS pain intensity rating for severe pain); and 3) High Rating subgroup (high VAS pain intensity ratings across all the pain severity categories). Overall, differences between pain conditions were small: muscle soreness pain intensity was consistently rated lower than the other pain types across severities. The highest pain ratings varied between joint injury and general pain, depending on severity level. No effects of sex or current experience of pain were noted. Conclusion The results indicate that: 1) three distinct pain schemas were present in this community-based sample, indicating significant variation in how pain scales are utilized and/or interpreted between clusters of individuals; 2) pain ratings vary by condition, but these differences are minor; and 3) pain rating schemas are not significantly different between males and females or between individuals with and without current pain.
Hydrogels With Integrin-Binding Angiopoietin-1–Derived Peptide, QHREDGS, for Treatment of Acute Myocardial Infarction

Background—Hydrogels are being actively investigated for direct delivery of cells or bioactive molecules to the heart after myocardial infarction (MI) to prevent cardiac functional loss. We postulate that immobilization of the prosurvival angiopoietin-1–derived peptide, QHREDGS, to a chitosan-collagen hydrogel could produce a clinically translatable thermoresponsive hydrogel to attenuate post-MI cardiac remodeling. Methods and Results—In a rat MI model, QHREDGS-conjugated hydrogel (QHG213H), control gel, or PBS was injected into the peri-infarct/MI zone. By in vivo tracking and chitosan staining, the hydrogel was demonstrated to remain in situ for 2 weeks and was cleared in ≈3 weeks. By echocardiography and pressure–volume analysis, the QHG213H hydrogel significantly improved cardiac function compared with the controls. Scar thickness and scar area fraction were also significantly improved with QHG213H gel injection compared with the controls. There were significantly more cardiomyocytes, determined by cardiac troponin-T staining, in the MI zone of the QHG213H hydrogel group; and hydrogel injection did not induce a significant inflammatory response as assessed by polymerase chain reaction and an inflammatory cytokine assay. The interaction of cardiomyocytes and cardiac fibroblasts with QHREDGS was found to be mediated by &bgr;1-integrins. Conclusions—We demonstrated for the first time that the QHG213H peptide–modified hydrogel can be injected in the beating heart where it remains localized for a clinically effective period. Moreover, the QHG213H hydrogel induced significant cardiac functional and morphological improvements after MI relative to the controls.
The rendezvous algorithm: multiclass semi-supervised learning with Markov random walks

We consider the problem of multiclass classification where both labeled and unlabeled data points are given. We introduce and demonstrate a new approach for estimating a distribution over the missing labels where data points are viewed as nodes of a graph, and pairwise similarities are used to derive a transition probability matrix P for a Markov random walk between them. The algorithm associates each point with a particle which moves between points according to P. Labeled points are set to be absorbing states of the Markov random walk, and the probability of each particle to be absorbed by the different labeled points, as the number of steps increases, is then used to derive a distribution over the associated missing label. A computationally efficient algorithm to implement this is derived and demonstrated on both real and artificial data sets, including a numerical comparison with other methods.
On-the-fly appearance quantization on the GPU for 3D broadcasting

This paper presents an improved client-server system that increases the availability of remote 3D data. In order to reduce the required bandwidth, the data related to the appearance (color and normal) involved in the rendering of meshes and point clouds is quantized on-the-fly during the transmission to the final client, without reducing the geometric complexity. Our new quantization technique for the appearance that can be implemented on the GPU, strongly reduces the CPU load on the server-side and the transmission time is largely decreased.
Mortality Associated with Influenza in Tropics, State of São Paulo, Brazil, from 2002 to 2011: The Pre-Pandemic, Pandemic, and Post-Pandemic Periods

The impact of the seasonal influenza and 2009 AH1N1 pandemic influenza on mortality is not yet completely understood, particularly in tropical and subtropical countries. The trends of influenza related mortality rate in different age groups and different outcomes on a area in tropical and subtropical climate with more than 41 million people (State of São Paulo, Brazil), were studied from 2002 to 2011 were studied. Serfling-type regression analysis was performed using weekly mortality registries and virological data obtained from sentinel surveillance. The prepandemic years presented a well-defined seasonality during winter and a clear relationship between activity of AH3N2 and increase of mortality in all ages, especially in individuals older than 60 years. The mortality due to pneumonia and influenza and respiratory causes associated with 2009 pandemic influenza in the age groups 0–4 years and older than 60 was lower than the previous years. Among people aged 5–19 and 20–59 years the mortality was 2.6 and 4.4 times higher than that in previous periods, respectively. The mortality in all ages was higher than the average of the previous years but was equal mortality in epidemics of AH3N2. The 2009 pandemic influenza mortality showed significant differences compared to other years, especially considering the age groups most affected.
Microstructural imaging of the eye and mechanical mapping of retinal tissue using Atomic Force Microscopy (AFM)

The objective of this study is to investigate the structures and mechanical properties of mouse eyes in correspondence with their functions. Moreover, my work places particular emphasis on the retina as it is associated with several diseases. To measure the mechanical properties of retinal tissue, eye samples of mice are taken and analyzed utilizing Force Spectroscopy to determine the Young’s modulus. Force mapping of the sample is done by nanoindentation (force curves), and Atomic Force Microscopy (AFM) is used to image the topography of our sample. AFM and force mapping provide key information on the nanoscale mechanical properties and structure of normal tissue. This fine level of detail provides insight on a length scale relevant to an individual cell. Our results also provide a baseline structure to enable the identification of mechanical indicators for disease. Most of the diseases that affect the eyes, including glaucoma and macular degenerations involve structural changes in the eyes, for example, affecting the photoreceptor or degeneration of layers thus causing eye damage. Damage on the nanoscale is not obvious given that research in that area is still underdeveloped. Therefore, the use of nanomechanical mapping has proved to be very useful because of providing in-depth knowledge regarding the characteristic microstructure and mechanical features of the normal eye.
Chapter 1 Generalizability Theory and Item Response Theory

Item response theory is usually applied to items with a selected-response format, such as multiple choice items, whereas generalizability theory is usually applied to constructed-response tasks assessed by raters. However, in many situations, raters may use rating scales consisting of items with a selected-response format. This chapter presents a short overview of how item response theory and generalizability theory were integrated to model such assessments. Further, the precision of the estimates of the variance components of a generalizability theory model in combination with twoand three-parameter models is assessed in a small simulation study.
Pedestrian Localization and Trajectory Reconstruction in a Surveillance Camera Network

In this paper, we propose a high accuracy solution for locating pedestrians from video streams in a surveillance camera network. For each camera, we formulate the vision-based localization service as detecting foot-points of pedestrians in the ground plane. We address two critical issues that strongly affect the foot-point's detection results: casting shadows and pruning detection results due to occlusion. For the first issue, we adopt a removing shadow technique based on a learning-based approach. For the second issue, a regression model is proposed to prune the wrong foot-point detection results. The regression model plays a role in estimating the position by using the human factors such as height, width and its ratio. A correlation of the detected foot-points and the results estimated from the regression model is examined. Once a foot-point is missed due to uncorrelated problem, a Kalman filter is deployed to predict the current location. To link the trajectory of the human in the camera network, we base on an observation about the same ground-plane/floor in view of cameras then the transformation between a pair of cameras could be computed offline. In the experiments, a high accuracy performance for locating the pedestrians and a real-time computation are achieved.
Effect of hyperbaric oxygen treatment on incorporation of an autogenous cancellous bone graft in a nonunion diaphyseal ulnar defect in cats.

OBJECTIVE To determine whether hyperbaric oxygen treatment (HBOT) would affect incorporation of an autogenous cancellous bone graft in diaphyseal ulnar defects in cats. ANIMALS 12 mature cats. PROCEDURE Bilateral nonunion diaphyseal ulnar defects were created in each cat. An autogenous cancellous bone graft was implanted in 1 ulnar defect in each cat, with the contralateral ulnar defect serving as a nongrafted specimen. Six cats were treated by use of hyperbaric oxygen at 2 atmospheres absolute for 90 minutes once daily for 14 days, and 6 cats were not treated (control group). Bone labeling was performed, using fluorochrome markers. Cats were euthanatized 5 weeks after implanting, and barium sulfate was infused to evaluate vascularization of grafts. Ulnas were evaluated by use of radiography, microangiography, histologic examination, and histomorphometric examination. RESULTS Radiographic scores did not differ between treatment groups. Microangiographic appearance of grafted defects was similar between groups, with all having adequate vascularization. Differences were not observed between treated and nontreated groups in the overall histologic appearance of decalcified samples of tissue in grafted defects. Mean distance between fluorescent labels was significantly greater in cats given HBOT than in nontreated cats. Median percentage of bone formation in grafted defects was significantly greater in cats given HBOT. CONCLUSIONS Hyperbaric oxygen treatment increased the distance between fluorescent labels and percentage of bone formation when incorporating autogenous cancellous bone grafts in induced nonunion diaphyseal ulnar defects in cats, but HBOT did not affect revascularization, radiographic appearance, or qualitative histologic appearance of the grafts.
Matrix Metalloproteinases 2 and 9 Polymorphism in Patients With Myeloproliferative Diseases

AbstractChronic myeloproliferative disorders such as polycythemia vera (PV), essential thrombocytosis (ET), and idiopathic myelofibrosis arise from clonal proliferation of neoplastic stem cells in the bone marrow. Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that have potential to degrade all types of extracellular matrix (ECM) and also play a role in remodeling of the ECM. It is known that MMPs play a role in bone marrow remodeling.The primary goal of our study is to explore the relationship between chronic myeloproliferative diseases and some of MMP gene polymorphisms. The demonstration of a relationship will help to understand whether these polymorphisms may be a potential early diagnosis marker of the diseases.Patients were selected from outpatient clinics of Turgut Ozal University Hospital, Ankara, Turkey, between December 2010 and May 2011. Twenty-eight patients that previously diagnosed and followed-up with PV, 17 with secondary polycythemia (SP), and 12 with ET were enrolled in the study, along with a control group of 22 healthy people.DNA was isolated from peripheral blood. Using polymerase chain reaction–restriction fragment length polymorphism method, MMP2 and MMP9 gene polymorphisms were analyzed with agarose gel electrophoresis. There was a statistically significant difference between the study groups and the control group in terms of Gln279Arg polymorphisms rates of MMP9. The highest MMP9 Gln279Arg polymorphism rate was observed in the ET group. But nobody from the control group had polymorphic MMP9. There was no statistically significant difference between the groups in terms of MMP2-735 C > T polymorphism rates.In conclusion, MMP9 gene Gln279Arg polymorphism was associated with ET, SP, and PV diseases. Hence, we believe that these gene polymorphisms may play a role in the mechanism of bone marrow fibrosis and may be a factor that increases the risk of thrombosis. Illumination of the molecular basis of the relationship between MMP-thrombosis and MMP-fibrosis provides a better understanding of the pathophysiology of PV and ET diseases and will allow new approaches to diagnosis and treatment.
Metamaterial nanotips with multi-frequency local field enhancement

In the paper metamaterial nanotips with multi-frequency local field enhancement are proposed and studied theoretically and numerically. The nanotips are in form of pyramids built from silver nanoplates embedded in a dielectric block. The pyramids are layered structures with subsequent plates parallel to the pyramid base. Thickness of nanoplates and their transversal size is chosen to efficiently convert the light impinging on the pyramid base into hot spots near the pyramid apex, and also to support large number of plasmonic resonances which allow for multi-frequency enhancement of the light intensity. Geometrical parameters are designed to cover the visible light range.
Current smoking differentially affects blood mononuclear cells from patients with crohn's disease and ulcerative colitis: Relevance to its adverse role in the disease

Background: Epidemiologic data suggest that smoking increases the risk and the severity of Crohn's disease (CD), although it may protect patients with ulcerative colitis (UC). To investigate this paradox, we evaluated the effect of cigarette smoke in the function of blood mononuclear cells from healthy subjects and patients with CD or UC in flare up. Methods: The production of mediators associated with inflammation but also with protective functions was evaluated by enzyme‐linked immunosorbent assay (ELISA) and enzyme immunoassay (EIA), following either in vivo or in vitro exposure to cigarette smoke. Results: We found that mononuclear cells from smokers with CD were functionally impaired. These cells secreted lower levels of chemokines and cytokines as compared with nonsmoker counterparts, whereas healthy smokers or smokers with UC were not affected. Similar findings were noted after in vitro exposure to cigarette smoke extract. In addition, cells from patients with CD who smoke presented a defective sensitivity to antiinflammatory or antioxidant protection, and particularly synthesized lower levels of cytoprotective Hsp70. The effects observed were not due to diminished cell viability. Our experiments suggest that cigarette smoke‐related responses were largely dependent on oxidative stress generated, and not on the nicotine component. Conclusions: Overall, our data point out the presence of biological differences between blood mononuclear cells from patients with CD and UC toward cigarette smoke that might support its opposite role in both diseases. (Inflamm Bowel Dis 2012;)
The Grammatical Structure of Protein Sequences in a Single Non-linear Hidden Markov Model ; Prediction of Coding Regions , Secondary and Tertiary Structure

We describe a hidden Markov model, HMMSTR, for general protein sequence based on the I-sites library of sequence-structure motifs [1]. Unlike the linear HMMs used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the database, and achieves a great reduction in parameters by representing overlapping motifs in a much more compact form. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.6% and backbone torsion angles better than any previously reported method, and predicts the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction.
Research on event-B based formal modeling and verification of automatic production line

Before the automatic production line put into practical use in industrial domain, it must go through a large number of long-term rigorous test to detect errors in the design process. However in the actual test process, the same mistake leads to different results due to the different test methods and there are some special conditions resulting from the limitation of field test environment what can't be used to be tested. The formal method, by using the method of discrete mathematics to practical system mathematical modeling and validation, can replace the methods what can not been tested under the conditions of system verification. The formal method is also suitable for developing large reactive and distributed systems. In this paper, the specific formal method which is called Event-B improves the high security and reliability of system. Moreover the related tools such as Rodin are used for modeling, refinement and verification in the PLC (Programmable Logic Controller) automatic production line. The result in this paper shows that our approach contributes to reducing system details during the early development stage and leads to simpler proofs and more automated proofs. Thus it provides a new method for reference for higher requirements in the reliability in engineering projects, so as to ensure the correctness of the designed software.
Multi-sensor image fusion based on fourth order partial differential equations

In this paper, a new image fusion algorithm based on fourth order partial differential equations and principal component analysis is introduced. This is for the first time fourth order partial differential equations brought into the context of image fusion. The proposed algorithm is as follows: First, fourth order partial differential equations are applied on each source image to obtain approximation and detail images. Second, principal component analysis is applied on detail images to obtain optimal weights. Third, final detail image is obtained by fusing these detail images with help of optimal weights. Fourth, final approximation image is obtained by employing an average operation on approximation images. Finally, resultant fused image is calculated by combining the final approximation and detail images. Experiments are conducted on standard fusion datasets. Results are analyzed with help of petrovic metrics and further compared with traditional and recent fusion methods. Results justify that performance of the proposed method is superior to state-of-the-art fusion methods. Moreover, reasonable computational time, easy and effective implementation of the proposed method makes it suitable for real time applications.
Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA‐bending protein Hbb

The genome of the Lyme disease‐causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or ‘DNABII’ family of nucleoid‐associated proteins – Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb–DNA complex in which the DNA is bent by over 180°. We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.
Controlling the Error Floor in LDPC Decoding

The error floor of LDPC is revisited as an effect of dynamic message behavior in the so-called absorbing sets of the code. It is shown that if the signal growth in the absorbing sets is properly balanced by the growth of set-external messages, the error floor can be lowered to essentially arbitrarily low levels. Importance sampling techniques are discussed and used to verify the analysis, as well as to discuss the impact of iterations and message quantization on the code performance in the ultra-low BER (error floor) regime.
Traditional allometric analysis fails to provide a valid predictive model for mammalian metabolic rates

SUMMARY The field of biological allometry was energized by the publication in 1997 of a theoretical model purporting to explain 3/4-power scaling of metabolic rate with body mass in mammals. This 3/4-power scaling exponent, which was first reported by Max Kleiber in 1932, has been derived repeatedly in empirical research by independent investigators and has come to be known as `Kleiber's Law'. The exponent was estimated in virtually every instance, however, by fitting a straight line to logarithmic transformations of data and by then re-expressing the resulting equation in the arithmetic scale. Because this traditional method may yield inaccurate and misleading estimates for parameters in the allometric equation, we re-examined the comprehensive data set that led Savage and colleagues to reaffirm the view that the metabolic rate of mammals scales to the 3/4-power of body mass. We found that a straight line fitted to logged data for the basal metabolic rate (BMR) of mammals ranging in size from a 2.4 g shrew to a 3672 kg elephant does not satisfy assumptions underlying the analysis and that the allometric equation obtained by back-transformation underestimates BMR for the largest species in the sample. Thus, the concept of 3/4-power scaling of metabolic rate to body mass is not well supported because the underlying statistical model does not apply to mammalian species spanning the full range in body size. Our findings have important implications with respect to methods and results of other studies that used the traditional approach to allometric analysis.