gebhart/patrepeval huggingface dataset:
Modeling log-compressed ultrasound images for radio frequency signal recovery (2008)

This paper presents an algorithm for recovering the radio frequency (RF) signal provided by the ultrasound probe from the log-compressed ultrasound images displayed in ultrasound equipment. Commercial ecographs perform nonlinear image compression to reduce the dynamic range of the Ultrasound (US) signal in order to improve image visualization. Moreover, the clinician may adjust other parameters, such as brightness, gain and contrast, to improve image quality of a given anatomical detail. These operations significantly change the statistical distribution of the original RF raw signal, which is assumed, based on physical considerations on the signal formation process, to be Rayleigh distributed. Therefore, the image pixels are no longer Rayleigh distributed and the RF signal is not usually available in the common ultrasound equipment. For statistical data processing purposes, more important than having "good looking" images, it is important to have realistic models to describe the data. In this paper, a nonlinear compression parametric function is used to model the pre-processed image in order to recover the original RF image as well the contrast and brightness parameters. Tests using synthetic and real data and statistical measures such as the Kolmogorov-Smirnov and Kullback-Leibler divergences are used to assess the results. It is shown that the proposed estimation model clearly represents better the observed data than by taking the general assumption of the data being modeled by a Rayleigh distribution.
Glutathione Peroxidase-3 Deficiency Promotes Platelet-Dependent Thrombosis In Vivo (2011)

These findings demonstrate that GPx-3 deficiency results in a prothrombotic state and vascular dysfunction that promotes platelet-dependent arterial thrombosis. These data illustrate the importance of this plasma antioxidant enzyme in regulating platelet activity, endothelial function, platelet-dependent thrombosis, and vascular thrombotic propensity.
Complete Protection in Macaques Conferred by Purified Inactivated Zika Vaccine: Defining a Correlate of Protection (2020)

A critical global health need exists for a Zika vaccine capable of mitigating the effects of future Zika epidemics. In this study we evaluated the antibody responses and efficacy of an aluminum hydroxide adjuvanted purified inactivated Zika vaccine (PIZV) against challenge with Zika virus (ZIKV) strain PRVABC59. Indian rhesus macaques received two doses of PIZV at varying concentrations ranging from 0.016 µg - 10 µg and were subsequently challenged with ZIKV six weeks or one year following the second immunization. PIZV induced a dose-dependent immune response that was boosted by a second immunization. Complete protection against ZIKV infection was achieved with the higher PIZV doses of 0.4 µg, 2 µg, and 10 µg at 6 weeks and with 10 ug PIZV at 1 year following vaccination. Partial protection was achieved with the lower PIZV doses of 0.016 µg and 0.08 µg. Based on these data, a neutralizing antibody response above 3.02 log<sub>10</sub> EC50 was determined as a correlate of protection in macaques. PIZV elicited a dose-dependent neutralizing antibody response which is protective for at least 1 year following vaccination.
Transfer of the ADA Gene into Bone Marrow Cells and Peripheral Blood Lymphocytes for the Treatment of Patients Affected by ADA-Deficient SCID (1993)

Severe combined immunodeficiency (SCID) caused by deficiency of the enzyme adenosine deaminase (ADA) is the first genetic disorder considered for human somatic cell gene therapy. ADA-SCID patients can be cured by HLA-matched sibling donor bone marrow transplantation. Alternative transplantation strategies as well as enzyme replacement are being tested in those patients who do not have a suitable matched sibling donor. Some ADA-SCID patients may not be candidates for cytoablation due to infectious damage to the lung or liver, or may have a milder phenotype that does not justify the risks associated with haploidentical bone marrow transplantation. Replacement therapy with PEG-ADA has resulted in improvement in growth, a variable increase in the number of peripheral blood lymphocytes, and a decrease in the incidence of severe infections. Another approach to the treatment of severe genetic diseases is now represented by somatic cell gene therapy. We and others have conducted experiments in vitro and in vivo that have documented that T-lymphocytes are suitable vehicles for gene transfer. Although the pluripotent stem cell remains the ideal target cell for somatic cell gene therapy of disorders of the hematopoietic system, the use of T-lymphocytes as gene therapy vehicles is specifically indicated for ADA-deficient patients where they represent the affected cells. Furthermore, the selective engraftment of T-cells only, following bone marrow transplantation, has resulted in reconstitution of cellular and humoral immunity. A model for the functional analysis in vivo of the human immune system has been utilized for the preclinical evaluation of this approach.(ABSTRACT TRUNCATED AT 250 WORDS)
[Clinical tolerance of a new antidepressant -- milnacipran]. (1999)

Milnacipran is a new antidepressant which has been developed for its selective inhibition of both serotonin and noradrenaline reuptake with a good safety and tolerability profile. The efficacy and tolerance profile of this antidepressant have been compared with those of tricyclic and selective serotonin reuptake inhibitor antidepressants (SSRIs) in open-label and placebo-controlled trials. But no data in clinical practice are available. The authors studied the tolerability of milnacipran (100 to 200 mg/d) in 28 depressed inpatients receiving usual comedications during a mean period of 33 days (3 to 107 days). The incidence of adverse events was determined with the help of the Pharmacovigilance Center of the Centre Hospitalo-Universitaire (Besançon, France). Among the 28 patients, milnacipran was well tolerated by 18 of them. Side-effects were noted in 10 patients, but they led to withdrawal of the antidepressant in only 2 cases, where dyspnea, palpitations, pollakiuria in a case and headache, nausea, dysuria in the other case occurred. The most frequent adverse event observed was hypotension (n = 6), but in each case it occurred just after the addition of sedative phenothiazines (n = 5) or of a comedication with phenothiazines and valpromide (n = 1). So this side-effect could not be attributed to milnacipran alone. Treatments with heptaminol or theodrenaline and cafedrine were useful. An increase of the cardiac frequency seemed to occur with milnacipran (p < 0.06). It was observed in the 5 inpatients for whom this cardiovascular parameter was recorded before and during the milnacipran treatment. In 5 other patients, the cardiac frequency seemed to decrease when milnacipran was stopped for lack of good efficacy or adverse events. Gastrointestinal disturbances were scarce isolated (nausea n = 1), but necessitated a treatment with metopimazine. The milnacipran prescription (100 mg/d) after an other antidepressant treatment had been done without a withdrawal period and without problem, even when the previous antidepressant was a SSRIs with a long half-life and CYP450 inhibitory properties. The authors concluded to the good tolerability of milnacipran in usual clinical practice.
Extension and discussion of the Palmer-Tomasko method of radiometric normalization (1983)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text William L. Wolfe, "Extension and discussion of the Palmer-Tomasko method of radiometric normalization," Appl. Opt. 22, 370-371 (1983) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Synergistic airway gland mucus secretion in response to vasoactive intestinal peptide and carbachol is lost in cystic fibrosis (2007)

Cystic fibrosis (CF) is caused by dysfunction of the CF transmembrane conductance regulator (CFTR), an anion channel whose dysfunction leads to chronic bacterial and fungal airway infections via a pathophysiological cascade that is incompletely understood. Airway glands, which produce most airway mucus, do so in response to both acetylcholine (ACh) and vasoactive intestinal peptide (VIP). CF glands fail to secrete mucus in response to VIP, but do so in response to ACh. Because vagal cholinergic pathways still elicit strong gland mucus secretion in CF subjects, it is unclear whether VIP-stimulated, CFTR-dependent gland secretion participates in innate defense. It was recently hypothesized that airway intrinsic neurons, which express abundant VIP and ACh, are normally active and stimulate low-level gland mucus secretion that is a component of innate mucosal defenses. Here we show that low levels of VIP and ACh produced significant mucus secretion in human glands via strong synergistic interactions; synergy was lost in glands of CF patients. VIP/ACh synergy also existed in pig glands, where it was CFTR dependent, mediated by both Cl(-) and HCO(3) (-), and clotrimazole sensitive. Loss of "housekeeping" gland mucus secretion in CF, in combination with demonstrated defects in surface epithelia, may play a role in the vulnerability of CF airways to bacterial infections.
Characterization of the major locus of immediate-early genes of rat cytomegalovirus (1993)

A major locus of rat cytomegalovirus (RCMV) immediate-early (IE) RNA transcription was identified. A cDNA library from rat embryo fibroblasts infected with RCMV under IE conditions was constructed and screened by using appropriate RCMV DNA probes, revealing at least two IE genes (IE1 and IE2) transcribed from this locus by differential splicing. The first three exons (the first is noncoding) are spliced to exon 4 to form IE1 and to exon 5 to form IE2. The structural organization of the RCMV major IE region is therefore similar to that of human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV). When we compared the predicted amino acid sequences of the IE1 proteins of RCMV, HCMV, and MCMV, no areas of homology were found across all three proteins, while a few small areas of homology were found between RCMV IE1 and MCMV IE1. In contrast, large areas of homology were found across the carboxyl half of RCMV IE2, HCMV IE2, and MCMV ie3 proteins. In addition, similarities were found at the beginning of exon 5 of RCMV and MCMV. The possible significance of these conserved regions is discussed. Dinucleotide frequency analysis demonstrated a decrease in CpG frequency over the IE region. The IE gene products were able to transactivate heterologous promoters.
New Photoactivated Protecting Groups. 6. p-Hydroxyphenacyl:  A Phototrigger for Chemical and Biochemical Probes1,2 (1997)

p-Hydroxyphenacyl, a new photoactive, aqueous soluble protecting group is proposed as a second generation α-keto “cage” reagent, a phototrigger for the efficient, rapid release of bioactive phosphates, e.g., inorganic phosphate (Pi) and ATP (Givens, R. S.; Park, C.-H. Tetrahedron Lett. 1996, 37, 6259−6262). p-Hydroxyphenacyl esters 6c and 7 trigger the release of Pi and ATP when irradiated at wavelengths between 300−350 nm also yielding p-hydroxyphenylacetic acid (8) from the rearrangement of the intermediate α-keto carbocation or its equivalent. In contrast, unsubstituted and m-substituted phenacyl esters yield only photoreduction and radical coupling products and none of the rearrangement product. Quantum efficiencies of 0.38 ± 0.04 were measured for the disappearance of the p-hydroxyphenacyl phosphate esters 6c and 7; the appearance efficiencies for 8 and ATP were 0.30 ± 0.03. Rates of release of ∼107 s-1 or better are observed for these esters with only minor variations in efficiencies and rate constants between these two examples of the p-hydroxyphenacyl phototrigger. Just as was found for the desyl “cage” series reported earlier (Givens, R. S.; Athey, P. S.; Kueper, L. W., III; Matuszewski, B.; Xue, J.-y.; Fister, T. J. Am. Chem. Soc. 1993, 115, 6001−6010), the p-hydroxyphenacyl derivatives react via their triplet states. Amino substituents, i.e., p-amino-, p-acetamido-, and p-(carbomethoxyamino)phenacyl phosphates 6f−h, were also investigated, but these analogues proved to be inferior as phototriggers when compared with p-hydroxyphenacyl.
Effects of hyaluronic acid on cardiac cushion tissue cells in collagen matrix cultures. (1979)

To initiate the experimental exploration of the role of extracellular macromolecules in influencing developmental events in the heart, a 3-dimensional substrate culture model of the developing cardiac cushion was devised. One cardiac jelly component, hyaluronic acid, was tested for its effects on morphology and migratory capacity of cushion tissue cells within the collagen matrix substrate. Hyaluronate treatment resulted in: (1) an increase in the number and extent of filopodia, reflected as an increase in cell surface area, and (2) an increase in migratory capacity, reflected as an increase in maximum depth to which cells migrate through the collagen lattice. These results suggest one major role for hyaluronate in the early cardiac cushion is the promotion of a high level of motility capability in the newly seeded cushion tissue cells, required for the key event of cell migration across the developing cushion.
RcsCDB His‐Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli (2003)

The genes involved in flagellum synthesis, motility and chemotaxis in Escherichia coli are expressed in a hierarchical fashion. At the top of the hierarchy lies the master regulator FlhDC, required for the expression of the whole set of genes. The operon flhDC is controlled by numerous regulators including H-NS, CRP, EnvZ/OmpR, QseBC and LrhA. In the present work, we report that the flhDC operon is also negatively regulated by the His-Asp phosphorelay system RcsCDB. The regulation is potentiated by the RcsB cofactor RcsA. Genetic analysis indicates that an RcsAB box, located downstream of the promoter, is required for the regulation. The binding of RcsB and RcsA to this site was demonstrated by gel retardation and DNase I protection assays. In addition, mutation analysis suggests that RcsA-specific determinants lie in the right part of the 'RcsAB box'.
PP.13.03 (2015)

Objective: Angiotensin 2-induced endothelial inflammation is a big risk for vascular diseases. Our work found that both ATF3 expression and SUMOylation were induced by Angiotensin 2 in endothelia cells,so we aimed to explore how ATF3 and its SUMOylation participated in endothelial inflammation caused by Angiotensin 2.Design and method: Mice were sacrificed after infusion of Angiotensin 2(Ang2) for 14 days, thoracic aorta immunofluorescence showed that both ATF3 and SUMO1 expressions increased, and merge analysis exhibited ATF3 was SUMOylated. Human Umbilical Vein Endothelial Cells(HUVECs) in culture were exposed to Ang2,western blot and co-immunoprecipitation(co-IP) exhibited both ATF3 expression and ATF3 SUMOylation were up-regulated. When Anacardic acid,an inhibitor of SUMOylation and SUMO1 siRNA were introduced to HUVECs, Ang2 failed to increase ATF3 protein level. Co-IP experiment demonstrated that when SUMO1 and ubiqutin were overexpressed at the same time, ATF3 combined SUMO1 rather than ubiqutin, means that ATF3 SUMOylation avoided its ubiquitination. Real-time PCR and Elisa confirmed that both ATF3 siRNA and SUMO1 siRNA blocked Ang2-induced transcriptions and expressions of IL6, TNF-α and IL-8. As a member of AP-1 complex, overexpressed ATF3 plasmid alone failed to increase inflammation cytokines. But inflammation responses were triggered when ATF3 and AP-1 members plasmids demonstrated to HUVEC together. Results: Ang2 induce ATF3 expression and ATF3 sumoylation in vascular endothelium. ATF3 sumoylation stabilize itself by keep it from ubiquitination. ATF3 contributed to inflammation induced by Ang2 and regulated by ATF3 sumoylation ATF3 activates inflammatory gene transcription dimerise with AP-1 members. Conclusions: Angiotensin 2 induced ATF3 SUMOylation protected ATF3 from ubiquitination .ATF3 heterdimer with AP-1 members increases endothelial inflammation. SUMOylation may be a potential therapeutic target for the treatment of vascular diseases caused by endothelial inflammation.
Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis (2002)

Comparison of the whole-genome sequence of Bacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracis chromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.
The Role of TLRs in Anti-cancer Immunity and Tumor Rejection (2019)

In recent years, a lot of scientific interest has focused on cancer immunotherapy. Although chronic inflammation has been described as one of the hallmarks of cancer, acute inflammation can actually trigger the immune system to fight diseases, including cancer. Toll-like receptor (TLR) ligands have long been used as adjuvants for traditional vaccines and it seems they may also play a role enhancing efficiency of tumor immunotherapy. The aim of this perspective is to discuss the effects of TLR stimulation in cancer, expression of various TLRs in different types of tumors, and finally the role of TLRs in anti-cancer immunity and tumor rejection.
Robust Statistical Label Fusion Through Consensus Level, Labeler Accuracy, and Truth Estimation (COLLATE) (2011)

Segmentation and delineation of structures of interest in medical images is paramount to quantifying and characterizing structural, morphological, and functional correlations with clinically relevant conditions. The established gold standard for performing segmentation has been manual voxel-by-voxel labeling by a neuroanatomist expert. This process can be extremely time consuming, resource intensive and fraught with high inter-observer variability. Hence, studies involving characterizations of novel structures or appearances have been limited in scope (numbers of subjects), scale (extent of regions assessed), and statistical power. Statistical methods to fuse data sets from several different sources (e.g., multiple human observers) have been proposed to simultaneously estimate both rater performance and the ground truth labels. However, with empirical datasets, statistical fusion has been observed to result in visually inconsistent findings. So, despite the ease and elegance of a statistical approach, single observers and/or direct voting are often used in practice. Hence, rater performance is not systematically quantified and exploited during label estimation. To date, statistical fusion methods have relied on characterizations of rater performance that do not intrinsically include spatially varying models of rater performance. Herein, we present a novel, robust statistical label fusion algorithm to estimate and account for spatially varying performance. This algorithm, COnsensus Level, Labeler Accuracy and Truth Estimation (COLLATE), is based on the simple idea that some regions of an image are difficult to label (e.g., confusion regions: boundaries or low contrast areas) while other regions are intrinsically obvious (e.g., consensus regions: centers of large regions or high contrast edges). Unlike its predecessors, COLLATE estimates the consensus level of each voxel and estimates differing models of observer behavior in each region. We show that COLLATE provides significant improvement in label accuracy and rater assessment over previous fusion methods in both simulated and empirical datasets.
Endarterectomy versus Stenting in Patients with Symptomatic Severe Carotid Stenosis (2006)

In this study of patients with symptomatic carotid stenosis of 60% or more, the rates of death and stroke at 1 and 6 months were lower with endarterectomy than with stenting. (ClinicalTrials.gov number, NCT00190398 [ClinicalTrials.gov].).
Islet Cell and Extrapancreatic Expression of the LIM Domain Homeobox Geneisl-1 (1991)

The phenotypically distinct cell types of the islets of Langerhans express a number of different hormone genes in a regulated and cell-specific manner. Analysis of the molecular factors important for the control of insulin gene transcription has led to the identification of a number of insulin gene-binding proteins. The cDNAs for several of these proteins have been isolated, including isl-1, a LIM domain homeobox protein reported to be preferentially expressed in islet cells. We now report that isl-1 mRNA transcripts are present not only in islet cells, but also in pheochromocytoma (PC-12) cell lines. Isl-1 mRNA transcripts were also detected in several different regions of rat brain as well as in rat kidney. Analysis of the patterns of gene expression in rate islet cell lines and human pancreatic endocrine tumors demonstrated a variable relationship between the hormonal phenotype of the tumor and expression of the isl-1 and insulin genes. Immunocytochemical studies demonstrated both cytoplasmic and nuclear staining for isl-1 in human pancreatic endocrine tumors, in normal pancreatic A, B, D, and PP cells, and in distal tubular cells of the kidney. Isl-1 immunoreactivity was also widely distributed in neurons in both the central and peripheral nervous system, pituitary, and several human pituitary tumors and pheochromocytomas. The results of these studies implicate a potential role for isl-1 outside the endocrine pancreas in the nervous system and kidney.
Generation and characterization of monoclonal antibodies specific for the human neu oncogene product, p185. (1989)

A series of monoclonal antibodies specific for the extracellular domain of the human neu gene product (p185) have been produced. The generation of these monoclonal antibodies, and their biochemical and immunological characterization is described. The immunization protocol utilized a series of injections of NIH3T3 cells, cyclophosphamide, and a neu transfected NIH3T3 cell line (designated 18-3-7) which expressed the full length human neu-encoded protein. This immunization regimen induced an immune response to the extracellular portion of p185 on the 18-3-7 cells. A panel of ten hybridomas were identified which secreted monoclonal antibodies with a variety of epitope specificities, and reacted with p185 in a number of different experimental formats. As the neu gene product has been associated with human breast cancers, a series of monoclonal antibodies such as these could prove useful in the diagnosis, prognosis and/or treatment of these human malignancies.