gebhart/patrepeval huggingface dataset:
High-Speed PIV Analysis Using Compressed Image Correlation (1998)

With the development of Holographic PIV (HPIV) and PIV Cinematography (PIVC), the need for a computationally efficient algorithm capable of processing images at video rates has emerged. This paper presents one such algorithm, sparse array image correlation. This algorithm is based on the sparse format of image data—a format well suited to the storage of highly segmented images. It utilizes an image compression scheme that retains pixel values in high intensity gradient areas eliminating low information background regions. The remaining pixels are stored in sparse format along with their relative locations encoded into 32 bit words. The result is a highly reduced image data set that retains the original correlation information of the image. Compression ratios of 30:1 using this method are typical. As a result, far fewer memory calls and data entry comparisons are required to accurately determine tracer particle movement. In addition, by utilizing an error correlation function, pixel comparisons are made through single integer calculations eliminating time consuming multiplication and floating point arithmetic. Thus, this algorithm typically results in much higher correlation speeds and lower memory requirements than spectral and image shifting correlation algorithms. This paper describes the methodology of sparse array correlation as well as the speed, accuracy, and limitations of this unique algorithm. While the study presented here focuses on the process of correlating images stored in sparse format, the details of an image compression algorithm based on intensity gradient thresholding is presented and its effect on image correlation is discussed to elucidate the limitations and applicability of compression based PIV processing.
A phase II trial of recombinant tumor necrosis factor in patients with metastatic colorectal adenocarcinoma: a Southwest Oncology Group study. (1990)

Tumor necrosis factor (TNF) induces hemorrhagic necrosis in the Meth A mouse tumor model and has shown cytostatic and cytotoxic antitumor effects against a wide range of human tumors both in vitro and as human tumor xenografts in nude mice. Because of in vitro activity against colorectal tumors and antitumor responses in colon cancer patients in phase I trials, this phase II study was undertaken. Patients were treated with TNF administered daily for 5 days/week every other week at a dose of 150 micrograms/m2/day as a 30-min i.v. infusion. One cycle consisted of 4 weeks of treatment over an 8-week period. Twenty-five patients have been entered into this study with three patients ineligible. The 22 eligible patients ranged in age from 38-73 years and had initial performance status of 0 in 10 patients, 1 in 10 patients, and 2 in 2 patients. No complete or partial responses were seen. Two patients had stable disease (no response) and 18 patients progressed. Two patients had no evaluation and were assumed to have had no response. The response rate is therefore 0%, with a 95% exact confidence interval of 0% to 15%. There was one grade 4 toxicity consisting of nausea and vomiting. Most common grade 3 toxicities were chills and fever in four patients, nausea and vomiting in three patients, and anemia and elevated liver enzymes in two patients. Headache, myalgia/arthralgia, and elevated serum triglycerides were frequently seen. Mildly elevated levels of fibrin split products were seen after TNF treatment in 5/13 evaluable patients and one ineligible patient.(ABSTRACT TRUNCATED AT 250 WORDS)
Locked Nucleic Acid Aptamers (2009)

The aptamer technology has been introduced in the early 1990s. With this technique ligands for organic dyes and proteins have been identified in many research field, providing various inhibitory molecules that allow functional interference in biological systems. Aptamers can therefore be employed for various applications ranging from diagnostic to therapeutic assay formats. Locked nucleic acid aptamers (LNA-Aps) are oligonucleotides containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking sugar conformation, evolved in vitro to bind target ligands with high affinity and specificity. LNA-Aps are attractive alternatives to antibody- and small-molecule-based therapeutics due to their stability, low toxicity and immunogenecity.
Production of laminin and fibronectin by Schwannoma cells: cell-protein interactions in vitro and protein localization in peripheral nerve in vivo. (1983)

We studied a rat Schwannoma cell line (RN22F) to determine if it produced the basement membrane glycoproteins laminin and fibronectin, and how it interacted with these proteins in vitro. We used antisera to laminin and fibronectin for immunoprecipitation experiments and immunocytochemical localization at the electron microscope level. Polyacrylamide gels of antilaminin immunoprecipitates of conditioned medium and solubilized Schwannoma cells contained bands of reduced Mr 200,000 and 150,000. Antilaminin immunoprecipitates of conditioned medium contained nonreduced bands of 850,000 daltons and 150,000, and immunoprecipitates of solubilized cells contained nonreduced bands of 850,000, 400,000, 200,000, and 150,000 daltons. Antifibronectin immunoprecipitates of conditioned medium contained a reduced band of 220,000 daltons, and nonreduced bands of 440,000 and 220,000 daltons. Radio-labeled protein was not detected in antifibronectin immunoprecipitates of solubilized cells. By immunocytochemistry, laminin was found along the cell surface in a continuous band, whereas fibronectin was only sparsely distributed along the cell surface. In cell adhesion assays, Schwannoma cells bound preferentially to laminin-coated substrates as compared to fibronectin or noncoated substrates. A number of Schwannoma cells displayed a curved and elongated morphology on laminin substrates, as compared to a uniformly spread morphology on fibronectin, and a round, nonspread morphology on noncoated substrates. Immunofluorescent staining showed laminin in the endoneurium and perineurium and fibronectin predominantly in the perineurium of mouse sciatic nerve in vivo. The production of laminin and fibronectin by Schwann cells may be important in the development and myelination of peripheral nerves, and the proper regeneration of axons following nerve injury.
Smooth ocular pursuit in Chiari type II malformation (2007)

Chiari type II malformation (CII) is a congenital anomaly of the cerebellum and brainstem, both important structures for processing smooth ocular pursuit. CII is associated with myelomeningocele and hydrocephalus. We investigated the effects of CII on smooth pursuit (SP) eye movements, and determined the effects of spinal lesion level, number of shunt revisions, nystagmus, and brain dysmorphology on SP. SP was recorded using an infrared eye tracker in 21 participants with CII (11 males, 10 females; age range 8-19y, mean 14y 3mo [SD 3y 2mo]). Thirty-eight healthy children (21 males, 17 females) constituted the comparison group. Participants followed a visual target moving sinusoidally at +/- 10 degrees amplitude, horizontally and vertically at 0.25 or 0.5Hz. SP gains, the ratio of eye to target velocities, were abnormal in the CII group with nystagmus (n= 8). The number of shunt revisions (range 0-10), brain dysmorphology, or spinal lesion level (n= 15 for lower and n= 6 for upper spinal lesion level) did not correlate with SP gains. SP is impaired in children with CII and nystagmus. Abnormal pursuit might be related to the CII dysgenesis or to effects of hydrocephalus. The lack of effect of shunt revisions and abnormal tracking in participants with nystagmus provide evidence that it is related primarily to the cerebellar and brainstem malformation.
Suppression of erythropoiesis in malarial anemia is associated with hemozoin in vitro and in vivo (2006)

Malarial anemia is a global public health problem and is characterized by a low reticulocyte response in the presence of life-threatening hemolysis. Although cytokines, in particular tumor necrosis factor-alpha (TNF-alpha), can suppress erythropoiesis, the grossly abnormal bone marrow morphology indicates that other factors may contribute to ineffective erythropoiesis. We hypothesized that the cytotoxic hemozoin (Hz) residues from digested hemoglobin (Hb) significantly contribute to abnormal erythropoiesis. Here, we show that not only isolated Hz, but also delipidated Hz, inhibits erythroid development in vitro in the absence of TNF-alpha. However, when added to cultures, TNF-alpha synergizes with Hz to inhibit erythropoiesis. Furthermore, we show that, in children with malarial anemia, the proportion of circulating monocytes containing Hz is associated with anemia (P < .001) and reticulocyte suppression (P = .009), and that this is independent of the level of circulating cytokines, including TNF-alpha. Plasma Hz is also associated with anemia (P < .001) and reticulocyte suppression (P = .02). Finally, histologic examination of the bone marrow of children who have died from malaria shows that pigmented erythroid and myeloid precursors are associated with the degree of abnormal erythroid development. Taken together, these observations provide compelling evidence for inhibition of erythropoiesis by Hz.
Acetyl-lysine Binding Site of Bromodomain-Containing Protein 4 (BRD4) Interacts with Diverse Kinase Inhibitors (2014)

Members of the bromodomain and extra terminal (BET) family of proteins are essential for the recognition of acetylated lysine (KAc) residues in histones and have emerged as promising drug targets in cancer, inflammation, and contraception research. In co-crystallization screening campaigns using the first bromodomain of BRD4 (BRD4-1) against kinase inhibitor libraries, we identified and characterized 14 kinase inhibitors (10 distinct chemical scaffolds) as ligands of the KAc binding site. Among these, the PLK1 inhibitor BI2536 and the JAK2 inhibitor TG101209 displayed strongest inhibitory potential against BRD4 (IC50=25 nM and 130 nM, respectively) and high selectivity for BET bromodomains. Comparative structural analysis revealed markedly different binding modes of kinase hinge-binding scaffolds in the KAc binding site, suggesting that BET proteins are potential off-targets of diverse kinase inhibitors. Combined, these findings provide a new structural framework for the rational design of next-generation BET-selective and dual-activity BET-kinase inhibitors.
Root Cause Analysis of Tungsten-Induced Protein Aggregation in Pre-filled Syringes. (2016)

Particles isolated from a pre-filled syringe containing a protein-based solution were identified as aggregated protein and tungsten. The origin of the tungsten was traced to the tungsten pins used in the supplier's syringe barrel forming process. A tungsten recovery study showed that the vacuum stopper placement process has a significant impact on the total amount of tungsten in solutions. The air gap formed in the syringe funnel area (rich in residual tungsten) becomes accessible to solutions when the vacuum is pulled. Leachable tungsten deposits that were not removed by the supplier's wash process are concentrated in this small area. Extraction procedures used to measure residual tungsten in empty syringes would under-report the tungsten quantity unless the funnel area is wetted during the extraction. Improved syringe barrel forming and washing processes at the supplier have lowered the residual tungsten content and significantly reduced the risk of protein aggregate formation. This experience demonstrates that packaging component manufacturing processes, which are outside the direct control of drug manufacturers, can have an impact on the drug product quality. Thus close technical communication with suppliers of product contact components plays an important role in making a successful biotherapeutic.
Dysregulation of the NLRP3 inflammasome complex and related cytokines in patients with multiple myeloma (2015)

This study demonstrated that dysregulated expression of NLRP3-caspase-1-IL-1beta axis was observed in patients with MM, suggesting they might be involved in the pathogenesis of MM.
Cutaneous lupus erythematosus: recent lessons from animal models (2010)

Cutaneous lupus erythematosus (CLE) may present as a clinically heterogeneous group of lupus-specific skin lesions that have common histopathological findings. Determination of the immunopathological sequence of events in this group of disorders has been challenging for dermatologists and immunologists but is vital for therapeutic targeting. We review animal models in which different aspects of immune alteration in CLE have been addressed. The MRL/lpr mouse develops spontaneous skin disease with some features of CLE. Study of this strain and related gene-manipulated strains has revealed roles for multiple cytokines, including interleukin (IL)-6, IL-18, and IL-21, in disease pathogenesis. A role for the growth factor colony stimulating factor 1 and the inflammatory protein high-mobility group box 1 has also been suggested. We discuss potential novel treatment options suggested by these models.
Therapeutic potential of CB2 targeting in multiple sclerosis (2008)

This review discusses the importance of glial cells in sustaining these effects, as well as the putative secondary effects that would limit the use of CB2 agonists in the treatment of MS.
Organosulfur compounds. 14. Dimethyl selenoxide oxidation of trivalent phosphorus compounds, thio- and selenophosphoryl compounds, and thiocarbonyl compounds. Stereochemical studies and selective modification of the thiocarbonyl-containing nucleic acid components (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganosulfur compounds. 14. Dimethyl selenoxide oxidation of trivalent phosphorus compounds, thio- and selenophosphoryl compounds, and thiocarbonyl compounds. Stereochemical studies and selective modification of the thiocarbonyl-containing nucleic acid componentsMarian Mikolajczyk and Jerzy LuczakCite this: J. Org. Chem. 1978, 43, 11, 2132–2138Publication Date (Print):May 1, 1978Publication History Published online1 May 2002Published inissue 1 May 1978https://pubs.acs.org/doi/10.1021/jo00405a010https://doi.org/10.1021/jo00405a010research-articleACS PublicationsRequest reuse permissionsArticle Views370Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
National estimates and race/ethnic‐specific variation of selected birth defects in the United States, 1999–2001 (2006)

This study can be used to evaluate individual state surveillance data, and to help plan for public health care and educational needs. It also provides valuable data on racial/ethnic patterns of selected major birth defects.
Mesoporous carbon nanospheres with an excellent electrocapacitive performance (2010)

Mesoporous carbon nanospheres (MCS) with particle size of about 65 nm and primary mesopores of about 2.7 nm in diameter were prepared and used as supercapacitor electrodes. Ferrocene was employed as the carbon precursor and mesoporous silica nanospheres were used as the template. High-resolution transmission electron microscopy revealed that the MCS consisted of graphene sheets in small domains and exhibited a specific surface area and pore volume of 2396 m2 g−1 and 2.9 cm3 g−1, respectively. The electrocapacitive performance of the MCS electrode was investigated by using cyclic voltammetry, galvanostatic charge–discharge, and electrochemical impedance spectroscopy techniques with both aqueous and non-aqueous electrolytes. The mesopores and short length of the MCS electrode were found to favor the diffusion of electrolyte ions. A symmetric supercapacitor with the MCS as the electrodes exhibited a specific capacitance of 180 F g−1 and delivered energy densities of 62.8 W h kg−1 and 9.1 W h kg−1 at power densities of 0.16 kW kg−1 and 32 kW kg−1, respectively, in a 1.5 mol L−1tetraethylammonium tetrafluoroborate in acetonitrile electrolyte. In addition, the MCS supercapacitor displayed a good cyclability, with 78% energy density and more than 90% power density remained after 700 cycles at a current density of 3.0 A g−1.
Delayed early morning turn "ON" in response to a single dose of levodopa in advanced Parkinson's disease: pharmacokinetics should be considered (2004)

The pathophysiology underlying the fluctuations in response following oral levodopa therapy is complex and includes peripheral and central factors. The short half-life of levodopa, erratic gastrointestinal absorption, and competitive transport across the blood–brain barrier have been regarded as factors responsible for the fluctuating plasma and striatal concentrations of levodopa. Indeed, failure of an oral dose to produce an effect or delay in the onset of action have been associated with problems in absorption.1,2

We studied the pharmacokinetics of levodopa in 19 patients with advanced Parkinson’s disease (12 men, seven women; period of evolution of illness more than 10 years) with and without a delayed response to the first drug dose in the morning (delayed early morning turn “ON”). The patients were selected according to the UK Brain Bank criteria; those who could not tolerate an assessment after 12 hours without taking their antiparkinsonian medication were excluded. All patients signed an informed consent form before being included in the study.

Medication and food were withheld after midnight the night before the study day. All patients’ regular therapeutic first (morning) levodopa/carbidopa dose was between 125 mg and 250 mg. Therefore all patients received a single oral dose of levodopa/carbidopa (250/25 mg) at 9:00 am, to ensure that all had a response. …
Synonymous codon usage in bacteria. (2001)

In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid conservation, protein hydropathy, transcriptional selection and even RNA stability. The review discusses these factors and their contribution to bias in synonymous codon usage in bacterial genomes.
Development of a Human Gamma Interferon Enzyme Immunoassay and Comparison with Tuberculin Skin Testing for Detection ofMycobacterium tuberculosisInfection (1998)

A sensitive two-step simultaneous enzyme immunoassay (EIA) for human gamma interferon (IFN-gamma) has been developed and used as an in vitro test for human tuberculosis (TB) in comparison with tuberculin skin testing. The EIA was shown to be highly sensitive, detecting less than 0.5 IU of recombinant human IFN-gamma per ml within a linear detection range of 0.5 to 150 IU/ml. The assay was highly reproducible and specific for native IFN-gamma. In addition, the assay detected chimpanzee, orangutan, gibbon, and squirrel monkey IFN-gammas. Cross-reactions with other human cytokines or with IFN-gammas derived from mice, cattle, or Old World monkeys were not evident. The assay was used to detect TB infection by incubating whole blood overnight with human, avian, and bovine tuberculin purified protein derivatives (PPDs), as well as positive (mitogen)- and negative-control preparations. The levels of IFN-gamma in plasma supernatants were then determined. Blood from 10 tuberculin skin test-positive individuals responded predominantly to the human tuberculin PPD antigen and to a lesser extent to bovine and avian PPD antigens. By contrast, blood from 10 skin test-negative individuals showed minimal responses or no response to any of the tuberculin PPDs. Detectable levels of IFN-gamma were present in all blood samples stimulated with mitogen. In vivo tuberculin reactivity was correlated with IFN-gamma responsiveness in vitro. These results support the further study of the blood culture-IFN-gamma EIA system as an alternative to skin testing for the detection of human TB infection.
N-Hydroxy Compounds as New Internal Standards for the 31P-NMR Determination of Lignin Hydroxy Functional Groups (2001)

Article N-Hydroxy Compounds as New Internal Standards for the 31P-NMR Determination of Lignin Hydroxy Functional Groups was published on April 25, 2001 in the journal Holzforschung (volume 55, issue 3).
Cold comfort farm: the acclimation of plants to freezing temperatures (2000)

ABSTRACT Plant acclimation to freezing temperatures is very complex. Many temperate plants increase in freezing tolerance upon exposure to a period of low but non‐freezing temperatures, an adaptive process known as cold acclimation. This acclimation phenomenon has encouraged investigations of physiological, biochemical, and molecular changes that are associated with the development of freezing tolerance. Although many biochemical and gene‐expression changes occur during cold acclimation, few have been unequivocally demonstrated to contribute to the development of freezing tolerance. However, in the last few years, exciting new progress has been made through the use of mutational analysis and molecular genetic approaches. We now recognize that several interacting signal pathways are activated to bring about cold acclimation and ensure the winter survival of plants. The challenge for the future is to understand these pathways at a mechanistic level. Facile map‐based cloning in Arabidopsis and techniques (such as DNA micro‐arrays) for transcript profiling will provide the tools needed for this task.