Miracle-dz/UniFAR-FTUs huggingface dataset:
Design of the Polish Colonoscopy Screening Program: a randomized health services study

Background and study aims: Colonoscopy screening for colorectal cancer has been implemented without evidence from randomized controlled trials quantifying its benefit and invariably as an opportunistic program, both of which are contrary to the European Union guideline recommendations. The aim of this paper is to describe the rationale and design of the first population-based colonoscopy screening program (PCSP), which was launched in Poland in 2012 as a randomized health services (RHS) study. Methods: The PCSP is a natural extension of opportunistic colonoscopy screening implemented in 2000. It uses colonoscopy capacity, a quality assurance program, and a network of 92 centers built up during the opportunistic screening phase to develop a countrywide PCSP. Within the PCSP, single screening colonoscopy is offered to a target population aged 55 – 64 years. The PCSP uses an RHS design, which means that eligible individuals drawn from population registries are randomly assigned to immediate or postponed invitation to screening. Individuals from birth cohorts that will reach the upper age limit for screening before full implementation of the PCSP are randomly assigned, in a 1:1:1 ratio, to “immediate” screening, “postponed” screening, or a “never invited” control group. The RHS design is a natural platform that will evaluate the effectiveness of screening, and compare different age ranges for screening, invitation procedures, and quality improvement interventions. Up to 2015, 24 centers have been developed, with 34.2 % geographic coverage and 851 535 individuals enrolled. Conclusions: The PCSP sets an example for implementation of population-based colonoscopy screening with experimental design to ensure proper evaluation of its effectiveness. RHS registration number: 007_2015_1_RHS.
Nanocrystalline carbon coatings and powders for medicine

All the allotropic forms of carbon, i.e., diamond, graphite and carbine, find applications in different areas of medicine, but diamond is specifically preferred. The unique properties of thin diamond layers, due to the highest biocompatibility of carbon resulting from the presence of this element in human body, make them candidates for producing biomaterials. Especially carbon in the form of a nanocrystalline diamond film has found industrial applications in the area of medical implants. Diamond Powder Particles (DPP), as an extended surface NCD, are useful for medical examinations. Different medical implants are covered with Nanocrystalline Diamond Coatings (NCD). NCD forms a diffusion barrier between implant and human environment.
Situation Change: Stability and Change of Situation Variables between and within Persons

When, how, and why situations flow into one another is important for understanding dynamic personality processes, but the topic of situation change has traditionally been a thorny issue in personality/social psychology. We explore conceptual and methodological issues in research on situation change: (1) What is situation change, which variables could we measure, and how can situation change be methodologically captured and analyzed (at between- and within-person levels)? (2) Which person-situation transaction mechanisms (situation management strategies) could entail stability and change of situations in daily life? (3) How do single or repeated instances of situation change impact short-, middle-, and long-term outcomes (e.g., intra- and interpersonal adjustment)? Besides laying out a research program for situation change, we present preliminary data from participants who wore mini-video cameras recording their situations so that they could be rated later in the lab. We demonstrate rater consensus on when situations change, mean-level changes of situation characteristics across situations, similarity of situation characteristics across adjacent situations, and inter-individual differences in intra-individual situation change in change networks.
Heterogeneous product description in electronic commerce

The heterogeneity of product descriptions is an impediment to successful interactions among buyers and vendors in electronic commerce. There is no uniform description even for the same product type among different vendors. In electronic commerce activities involving interactions among different vendors (business-to-business) or between a buyer and vendors (consumer-to-business), a common ontology for products is critical. There are two approaches to resolve the information heterogeneity problem in electronic commerce: standardization and integration. This short paper presents an overview of these approaches and shows that even with standardization efforts, some form of integration would still be required due to the potential multiplicity of standards and their degree of acceptance.
Optogenetic skeletal muscle-powered adaptive biological machines

Significance Understanding the design rules that govern the structure and function of natural biological systems gives us the ability to forward engineer machines integrated with and powered by biological components. Such machines, or “bio-bots,” can sense, process, and respond to dynamic environmental signals in real time, enabling a variety of applications. Here we present a modular optogenetic muscle actuator used to power actuation and locomotion of 3D printed flexible skeletons. Observing and controlling the functional response of such muscle-powered machines helps replicate the complex adaptive functionality we observe in natural biological systems. This demonstration thus sets the stage for building the next generation of bio-integrated machines and systems targeted at a diverse array of functional tasks. Complex biological systems sense, process, and respond to their surroundings in real time. The ability of such systems to adapt their behavioral response to suit a range of dynamic environmental signals motivates the use of biological materials for other engineering applications. As a step toward forward engineering biological machines (bio-bots) capable of nonnatural functional behaviors, we created a modular light-controlled skeletal muscle-powered bioactuator that can generate up to 300 µN (0.56 kPa) of active tension force in response to a noninvasive optical stimulus. When coupled to a 3D printed flexible bio-bot skeleton, these actuators drive directional locomotion (310 µm/s or 1.3 body lengths/min) and 2D rotational steering (2°/s) in a precisely targeted and controllable manner. The muscle actuators dynamically adapt to their surroundings by adjusting performance in response to “exercise” training stimuli. This demonstration sets the stage for developing multicellular bio-integrated machines and systems for a range of applications.
Vasopressin Decreases Pulmonary–to–Systemic Vascular Resistance Ratio in a Porcine Model of Severe Hemorrhagic Shock

ABSTRACT Vasopressors are gaining renewed interest as treatment adjuncts in hemorrhagic shock. The ideal vasoconstrictor will increase systemic blood pressure without increasing pulmonary vascular resistance (PVR), which hinders pulmonary perfusion and exacerbates hypoxemia. However, the selectivity of pressors for pulmonary versus systemic vasoconstriction during hemorrhage has not been characterized. The purpose of this study was to test the hypothesis that vasopressin (VP) has distinct effects on pulmonary versus systemic hemodynamics, unlike the catecholamine vasopressors norepinephrine (NE) and phenylephrine (PE). Anesthetized and ventilated pigs were assigned to resuscitation with saline only (n = 7) or saline with VP (n = 6), NE (n = 6), or PE (n = 6). Animals were hemorrhaged to a target volume of 30 mL/kg and a mean arterial pressure of 35 mmHg. One hour after the start of hemorrhage, animals were resuscitated with saline up to one shed blood volume, followed by either additional saline or a vasopressor. Hemodynamics and oxygenation were measured hourly for 4 h after the start of hemorrhage. Vasopressin increased systemic vascular resistance (SVR) while sparing the pulmonary vasculature, leading to a 45% decrease in the PVR/SVR ratio compared with treatment with PE. Conversely, NE induced pulmonary hypertension and led to an increased PVR/SVR ratio associated with decreased oxygen saturation. Phenylephrine and crystalloid had no significant effect on the PVR/SVR ratio. Sparing of pulmonary vasoconstriction occurs only with VP, not with administration of crystalloid or catecholamine pressors. The ability of VP to maintain blood oxygenation indicates that VP may prevent hypoxemia in the management of hemorrhagic shock.
High risk mammographic parenchymal patterns and diet: a case–control study

Mammographic parenchymal patterns are related to breast cancer risk and are also thought to be affected by diet. We designed a case–control study comprising 200 cases with high-risk (P2 and DY) mammographic parenchymal pattern and 200 controls with low-risk (N1 and P1) patterns in order to investigate the effect of food and nutrient intake on mammographic patterns. Mammograms were evaluated according to the Wolfe classification system. Dietary data were obtained from 7-day food diaries. Mean daily intake of nutrients was computed from standard UK food tables. The adjusted odds ratio (OR) of having a high-risk pattern in women in the highest tertile of total protein and carbohydrate intake was twice that of women in the lowest tertile (OR = 2.00; 95% confidence interval (CI) 1.06–3.77; P = 0.04 and OR = 1.93; 95% CI 1.03–3.59; P = 0.04 respectively). There was no excess risk for fat intake. In addition, there was no association between intake of vitamins and mammographic parenchymal patterns. Total meat intake was strongly and positively associated with high-risk patterns among post-menopausal women (OR = 2.50, 95% CI 1.09–5.69, P = 0.03). Our study suggests that certain macronutrients and foods such as protein, carbohydrate and meat intake influence the risk of breast cancer through their effects on breast tissue morphology, whereas fat and vitamins do not affect mammographic density. It seems that parenchymal pattern acts as an informative biomarker of the effect of some macronutrient and foodstuffs intake on breast cancer risk. © 2000 Cancer Research Campaign
Preventable Hospitalizations and Emergency Department Visits for Angina, United States, 1995–2010

Introduction Preventable hospitalizations for angina have been decreasing since the late 1980s — most likely because of changes in guidance, physician coding practices, and reimbursement. We asked whether this national decline has continued and whether preventable emergency department visits for angina show a similar decline. Methods We used National Hospital Discharge Survey data from 1995 through 2010 and National Hospital Ambulatory Medical Care Survey data from 1995 through 2009 to study preventable hospitalizations and emergency department visits, respectively. We calculated both crude and standardized rates for these visits according to technical specifications published by the Agency for Healthcare Research and Quality, which uses population estimates from the US Census Bureau as the denominator for the rates. Results Crude hospitalization rates for angina declined from 1995–1998 to 2007–2010 for men and women in all 3 age groups (18–44, 45–64, and ≥65) and age- and sex-standardized rates declined in a linear fashion (P = .02). Crude rates for preventable emergency department visits for angina declined for men and women aged 65 or older from 1995–1998 to 2007–2009. Age- and sex-standardized rates for these visits showed a linear decline (P = .05). Conclusion We extend previous research by showing that preventable hospitalization rates for angina have continued to decline beyond the time studied previously. We also show that emergency department visits for the same condition have also declined during the past 15 years. Although these declines are probably due to changes in diagnostic practices in the hospitals and emergency departments, more studies are needed to fully understand the reasons behind this phenomenon.
Multivariable feedback particle filter

In recent work it is shown that importance sampling can be avoided in the particle filter through an innovation structure inspired by traditional nonlinear filtering combined with Mean-Field Game formalisms [9], [19]. The resulting feedback particle filter (FPF) offers significant variance improvements; in particular, the algorithm can be applied to systems that are not stable. The filter comes with an up-front computational cost to obtain the filter gain. This paper describes new representations and algorithms to compute the gain in the general multivariable setting. The main contributions are, (i) Theory surrounding the FPF is improved: Consistency is established in the multivariate setting, as well as well-posedness of the associated PDE to obtain the filter gain. (ii) The gain can be expressed as the gradient of a function, which is precisely the solution to Poisson's equation for a related MCMC diffusion (the Smoluchowski equation). This provides a bridge to MCMC as well as to approximate optimal filtering approaches such as TD-learning, which can in turn be used to approximate the gain. (iii) Motivated by a weak formulation of Poisson's equation, a Galerkin finite-element algorithm is proposed for approximation of the gain. Its performance is illustrated in numerical experiments.
Chronic Exposure to Rotenone Models Sporadic Parkinson's Disease in Drosophila melanogaster

Parkinson's disease (PD) is a movement disorder characterized by the selective degeneration of nigrostriatal dopaminergic neurons. Both familial and sporadic cases present tremor, rigidity, slowness of movement, and postural instability. Although major insights into the genes responsible for some rare hereditary cases have arisen, the etiology of sporadic cases remains unknown. Epidemiological studies have suggested an association with environmental toxins, mainly mitochondrial complex I inhibitors such as the widely used pesticide rotenone. In recent years, Drosophila melanogaster has been used as a model of several neurodegenerative diseases, including a genetic model of PD. Here, we studied the neurodegenerative and behavioral effects of a sublethal chronic exposure to rotenone in Drosophila. After several days, the treated flies presented characteristic locomotor impairments that increased with the dose of rotenone. Immunocytochemistry analysis demonstrated a dramatic and selective loss of dopaminergic neurons in all of the brain clusters. The addition of l-dopa (3,4-dihydroxy-l-phenylalanine) into the feeding medium rescued the behavioral deficits but not neuronal death, as is the case in human PD patients. In contrast, the antioxidant melatonin (N-acetyl-5-methoxytryptamine) alleviated both symptomatic impairment and neuronal loss, supporting the idea that this agent may be beneficial in the treatment of PD. Therefore, chronic exposure to pesticides recapitulates key aspects of PD in Drosophila and provides a new in vivo model for studying the mechanisms of dopaminergic neurodegeneration.
Experimental ultrasound system for real-time synthetic imaging

Digital signal processing is being employed more and more in modern ultrasound scanners. This has made it possible to do dynamic receive focusing for each sample and implement other advanced imaging methods. The processing, however, has to be very fast and cost-effective at the same time. Dedicated chips are used in order to do real time processing. This often makes it difficult to implement radically different imaging strategies on one platform and makes the scanners less accessible for research purposes. Here flexibility is the prime concern, and the storage of data from all transducer elements over 5 to 10 seconds is needed to perform clinical evaluation of synthetic and 3D imaging. This paper describes a real-time system specifically designed for research purposes. The purpose of the system is to make it possible to acquire multi-channel data in real-time from clinical multi-element ultrasound transducers, and to enable real-time or near real-time processing of the acquired data. The system will be capable of performing the processing for the currently available imaging methods, and will make it possible to perform initial trials in a clinical environment with new imaging modalities for synthetic aperture imaging, 2D and 3D B-mode and velocity imaging. The system can be used with 128 element transducers and can excite 128 channels and receive and sample data from 64 channels simultaneously at 40 MHz with 12 bits precision. Data can be processed in real time using the system's 80 signal processing units or it can be stored directly in RAM. The system has 24 GBytes RAM and can thus store 8 seconds of multi-channel data. It is fully software programmable and its signal processing units can also be reconfigured under software control. The control of the system is done over an Ethernet using C and Matlab. Programs for doing, e.g. B-mode imaging can directly be written in Matlab and executed on the system over the net from any workstation running Matlab. The overall system concept is presented and an example of a 20 lines script for doing phased array B-mode imaging is presented.
Rapid Slide Latex Agglutination Test for Detection of Methicillin Resistance in Staphylococcus aureus

ABSTRACT The MRSA screen test (Denka Seiken Co., Ltd.), a commercially available, rapid (20-min) slide latex agglutination test for the determination of methicillin resistance by detection of PBP 2a inStaphylococcus aureus, was compared with the oxacillin agar screen test and PCR detection of the mecA gene. A total of 563 S. aureus isolates were tested. Two hundred ninety-six of the isolates were methicillin-susceptible isolates from cultures of blood from consecutive patients. Also, 267 methicillin-resistant isolates that comprised 248 different phage types were tested. Methicillin resistance was defined as the presence of themecA gene. Of the 267 mecA gene-positive isolates, 263 were positive by the MRSA screen test (sensitivity, 98.5%), and all the mecA-gene negative strains were negative by the MRSA screen test (specificity, 100%). The oxacillin agar screen test detected methicillin resistance in 250 of themecA gene-positive isolates (sensitivity, 93.6%). The sensitivity of the MRSA screen test was statistically significantly higher than the sensitivity of the oxacillin agar screen test (P < 0.05). The MRSA screen test is a highly sensitive and specific test for the detection of methicillin resistance. Also, it offers results within half an hour and is easy to perform, which makes this test a valuable tool in the ongoing battle against methicillin-resistant S. aureus.
Beyond SIFT using binary features in Loop Closure Detection

In this paper a binary feature based Loop Closure Detection (LCD) method is proposed, which for the first time achieves higher precision-recall (PR) performance compared with state-of-the-art SIFT feature based approaches. The proposed system originates from our previous work Multi-Index hashing for Loop closure Detection (MILD), which employs Multi-Index Hashing (MIH) [1] for Approximate Nearest Neighbor (ANN) search of binary features. As the accuracy of MILD is limited by repeating textures and inaccurate image similarity measurement, burstiness handling is introduced to solve this problem and achieves considerable accuracy improvement. Additionally, a comprehensive theoretical analysis on MIH used in MILD is conducted to further explore the potentials of hashing methods for ANN search of binary features from probabilistic perspective. This analysis provides more freedom on best parameter choosing in MIH for different application scenarios. Experiments on popular public datasets show that the proposed approach achieved the highest accuracy compared with state-of-the-art while running at 30Hz for databases containing thousands of images.
Rotation, scale, and translation resilient watermarking for images

Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example, simple rotation, scaling, and/or translation (RST) of an image can prevent blind detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a one-dimensional (1-D) signal obtained by taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. Rotation of the image results in a cyclical shift of the extracted signal. Scaling of the image results in amplification of the extracted signal, and translation of the image has no effect on the extracted signal. We can therefore compensate for rotation with a simple search, and compensate for scaling by using the correlation coefficient as the detection measure. False positive results on a database of 10,000 images are reported. Robustness results on a database of 2000 images are described. It is shown that the watermark is robust to rotation, scale, and translation. In addition, we describe tests examining the watermarks resistance to cropping and JPEG compression.
The Comparative Toxicogenomics Database: update 2013

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical–gene, chemical–disease and gene–disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene–disease and pathway–chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a ‘slim list’ for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical–gene–disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
A Conserved Acetyl Esterase Domain Targets Diverse Bacteriophages to the Vi Capsular Receptor of Salmonella enterica Serovar Typhi

ABSTRACT A number of bacteriophages have been identified that target the Vi capsular antigen of Salmonella enterica serovar Typhi. Here we show that these Vi phages represent a remarkably diverse set of phages belonging to three phage families, including Podoviridae and Myoviridae. Genome analysis facilitated the further classification of these phages and highlighted aspects of their independent evolution. Significantly, a conserved protein domain carrying an acetyl esterase was found to be associated with at least one tail fiber gene for all Vi phages, and the presence of this domain was confirmed in representative phage particles by mass spectrometric analysis. Thus, we provide a simple explanation and paradigm of how a diverse group of phages target a single key virulence antigen associated with this important human-restricted pathogen.