Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting protein atom correlations using correlation of probability of recurrence

The dynamic cross‐correlation Map(DCCM) technique has been used extensively to study protein dynamics. In this work, we introduce the use of the method of correlation of probability of recurrence (CPR) as a complementary method to detect correlations between protein residue atoms. Time series of the distances of the Cα atoms of the β‐lactamase inhibitory protein (BLIP) from a reference position are analyzed using CPR and mutual information (MI). The results are compared to those provided by DCCM. In comparison to MI, CPR is found to detect more of the correlations present in DCCM. It is also able to detect a small number of significant correlations between distant residues that are not detected by DCCM. Proteins 2014; 82:2180–2189. © 2014 Wiley Periodicals, Inc.
Antimicrobial photodynamic therapy in a mouse model of Acinetobacter baumannii burn infection

Multi-drug resistant Acinetobacter baumanii infections represent a growing problem, especially in traumatic wounds and burns suffered by military personnel injured in Middle Eastern conflicts. Effective treatment using traditional antibiotics can be extremely difficult and new antimicrobial approaches are being investigated. One of these antimicrobial alternatives could be the combination of non-toxic photosensitizers (PS) and visible light known as photodynamic therapy (PDT). We report on the establishment of a new mouse model of full thickness thermal burns infected with a bioluminescent derivative of a clinical Iraqi isolate of A. baumannii and its PDT treatment by topical application of a PS produced by covalent conjugation chlorin(e6) to polyethylenimine followed by illumination of the burn surface with red light. Application of 108 A. baumannii cells to the surface of 10-second burns made on the dorsal surface of shaved female BALB/c mice led to chronic infections that lasted on average 22 days characterized by a remarkably stable bacterial bioluminescence. PDT carried out on day 0 soon after applying bacteria gave over three logs of loss of bacterial luminescence in a light exposure dependent manner, while PDT carried out on day 1 and day 2 gave approximately a 1.7-log reduction. Application of PS dissolved in 10% or 20% DMSO without light gave only modest reduction in bacterial luminescence from mouse burns. Some bacterial regrowth in the treated burn was observed but was generally modest. It was also found that PDT did not lead to inhibition of wound healing. The data suggest that PDT may be an effective new treatment for multi-drug resistant localized A. baumannii infections.
Modeling the sample distribution for clustering OCR

The paper re-examines a well-known technique in OCR, recognition by clustering followed by cryptanalysis, from a Bayesian perspective. The advantage of such techniques is that they are font-independent, but they appear not to have offered competitive performance with other pattern recognition techniques in the past. The analysis presented in this paper suggests an approach to OCR that is based on modeling the sample distribution as a mixture of Gaussians. Results suggest that such an approach may combine the advantages of cluster- based OCR with the performance of traditional classification algorithms.
Anthropometric Standardization Reference Manual

This abridged version of the "Anthropometric Standardisation Reference Manual" contains the heart of the original manual - complete procedures for 45 anthropometric measurements. Its style enables it to be used as a supplemental text for courses in fitness assessment and exercise prescription, kinanthropometry, body composition, nutrition, and exercise physiology. It can also be used as a reference for exercise scientists. For each of the 45 measurements included in this abridged edition, readers will find complete information on the recommended technique for making the measurement, the purpose and uses for the measurement, the literature on which the measurement technique is based, and the reliability of the measurement.
New and Future Medications for the Treatment of Type 2 Diabetes Mellitus

With almost 30 million individuals predicted to be diagnosed by the year 2025, type 2 diabetes mellitus (T2DM) has become one of the most prevalent diseases in the United States. Because of the progressive dysfunction of the pancreatic β-cells and increasing insulin resistance over time, the need for treatments with different mechanisms or addition of medications to a regimen is becoming commonplace. Because of this, developing new medications to treat T2DM has been the focus of a lot of recent research and drug development. Molecular substrates such as glucagon-like peptide-1 (GLP-1), dipeptidyl peptidase-4 (DPP-4), and the sodium glucose transporter-2 (SGLT2) have all become new therapeutic targets. GLP-1 agonists and DPP-4 inhibitors are 2 of the newest classes of Food and Drug Administration–approved medications for diabetes. By increasing GLP-1 to supraphysiologic levels (GLP-1 agonists) and delaying endogenous GLP-1 degradation (DPP-4 inhibitors), these drugs increase insulin secretion and decrease glucagon production. SGLT2 inhibitors, the newest antihyperglycemic class, promote glycosuria by inhibiting sodium and glucose reabsorption in the proximal tubule of the renal nephron. Other novel agents for the treatment of diabetes include the use of the dopamine agonist bromocriptine, the cholesterol medication colesevelam, and a new form of inhaled insulin.
Reconstructing polygonal approximations of 3D shapes through multiple-view matching on planes

We present a new algorithm that reconstructs 3D shapes from 2D images. Unlike previous algorithms that produce points or voxels representing the shapes, our algorithm produces their polygonal approximations. Such approximations are simpler, easier to manipulate, and more suitable for many graphics applications. The algorithm consists of the following steps. First, we project the 2D images onto a plane, called ``test plane. '' The test plane is chosen at random from the set of all planes that pass through the volume, where the object to be reconstructed exists. Next, we compare the projected images with each other. If the test plane is tangential to the object, the images will coincide at some regions on the plane. We then represent such regions using texture-mapped polygons. By collecting these polygons together, we can obtain a polygonal approximation of the 3D object. One important feature of our algorithm is its capability to incrementally refine the resulting approximations. This feature has turned out useful especially when the objects' shapes are very complex. We also show some examples to demonstrate that our algorithm works fine with partly noisy images.
A multi-source book review system for reducing information overload and accommodating individual styles

Purpose – The purpose of this paper is to evaluate the performance of the multi-source book review system (MBRS). MBRS was designed to reduce information overload using the internet and to accommodate different learner preferences. Design/methodology/approach – The authors experimentally compared MBRS with the Google search engine. MBRS first gathers reviews from online sources, such as bookstores and blogs. It reduces information overload through an advanced filtering and sorting algorithm and by providing a uniform user interface. MBRS accommodates different learning styles through various sort options and through adding video-mediated reviews. Findings – Results indicate that, compared with Google, MBRS: reduces the information overload associated with searching for online book reviews; increases users finding satisfactory book reviews; and allows users to find reviews more quickly. In addition, more than half of the participants found video-mediated book reviews more appealing than traditional text-ba.
Religion and Political Protest: A Cross-Country Analysis

Religion’s effect on individual tendency to engage in political protest is influenced both by the resources available to citizens at the individual level and opportunities provided to religious groups and organizations at the country level. Combining data from last two waves of the World Values Surveys with aggregate data on religious regulation, we show that private religious beliefs reduce an individual’s protest potential while involvement in religious social networks fosters it. At the country level, we find that government regulation of religion decreases individual tendency to protest, and has an especially detrimental effect on the likelihood of religious minorities joining peaceful protest activities. These findings are in line with opportunity structure theories that stress the importance of system openness for fostering political protest.
Robust and high-quality video watermarking with the use of temporal redundancy

In this paper, we present a new video watermarking technique, which utilize the characteristic of temporal redundancy of video sequence to improve the quality and robustness of the watermarked sequence. The proposed watermarking technique can be combined with many existing 2D image-watermarking algorithm to take advantage of their robustness against various attacks. For every watermark bit (formula available in paper), the pseudo random sequence (formula available in paper) is added to the mid-band coefficients of a block and the complementary sequence, (formula available in paper) is added to the same block in another frame of the insertion pair. To retrieve the embedded watermark bit, the block in the first frame is subtracted by the same block of the second frame, resulting in a watermark with double the magnitude (formula available in paper). Since adjacent video frames are highly correlated and the DCT coefficients are almost the same (especially in non-moving regions), the subtraction of the block pair also cancels out most of the interfering DCT coefficients originated from the host signal, such that the interference to the watermark signal from the host signal is minimized during detection. Experiment shows that the probability of receiving an error bit can be reduced or the picture quality is improved while maintaining the same probability of error.
Cooking Camp Provides Hands-On Nutrition Education Opportunity

Abstract Making healthy food choices requires far more than nutrition knowledge. Food preparation skills are essential in order to prepare healthful, palatable meals that meet dietary recommendations for children and for young adults. Children who cook are more likely to taste the foods they've prepared than those who are simply served meals. College-age individuals are likely to try new foods but they often lack the basic skills to plan menus, purchase appropriate ingredients and balance meals. They many want to cook but don't know how, or don't think they have the time. Children participated in a five day culinary program which covered eight different regions, each with a particularly distinctive culinary style and heritage. A nutritionist provided nutrition education and lab support and a kinesiology instructor planned games and activities that engaged the participants in outdoor physical activities for an hour each day. A validated evaluation tool, Eating Right is Fun: Food and Me for assessment indicated a positive change in knowledge and behavior of participants. Cooking Campand similar programs present unique opportunities for professional chefs to engage people of all ages in cooking activities that build confidence in home food preparation.
Perspective estimation for document images

There has been increasing interest in document capture with digital cameras, since they are often more convenient to use than conventional devices such as flatbed scanners. Unlike flatbed scanners, cameras can acquire document images with arbitrary perspectives. Without correction, perspective distortions are unappealing to human readers. They also make subsequent image analysis slower, more complicated and less reliable. The novel contribution of this paper is to view perspective estimation as a generalization of the well-studied skew estimation problem. Rather than estimating one angle of rotation we must determine four angles describing the perspective. In our method, separate estimates are made for angles describing lines that are parallel and perpendicular to text lines. Each of these estimates is based on a twice-iterated projection profile computation. We give a probabilistic argument for the method and describe an efficient implementation. Our results illustrate its primary benefits: it is robust and accurate. The method is efficient compared with the time required to warp the image to correct for perspective.
Key Applications for High-Assurance Systems

The paper consists of project summaries concerning high-assurance systems. Those who are grappling with practical high-assurance design issues report their strategies, the problems they solved, and the challenges that remain. The six summaries represent a cross-section of projects and domains with some strikingly similar challenges. Although they address diverse domains, these reports reveal a set of common criteria for high assurance. Generally speaking, the critical criteria are reliability, availability, safety, timeliness, security and evolvability.
Formulary Drug Reviews: Glecaprevir/Pibrentasvir

Each month, subscribers to The Formulary Monograph Service receive 5 to 6 well-documented monographs on drugs that are newly released or are in late phase 3 trials. The monographs are targeted to Pharmacy & Therapeutics Committees. Subscribers also receive monthly 1-page summary monographs on agents that are useful for agendas and pharmacy/nursing in-services. A comprehensive target drug utilization evaluation/medication use evaluation (DUE/MUE) is also provided each month. With a subscription, the monographs are available online to subscribers. Monographs can be customized to meet the needs of a facility. Through the cooperation of The Formulary, Hospital Pharmacy publishes selected reviews in this column. For more information about The Formulary Monograph Service, contact Wolters Kluwer customer service at 866-397-3433.
The clinical and pathohistological study on the schistosomiasis patients diagnosed by liver biopsy.

The precise diagnosis of schistosomiasis japonica consists in the detection of the eggs of schistosoma japonicum in patient's feces (1), (2), (3), (4). Accordingly, the skin test, the clinical symptoms such as acidopilie etc., or the examination of dwelling area of patient is only the help method of diagnosis•D As well known, cercariae, invaded to human body, develope to mature form and produce the eggs in the portal system, sometimes eggs acting as the embolus in the marginal region of liver. For the difficulty of detecting the eggs from the feces especially in the early stage of infection, Prof. Yoshizumi attempted to discover the eggs obstructing the marginal vessels in liver. Namely in the microscopic examination of specimen obtained by liver biopsy, the eggs are recognizable in the clear visual field. This method, the fresh liver slide method named by Prof. Yoshizumi, was added as a new diagnostic method of schistosomiasis by him, because many eggs are easily detectable even in the case without eggs within feces (5), (6). The detection of eggs by the fresh liver slide method and the histological examination of liver specimen are simultaneously made by the author. By these procedures, the diferenciation of schistosoma eggs from other parasite eggs, the measurement of real size of eggs, the decision of maturity, and the judgment of death are possible. Moreover, by this metod, the histological changes, especially the parasitogenic cirrhosis of liver can be
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. (2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. (3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. (4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. (5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. (6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. (7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas. Proteins 2016; 84(Suppl 1):4–14. © 2016 Wiley Periodicals, Inc.
Work conditions and occupational morbidity in Latvia

The aim of study was to analyse work conditions and occupational morbidity in Latvia during a 15-year period for recommendations to employment policy programmes. The study included the analysis of the database of occupational risk factor measurements in more than 7000 enterprises and companies performed in period 1995–2010 by the Laboratory of Hygiene and Occupational Diseases of the Institute of Occupational Safety and Environmental Health of Riga Stradins University. The analysis of registered occupational diseases according to the data from the Latvian State Registry of Occupational diseases run by the Centre of Occupational and Radiation Medicine of Pauls Stradins Clinical University Hospital for the same period was performed. Occupational diseases in Latvia are diagnosed and coded in accordance with the International Classification of Diseases. Results of measurements showed that for one third of measured occupational risk factors values exceeded recommended limits. The traditional work risk factors (chemical, physical, biological etc.) have been partly replaced by new risks (ergonomic and psychosocial factors). The results of the study indicated that the following enterprises form a major risk group of non-compliance with legislation regarding occupational health and safety: small enterprises; enterprises of private and non-governmental sectors; enterprises of different industries (construction, metal processing and wood processing). The number of firstly diagnosed occupational diseases and patients has gradually increased. The total number of firstly diagnosed and registered occupational patients per 100,000 employees was 11.2 in 1995 and 140.5 in 2009. The structure of
Human Factors Measurement for Future Air Traffic Control Systems

Objective: This article provides a critical review of research pertaining to the measurement of human factors (HF) issues in current and future air traffic control (ATC). Background: Growing worldwide air traffic demands call for a radical departure from current ATC systems. Future systems will have a fundamental impact on the roles and responsibilities of ATC officers (ATCOs). Valid and reliable methods of assessing HF issues associated with these changes, such as a potential increase (or decrease) in workload, are of utmost importance for advancing theory and for designing systems, procedures, and training. Method: We outline major aviation changes and how these relate to five key HF issues in ATC. Measures are outlined, compared, and evaluated and are followed by guidelines for assessing these issues in the ATC domain. Recommendations for future research are presented. Results: A review of the literature suggests that situational awareness and workload have been widely researched and assessed using a variety of measures, but researchers have neglected the areas of trust, stress, and boredom. We make recommendations for use of particular measures and the construction of new measures. Conclusion: It is predicted that, given the changing role of ATCOs and profound future airspace requirements and configurations, issues of stress, trust, and boredom will become more significant. Researchers should develop and/or refine existing measures of all five key HF issues to assess their impact on ATCO performance. Furthermore, these issues should be considered in a holistic manner. Application: The current article provides an evaluation of research and measures used in HF research on ATC that will aid research and ATC measurement.
Vision system for classification of metallic tokens using the selective stereo gradient method

This paper presents a vision system whose purpose is to detect topographies of high reflective, metallic surfaces of minted tokens. We call this technique 'Selective Stereo Gradient Method' (SSGM). The objective is to decide whether the token belongs to a reference class or not. The most important property of the SSGM is that the classification can not be deceived by a photographic image and hence yields high fraud protection. To achieve this a 3 sector 120# LED illumination is used for generating three images under different illumination directions. The comparison between these three sequentially taken images leads to a discrimination between a real object with 3 D topography and a photographic image. The experimental setup and special illumination conditions are described. Rotation and translation invariance of the recognition and classification process are implemented. This is achieved by image transformation into a suitable coordinate system. A specimen will be identified to belong to the class of interest if, in a subsequent template matching step, selected patterns taken from the class reference object, can be successfully identified. If a first pattern is found additional patterns will be searched for. The classification statistics results will be reported for metallic tokens.
Trying to understand social media users and usage: The forgotten features of social media platforms

Purpose – The purpose of this paper from the series “Monitoring the Media: Spotlight on Social Media Research” is to look into different approaches to study uses of social media platforms – from user statistics to motivations for using specific features within a platform. Design/methodology/approach – Based on a literature review some general findings on social media usage are summarized alongside with examples of user activities that are rarely studied. Findings – The paper concludes that social media research has neglected to question the use of more recent features in social media platforms, such as Twitter favorites or Facebook hashtags, as well as the more “destructive” activities in social networking such as unfollowing. Originality/value – The paper draws attention to some features of popular social media platforms which are currently understudied. It raises awareness for these specific gaps in social media research and could inspire future studies to close the gap.
On phase-locked loops and Kalman filters

Driessen (1994) and Christiansen (1994) independently showed that for a specific dynamic model, the proportional-integral phase-locked loop (PLL) has the same structure as the Kalman filter. In this paper, closed-form expressions of the corresponding Kalman gain values are derived both in acquisition and tracking modes of the PLL.