gebhart/patrepeval huggingface dataset:
SparkMaster: automated calcium spark analysis with ImageJ (2007)

Ca sparks are elementary Ca-release events from intracellular Ca stores that are observed in virtually all types of muscle. Typically, Ca sparks are measured in the line-scan mode with confocal laser-scanning microscopes, yielding two-dimensional images (distance vs. time). The manual analysis of these images is time consuming and prone to errors as well as investigator bias. Therefore, we developed SparkMaster, an automated analysis program that allows rapid and reliable spark analysis. The underlying analysis algorithm is adapted from the threshold-based standard method of spark analysis developed by Cheng et al. (Biophys J 76: 606-617, 1999) and is implemented here in the freely available image-processing software ImageJ. SparkMaster offers a graphical user interface through which all analysis parameters and output options are selected. The analysis includes general image parameters (number of detected sparks, spark frequency) and individual spark parameters (amplitude, full width at half-maximum amplitude, full duration at half-maximum amplitude, full width, full duration, time to peak, maximum steepness of spark upstroke, time constant of spark decay). We validated the algorithm using images with synthetic sparks embedded into backgrounds with different signal-to-noise ratios to determine an analysis criteria at which a high sensitivity is combined with a low frequency of false-positive detections. Finally, we applied SparkMaster to analyze experimental data of sparks measured in intact and permeabilized ventricular cardiomyocytes, permeabilized mammalian skeletal muscle, and intact smooth muscle cells. We found that SparkMaster provides a reliable, easy to use, and fast way of analyzing Ca sparks in a wide variety of experimental conditions.
HTLV-III in the Semen and Blood of a Healthy Homosexual Man (1984)

Human T-lymphotropic virus type III (HTLV-III) is the probable etiologic agent for the acquired immune deficiency syndrome (AIDS). HTLV-III was isolated from semen and blood of a healthy homosexual man whose serum contains antibodies to HTLV-III. The finding of virus in semen supports epidemiologic data that suggest that AIDS can be transmitted sexually. In addition, the demonstration of HTLV-III in the blood and semen of a healthy individual establishes an asymptomatic, virus-positive carrier state which may be important in the dissemination of HTLV-III and, consequently, AIDS.
A FLUORESCENCE IMAGING DEVICE FOR ENDOSCOPIC DETECTION OF EARLY STAGE CANCER – INSTRUMENTAL and EXPERIMENTAL STUDIES (1987)

Abstract Visible detection of early stage cancer labelled with the fluorescing porphyrin mixture of dihematoporphyrin‐ether and dihematoporphyrin‐ester (DHE) is often limited by a high and inhomogeneously distributed level of autofluorescence. A new imaging method for reducing autofluo‐rescence is described. The method uses alternating fluorescence excitation with laser light in the violet and blue spectral ranges. Subtraction of the corresponding fluorescence images results in contrast enhancement due to an effective reduction in the autofluorescence contribution. A prototype version of a highly sensitive fluorescence imaging device including a modified krypton ion laser, an image‐intensified solid‐state TV‐camera, a digital image‐processing system, and video recording and monitoring has been developed. Experiments performed with this fluorescence imaging system on a tumorous dog bladder showed that a dose of 0.2 mg DHE kg −1 body wt, which is far below the dose administered for photodynamic therapy (2‐5 mg kg − ’body wt), is sufficient to give a high‐contrast fluorescence image. The corresponding excitation power density was about 1 W m −2 . Photobleaching of DHE was observed during fluorescence detection at excitation power densities exceeding 1 kW m −2 . At these high excitation levels DHE fades out nearly completely within 0.25 min.
Dissection of T-cell Antigen Specificity in Human Melanoma (2012)

Tumor-infiltrating lymphocytes (TIL) isolated from melanoma patients and expanded in vitro by interleukin (IL)-2 treatment can elicit therapeutic response after adoptive transfer, but the antigen specificities of the T cells transferred have not been determined. By compiling all known melanoma-associated antigens and applying a novel technology for high-throughput analysis of T-cell responses, we dissected the composition of melanoma-restricted T-cell responses in 63 TIL cultures. T-cell reactivity screens against 175 melanoma-associated epitopes detected 90 responses against 18 different epitopes predominantly from differentiation and cancer-testis antigens. Notably, the majority of these responses were of low frequency and tumor-specific T-cell frequencies decreased during rapid expansion. A further notable observation was a large variation in the T-cell specificities detected in cultures established from different fragments of resected melanoma lesions. In summary, our findings provide an initial definition of T-cell populations contributing to tumor recognition in TILs although the specificity of many tumor-reactive TILs remains undefined.
Inhibition of the phosphatase PTEN protects mice against oleic acid‐induced acute lung injury (2008)

Treatment with bpV(phen) significantly reduced the severity of acute lung injury in mice indicating that additional investigation is warranted to understand the important role that this phosphatase may play in the lung.
Intra motion compensation and entropy coding improvements for HEVC screen content coding (2013)

Applications such as wireless displays, automotive infotainment, remote desktop, remote gaming, distance education, cloud computing etc. are becoming popular. Video in these applications often has mixed content consisting of natural video and screen content (text, graphics etc.) in the same picture. In text and graphics regions, patterns such as text characters, icons, lines etc. can repeat within a picture. Also since the graphics and text regions have sharp edges that are sometimes not predicted well by Intra prediction tools, the probability of prediction error having high amplitude increases. This paper presents two tools for improving the intra coding efficiency of the High Efficiency Video Coding (HEVC) standard when coding screen content. The first tool is a Coding Unit (CU)-level Intra motion compensation tool to eliminate redundancy from repeating patterns in text and graphics regions. The second tool is a modification to HEVC cRiceParam update process of coeff_abs_level_remaining entropy coding to adapt better to larger prediction errors in text and graphics regions. The combination of the two tools achieves an average bit-rate/Bjontegaard Delta-Rate savings in the range of 0.8% to 28.1% over HEVC Range Extensions Test Model on screen content test video sequences used in Range Extensions core experiments by the Joint Collaborative Team for Video Coding (JCT-VC).
Plasmid DNA Encoding IFN-γ-Inducible Protein 10 Redirects Antigen-Specific T Cell Polarization and Suppresses Experimental Autoimmune Encephalomyelitis (2002)

IFN-gamma-inducible protein 10 (IP-10) is a CXC chemokine that stimulates the directional migration of activated T cells, particularly Th1 cells. We demonstrate in this work that during activation this chemokine drives naive CD4(+) T cells into Th1 polarization. Administration of plasmid DNA encoding self IP-10 was found capable of breaking down immunological tolerance to IP-10, resulting in the generation of self-specific immunity to the gene product of the vaccine. Despite the CpG motif that drives T cells into Th1, the vaccine redirected the polarization of myelin basic protein-specific T cells into Th2 and conferred the vaccinated recipients a high state of resistance against experimental autoimmune encephalomyelitis, a T cell-mediated autoimmune disease of the CNS. The vaccine also suppressed full-blown ongoing disease in a mouse model of multiple sclerosis. Self-specific Ab to IP-10 developed in protected animals could inhibit leukocyte migration, alter the in vitro Th1/Th2 balance of autoimmune T cells, and adoptively transfer disease suppression. This demonstrates not only the pivotal role of a chemokine in T cell polarization and function but also its potential implications for plasmid DNA gene therapy.
Pitfalls of using conventional and discrete Radon transforms on poorly sampled data (1996)

Abstract The least-square discrete Radon transform (DRT) is currently one of the most popular methods used in the suppression of multiples and other coherent noise events on irregularly sampled data gathers used for prestack true amplitude analysis. Unfortunately, in the absence of a priori information, this technique suffers from the same aliasing problems as Fourier and conventional (τ, ρ) methods. Although the DRT is able to reconstruct the original image more accurately than conventional (τ, ρ) transforms, a harmful by-product is an increase in the amplitude of aliased events in the transform domain. In particular, the DRT will boost the amplitude of the aliases of true events that fall outside the p analysis window to help reconstruct the input data. These amplified aliases degrade signal periodicity in the (τ, ρ) domain. If muted, they can destroy subtle amplitude changes necessary for amplitude variation with offset (AVO) analysis. At the very least, one should carefully evaluate the choice of analysis window and mutes when designing a filter in the (τ, ρ) domain. Alternatively, one can exploit additional a priori information based on semblance. Iterative application of the DRT and mutes can also be used to suppress aliased events further.
Selective enhancement of surface-state emission and simultaneous quenching of interband transition in white-luminophor CdS nanocrystals using localized plasmon coupling (2008)

We propose and demonstrate the controlled modification and selective enhancement of surface-state emission in white-luminophor CdS nanocrystals (NCs) by plasmon-coupling them with proximal metal nanostructures. By carefully designing nano-Ag films to match their localized plasmon resonance spectrally with the surface-state emission peak of CdS NCs, we experimentally show that the surface-state emission is substantially enhanced in the visible wavelength, while the interband (band-edge) transition at the shorter wavelength far away from the plasmon resonance is simultaneously significantly suppressed. With such plasmon tuning and consequent strong plasmon coupling specifically for the surface-state transitions, the surface-state emission is made stronger than the band-edge emission. This corresponds to an enhancement factor of 12.7-fold in the ratio of the surface-state peak emission to the band-edge peak emission of the plasmon-coupled film sample compared with that in solution. Such a plasmonic engineering of surface-state emission in trap-rich CdS white nanoluminophors holds great promise for future solid-state lighting.
The Social ABCs caregiver‐mediated intervention for toddlers with autism spectrum disorder: Feasibility, acceptability, and evidence of promise from a multisite study (2015)

The Social ABCs is a parent-mediated intervention for toddlers with suspected or confirmed autism spectrum disorder (ASD). We undertook a multi-site pilot study to evaluate feasibility and acceptability, and to identify trends in child and parent behavior to inform future research using a larger sample and a rigorous research design. The program involved 12 weeks of parent coaching, followed by 12 weeks' implementation, and 3-month follow-up assessment for 20 parent-toddler dyads (age range: 12-32 months). Parents successfully learned the techniques and rated the intervention as highly acceptable. Paired samples t-tests revealed significant gains in children's functional communication (responsivity, initiations), and language gains (age-equivalents on standardized measures) commensurate with typical developmental rates. Significant increases in shared smiling and social orienting also emerged, but were attenuated at follow-up. Parents' fidelity was positively associated with child responsivity. Training parents as mediators is a feasible and highly acceptable approach that provides a potentially cost-effective opportunity for intensive intervention at a very young age at the first signs of ASD risk. Child and parent gains in several key variables demonstrate the promise of this intervention. Autism Res 2016, 9: 899-912. © 2015 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research.
CLINICAL EFFICACY OF TESTOSTERONE UNDECANOATE IN MALE HYPOGONADISM (1981)

Testosterone undecanoate (Restandol, Organon Laboratories Ltd) dissolved in oleic acid, was administered orally to seventy-six hypogonadal males for three consecutive 3-week periods and the subjective clinical response assessed by a standard interview. Plasma testosterone and testosterone undecanoate levels were determined by radioimmunoassay before the study and after 3, 6 and 9 weeks treatment. The treatment was effective in sixty of the sixty-six patients who completed the trial. Ten patients did not complete the trial; two for reasons unrelated to the drug and eight because of side effects, mainly gastro-intestinal. There was a significant rise in plasma testosterone levels during treatment and a positive correlation between plasma testosterone and testosterone undecanoate levels. Testosterone undecanoate is a potentially valuable drug for the oral treatment of male hypogonadism.
Autoimmune diseases: insights from genome-wide association studies (2008)

Autoimmune diseases occur when an individual's own immune system attacks and destroys his or her healthy cells and tissues. Although it is clear that environmental stimuli can predispose someone to develop autoimmune diseases, twin- and family-based studies have shown that genetic factors also play an important role in modifying disease risk. Because many of these diseases are relatively common (prevalence in European-derived populations: 0.01-1%) and exhibit a complex mode of inheritance, many DNA sequence variants with modest effect on disease risk contribute to the genetic burden. Recently, the completion of the HapMap project, together with the development of new genotyping technologies, has given human geneticists the tools necessary to comprehensively, and in an unbiased manner, search our genome for DNA polymorphisms associated with many autoimmune diseases. Here we review recent progress made in the identification of genetic risk factors for celiac disease, Crohn's disease, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus and type-1 diabetes using genome-wide association studies (GWAS). Strikingly, GWAS have increased the number of genetic risk variants associated with these autoimmune diseases from 15 before 2006 to 68 now. We summarize what this new genetic landscape teaches us in terms of the pathogenesis of these diseases, and highlight some of the outstanding challenges ahead. Finally, we open a discussion on ways to best maximize the impact of these genetic discoveries where it matters the most, that is for autoimmune disease patients.
Molecular Neuropharmacology: A Foundation for Clinical Neuroscience (2001)

An engagingly written, vibrantly illustrated reference that expertly links neurobiology, clinical psychiatry, and neurology Molecular Neuropharmacology first reviews the fundamental biochemistry of the functioning nervous system and then describes in clear, concise and consistent terms how nerve cells communicate with one another through numerous types of neurotransmitters involving amino acids, monoamines, neuropeptides, and neurotrophic factors, among several others. The neuropharmacology and neural circuits that underlie complex behaviors as well as major neural disorders are then discussed as are the drugs used to treat those conditions. In this final section, the authors use the concepts presented in the first two sections to explain how irregularities in the biochemistry of neuronal interactions can lead to a wide array of clinical manifestations. Key points begin every chapter for a brief overview. Each chapter is packed with figures, tables and text boxes (presented on every page and accessible with clear color coding). More than 300 detailed diagrams provide specific information on receptor and drug families, biosynthetic and metabolic pathways, and interactions between the nervous system and the rest of the body. Simple and elegant, these illustrations are rich enough in content to serve as brief overviews of each chapter when viewed alone. Features NEW chapter on neuroinflammation All chemical structure illustrations have been redrawn and improved Fully updated to reflect the latest breakthroughs and new drugs The best written and most easily understood work on the subject
An Introduction To Compressive Sampling [A sensing/sampling paradigm that goes against the common knowledge in data acquisition] (2008)

This article surveys the theory of compressive sampling, also known as compressed sensing or CS, a novel sensing/sampling paradigm that goes against the common wisdom in data acquisition. CS theory asserts that one can recover certain signals and images from far fewer samples or measurements than traditional methods use. To make this possible, CS relies on two principles: sparsity, which pertains to the signals of interest, and incoherence, which pertains to the sensing modality. &#13;\n&#13;\nOur intent in this article is to overview the basic CS theory that emerged in the works [1]–[3], present the key mathematical ideas underlying this theory, and survey a couple of important results in the field. Our goal is to explain CS as plainly as possible, and so our article is mainly of a tutorial nature. One of the charms of this theory is that it draws from various subdisciplines within the applied mathematical sciences, most notably probability theory. In this review, we have decided to highlight this aspect and especially the fact that randomness can — perhaps surprisingly — lead to very effective sensing mechanisms. We will also discuss significant implications, explain why CS is a concrete protocol for sensing and compressing data simultaneously (thus the name), and conclude our tour by reviewing important applications.
Intraocular pressure in rabbits by telemetry II: effects of animal handling and drugs. (1998)

Continuous telemetric measurement of intraocular pressure in rabbits permits the measurement of uncontrollable artifacts that occur with tonometric measurements and animal handling. If environmental conditions are rigidly controlled, this method is very sensitive for detecting therapeutic effects of candidates for ocular hypotensive drugs. When healthy animals are used, the method appears to be more sensitive for drugs that affect aqueous humor formation than for drugs that affect aqueous humor outflow resistance.
Footprint evaluation for volume rendering (1990)

This paper presents a forward mapping rendering algorithm to display regular volumetric grids that may not have the same spacings in the three grid directions. It takes advantage of the fact that convolution can be thought of as distributing energy from input samples into space. The renderer calculates an image plane footprint for each data sample and uses the footprint to spread the sample's energy onto the image plane. A result of the technique is that the forward mapping algorithm can support perspective without excessive cost, and support adaptive resampling of the three-dimensional data set during image generation.
From promotion to management: The wide impact of bacteria on cancer and its treatment (2014)

In humans, the intestine is the major reservoir of microbes. Although the intestinal microbial community exists in a state of homeostasis called eubiosis, environmental and genetics factors can lead to microbial perturbation or dysbiosis, a state associated with various pathologies including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Dysbiotic microbiota is thought to contribute to the initiation and progression of CRC. At the opposite end of the spectrum, two recently published studies in Science reveal that the microbiota is essential for chemotherapeutic drug efficacy, suggesting a beneficial microbial function in cancer management. The dichotomy between the beneficial and detrimental roles of the microbiota during cancer initiation, progression, and treatment emphasize the interwoven relationship between bacteria and cancer. Moreover, these findings suggest that the microbiota could be considered as a therapeutic target, not only at the level of cancer prevention, but also during management, i.e. by enhancing the efficacy of chemotherapeutics.
Ocular findings in a double-blind study of ivermectin versus diethylcarbamazine versus placebo in the treatment of onchocerciasis. (1987)

The effect of ivermectin, a new microfilaricide, was assessed in a double blind trial against diethylcarbamazine citrate (DEC) and placebo. Fifty-nine adult males with moderate to heavy infection with Onchocerca volvulus and with eye involvement were recruited from an area under Onchocerciasis Control Programme (OCP) vector control in Northern Ghana. They were randomly assigned to an eight-day treatment with ivermectin as a single dose of 12 mg on day 1 followed by placebo for the remaining seven days, or DEC, total dose 1.3 g, or placebo, and ophthalmological review was undertaken over a period of one year. DEC acted quickly to eliminate microfilariae from the eye and was associated with reactive ocular changes and in a few cases functional deficit. Ivermectin eliminated microfilariae slowly from the anterior chamber of the eye over a period of six months. The ocular inflammatory reaction was minimal and no functional deficit occurred. It is postulated that the observed slow action of ivermectin on the eye may be attributed in part to its instability to cross the blood-aqueous humour barrier because of its molecular size as a macrocyclic lactone causing microfilariae to leave the eye gradually along a newly created gradient. Ivermectin is an effective microfilaricide with minimal ocular adverse effect and could therefore be suitable for widespread application without strict supervision.
Responses of Gut Microbiota to Diet Composition and Weight Loss in Lean and Obese Mice (2011)

Maintenance of a reduced body weight is accompanied by a decrease in energy expenditure beyond that accounted for by reduced body mass and composition, as well as by an increased drive to eat. These effects appear to be due--in part--to reductions in circulating leptin concentrations due to loss of body fat. Gut microbiota have been implicated in the regulation of body weight. The effects of weight loss on qualitative aspects of gut microbiota have been studied in humans and mice, but these studies have been confounded by concurrent changes in diet composition, which influence microbial community composition. We studied the impact of 20% weight loss on the microbiota of diet-induced obese (DIO: 60% calories fat) mice on a high-fat diet (HFD). Weight-reduced DIO (DIO-WR) mice had the same body weight and composition as control (CON) ad-libitum (AL) fed mice being fed a control diet (10% calories fat), allowing a direct comparison of diet and weight-perturbation effects. Microbial community composition was assessed by pyrosequencing 16S rRNA genes derived from the ceca of sacrificed animals. There was a strong effect of diet composition on the diversity and composition of the microbiota. The relative abundance of specific members of the microbiota was correlated with circulating leptin concentrations and gene expression levels of inflammation markers in subcutaneous white adipose tissue in all mice. Together, these results suggest that both host adiposity and diet composition impact microbiota composition, possibly through leptin-mediated regulation of mucus production and/or inflammatory processes that alter the gut habitat.