gebhart/patrepeval huggingface dataset:
Mechanical Properties of Alkali-Silica Reaction Gel Measured by Nanoindenter (2015)

The mechanical properties, particularly the elastic modulus and hardness of alkali-silica reaction (ASR) gel are measured at the microscopic scale by nanoindentation. The ASR gels are simulated in the laboratory by reacting amorphous silica (i.e., borosilicate glass) with different alkali hydroxide solutions. The measured elastic modulus of gel, formed by reacting borosilicate glass in sodium hydroxide solution was found to have a mean value of 2.96 GPa, while the gel formed from a combination of sodium hydroxide, potassium hydroxide, and calcium hydroxide solution has the mean modulus of 5.17 GPa. The results show that the presence of potassium and calcium alkalis increases the elastic modulus and hardness of the gel. A student’s t-test performed on the results confirmed the statistical significance.
Immunoglobulin/T-cell receptor clonality diagnostics (2007)

Clonality testing in lymphoid malignancies has become technically relatively easy to perform in routine laboratories using standardized multiplex polymerase chain reaction protocols for Ig/T-cell receptor (TCR) gene analysis. Expertise with clonality diagnostics and knowledge about the biology of Ig/TCR recombination are essential for correct interpretation of the Ig/TCR clonality data. Several immunobiologic and technical pitfalls that should be taken into account to avoid misinterpretation of data are addressed in this review. Furthermore, the need to integrate the molecular data with that from (hemato-)pathology, and preferably also flowcytometric immunophenotyping for appropriate interpretation, is discussed. Such an interactive, multidisciplinary diagnostic model guarantees integration of all available data to reach the most reliable diagnosis.
Compact optical temporal processors (1995)

Optical signal processing can be done with time-lens devices. A temporal processor based on chirp-z transformers is suggested. This configuration is more compact than a conventional 4-ƒ temporal processor. On the basis of implementation aspects of such a temporal processor, we did a performance analysis. This analysis leads to the conclusion that an ultrafast optical temporal processor can be implemented.
TWO MAMMALIAN CELL INTERNALIZATION STRATEGIES USED BY PATHOGENIC BACTERIA (1994)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Ancient System Gets New Respect (2001)

INNATE IMMUNITYUnlike the so-called acquired immune system, with its disease-fighting cells and antibodies, innate immunity depends on peptides and small proteins to fight off dangerous microbes. As genomic information has flooded out of sequencing labs within the last few years, researchers have identified hundreds of these peptides from a broad range of species. They are also now working out exactly what trips these defenses and how they specialize to fight off the pathogens that attack each kind of organism--information that may make peptides a new source of antibiotics.
Sickle Hemoglobin (Hb S) Allele and Sickle Cell Disease: A HuGE Review (2000)

Sickle cell disease is caused by a variant of the beta-globin gene called sickle hemoglobin (Hb S). Inherited autosomal recessively, either two copies of Hb S or one copy of Hb S plus another beta-globin variant (such as Hb C) are required for disease expression. Hb S carriers are protected from malaria infection, and this protection probably led to the high frequency of Hb S in individuals of African and Mediterranean ancestry. Despite this advantage, individuals with sickle cell disease exhibit significant morbidity and mortality. Symptoms include chronic anemia, acute chest syndrome, stroke, splenic and renal dysfunction, pain crises, and susceptibility to bacterial infections. Pediatric mortality is primarily due to bacterial infection and stroke. In adults, specific causes of mortality are more varied, but individuals with more symptomatic disease may exhibit early mortality. Disease expression is variable and is modified by several factors, the most influential being genotype. Other factors include beta-globin cluster haplotypes, alpha-globin gene number, and fetal hemoglobin expression. In recent years, newborn screening, better medical care, parent education, and penicillin prophylaxis have successfully reduced morbidity and mortality due to Hb S.
Effects of highly concentrated omega-3 polyunsaturated fatty acids and acetylsalicylic acid, alone and combined, on bleeding time and serum lipid profile. (1989)

Twenty-two patients with stable coronary heart disease were randomly assigned to either of two groups. Group I (n = 11) was given acetylsalicylic acid (ASA) 300 mg daily for 1 week, whereafter a daily supplement of 3,4 g eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) as a highly concentrated ethylester, formulation ("K-85", Norsk Hydro) was added for another 4 weeks. Group II (n = 11) was given 3,4 g daily of EPA and DHA for 4 weeks, after which ASA 300 mg daily was added for another week. Determination of serum fatty acids confirmed satisfying absorption of EPA and DHA. A significant increase of the Ivy bleeding time was registered following administration of both "K-85" (240 to 270 sec, median values) and ASA (270 to 360 sec, median values) alone. A slighter increase was noted by a combination of the two principles. A reduction in serum triglycerides of 17% was noted after "K-85" (median values, both groups). Serum total cholesterol decreased after "K-85" administration in group I, but not so in group II. HDL-cholesterol remained unchanged. Serum lipids remained unaffected by ASA. During administration of "K-85" no adverse effects or bleeding episodes were seen.
Isolation of MHC Class I-Restricted Tumor Antigen Peptide and Its Precursors Associated with Heat Shock Proteins hsp70, hsp90, and gp96 (1999)

We have previously demonstrated that vaccination with heat shock proteins hsp70, hsp90, and gp96 elicits specific immunity against the tumor from which the hsps were purified. Although the association of tumor Ag peptides with these hsps have been suggested, the identification of the peptides or their precursors stripped from the hsps remained to be resolved. We show in this report that an Ld-restricted cytotoxic T lymphocyte epitope of a mouse leukemia RLmale symbol1 and its precursors are associated with the chaperones hsp90 and hsp70 in the cytosol and gp96 in the lumen of the endoplasmic reticulum. Hsp70 was associated with only final sized octamer, while hsp90 was found to associate with the octamer and two distinct precursor peptides. The gp96 was associated with the octamer and one of the two precursors. Thus, each of the hsps bound a distinct set of peptides. Our results have demonstrated for the first time that the hsps associate not only with final sized tumor Ag peptide but also with its precursors. The implication of this evidence is also discussed in terms of the roles of hsps in MHC class I Ag processing/presentation.
Diagnostic criteria for the sleep apnoea syndrome: time for consensus (1996)

The traditional diagnosis of sleep apnoea syndrome has been based on a particular apnoea frequency during sleep, and was originally set at ≥5 apnoeas·h-1 of sleep during the 1970s [1]. However, as experience developed with the clinical spectrum of patients with sleep apnoea, it was realized that hypopnoeas during sleep could have a similar clinical significance as complete apnoeas [2], and this realization led to the present clinical diagnostic criteria, which are based on the combined frequency of apnoeas and hypopnoeas during sleep. Unfortunately, there is not complete agreement as to what apnoea and hypopnoea frequency represents a clinically significant sleep apnoea syndrome, with some centres using a level of 10 episodes·h -1 [3‐5], and others 15 episodes·h -1 [6, 7]. A number of obvious deficiencies can be identified in the present approach to the diagnosis of obstructive sleep apnoea (OSA). Firstly, not all patients with an apnoea/hypopnoea index (AHI) of greater than 10 or 15 episodes·h-1 of sleep appear to have a clinically significant OSA syndrome. It has long been recognized that apnoeas during sleep become more frequent with advancing age, and many apparently normal elderly people have an AHI greater than the above thresholds [8, 9]. It is now accepted that a diagnosis of clinically significant OSA should be accompanied by compatible symptoms, and not be based simply on an arbitrary AHI threshold, particularly in borderline cases. Clinically significant OSA can occur, particularly among younger patients, at AHI frequencies below 10 episodes·h-1, and the recent description of the upper airway resistance syndrome [10] indicates that episodic partial upper airway obstruction without significant hypopnoea can mimic OSA in most
Femtosecond pulse shaping using spatial light modulators (2000)

We review the field of femtosecond pulse shaping, in which Fourier synthesis methods are used to generate nearly arbitrarily shaped ultrafast optical wave forms according to user specification. An emphasis is placed on programmable pulse shaping methods based on the use of spatial light modulators. After outlining the fundamental principles of pulse shaping, we then present a detailed discussion of pulse shaping using several different types of spatial light modulators. Finally, new research directions in pulse shaping, and applications of pulse shaping to optical communications, biomedical optical imaging, high power laser amplifiers, quantum control, and laser-electron beam interactions are reviewed.
Involvement of 29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication (2006)

Phi29 DNA polymerase achieves a functional coupling between its 3'-5' exonuclease and polymerization activities by means of important contacts with the DNA at both active sites. The placement and orientation of residues Lys538, Lys555, Lys557, Gln560, Thr571, Thr573 and Lys575 in a modelled phi29 DNA polymerase-DNA complex suggest a DNA-binding role. In addition, crystal structure of phi29 DNA polymerase-oligo (dT)5 complex showed Leu567, placed at the tip of the thumb subdomain, lying between the two 3'-terminal bases at the exonuclease site. Single replacement of these phi29 DNA polymerase residues by alanine was made, and mutant derivatives were overproduced and purified to homogeneity. The results obtained in the assay of their synthetic and degradative activities, as well as their coordination, allow us to propose: (1) a primer-terminus stabilization role at the polymerase active site for residues Lys538, Thr573 and Lys575, (2) a primer-terminus stabilization role at the exonuclease active site for residues Leu567 and Lys555 and (3) a primer-terminus binding role in both editing and polymerization modes for residue Gln560. The results presented here lead us to propose phi29 DNA polymerase thumb as the main subdomain responsible for the coordination of polymerization and exonuclease activities.
Detection and cloning of new HTLV-related endogenous sequences in man (1989)

Human T-cell leukemia virus (HTLV) type I-related endogenous sequences (HRES) have been cloned from a human genomic library. HRES-1/1 is present in DNA of all normal donors examined. By nucleotide sequence analysis, HRES-1/1 contains two potential open reading frames capable of encoding a p25 and a p15. A 684 bp flanking region 5' from the first ATG codon of p25 contains a TATA-box, a poly-adenylation signal, a putative tRNA primer binding site, and inverted repeats at locations which are typical of a retroviral long terminal repeat. Phylogenetic analysis suggests that HRES-1/1 entered the genome in primates, presumably as an exogenous retrovirus. From the deduced amino acid sequence of HRES-1/1 p25, residues 6-36 show a sequence homology of 32% and 39% to gag region segments of HTLV-I and HTLV-II, while residues 104-139 display a sequence homology of 33% and 28% to the gag regions of human immunodeficiency virus type 2 (HIV-2) and feline sarcoma virus (FSV), respectively. This suggests that the original exogenous virus infecting primate may be chimeric in structure. The HRES-1/1 genomic locus is transcriptionally active in lymphoid cells, melanoma cells, and embryonic tissues.
Quantum Dot Self-Assembly for Protein Detection with Sub-Picomolar Sensitivity (2008)

A novel approach to sensitive and rapid antigen detection is described. In the presence of a specific antigen, quantum dot-antibody conjugates rapidly self-assemble into agglomerates that are typically more than 1 order of magnitude larger than their individual components. The size distribution of the agglomerated colloids depends on, among other things, the relative concentration of quantum dot conjugates and antigen molecules. Quantum dot agglomerates mediated by antigen recognition were characterized by measuring their light scattering and fluorescence characteristics in an unmodified flow cytometer. Protein antigens angiopoietin-2 and mouse IgG were detected to sub-picomolar concentrations using this method. This simple technique enables the potential simultaneous detection of multiple antigenic biomarkers directly from physiological media and could be used for early detection and frequent screening of cancers and other diseases.
Identification of the cellulose-binding domain of the cellulosome subunit S1 from Clostridium thermocellum YS (1992)

The 3′ region of a gene designated cipB, which shows strong homology with cipA that encodes the cellulosome SL subunit of Clostridium thermocellum ATCC 27405, was isolated from a gene library of C. thermocellum strain YS. The truncated S1 protein encoded by the cipB derivative bound tightly to cellulose. The cellulose-binding domain in this polypeptide consisted of a C-terminal proximal 167 residue sequence which showed complete identity with residues 337–503 of mature SL from C. thermocellum strain ATCC 27405. The cellulose-binding domain interacted with both crystalline and amorphous cellulose, but not with xylan.
Proxemic interactions (2011)

research-article Proxemic interactions: the new ubicomp? Share on Authors: Saul Greenberg University of Calgary University of CalgaryView Profile , Nicolai Marquardt University of Calgary University of CalgaryView Profile , Till Ballendat University of Calgary and Ludwig-Maximilians-Universität University of Calgary and Ludwig-Maximilians-UniversitätView Profile , Rob Diaz-Marino University of Calgary University of CalgaryView Profile , Miaosen Wang University of Calgary University of CalgaryView Profile Authors Info & Claims InteractionsVolume 18Issue 1January + February 2011 pp 42–50https://doi.org/10.1145/1897239.1897250Online:01 January 2011Publication History 265citation8,470DownloadsMetricsTotal Citations265Total Downloads8,470Last 12 Months1,400Last 6 weeks135 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Galeterone in men with CRPC: Results in four distinct patient populations from the ARMOR2 study. (2014)

5029 Background: Galeterone is a 1st in class oral small molecule that disrupts androgen receptor (AR) signaling via multi-targeted mechanism of action (1) selective inhibition of CYP17 lyase; (2) competitive antagonism of androgen binding to AR; and (3) degrading of AR protein. CYP17 enzyme inhibition (abiraterone) and AR antagonism (enzalutamide) separately have shown significant activity in metastatic castrate resistant prostate cancer (mCRPC) and considered standard treatment for these pts. Galeterone is a single molecule that has the potential advantage to target both mechanisms. Methods: ARMOR2 (NCT# 01709734) is a 2 Pt Phase 2 study designed to confirm dose of reformulated galeterone (spray dry dispersion; SDD) (Pt 1) and assess the safety and efficacy of the dose, 2550 mg QD for 12 wks, in 4 distinct CRPC pt cohorts; non-metastatic tx naïve (M0 TN, n= 7, median PSA=15.6 ng/dL, median PSA DT=2.30 mo), metastatic tx naïve (M1 TN, n=24, median PSA = 22.9 ng/dL, median PSA DT=2.3 mo), abiraterone refractory (Abi-R, n=11, median PSA=35.8 ng/dL, median PSA DT=1.57 mo) and enzalutamide refractory (Enza-R, n=2, median PSA = 72.85 ng/dL, median PSA DT=1.97 mo). This abstract presents interim results of the 2550 mg dose for pts treated in both Pt 1 and 2. Results: Response was seen at 2550 mg in all tx groups, including decreases in PSA. In the most mature dataset of 24 M1 TN pts, PSA decreases of 30% (92%), and 50% (83%) were reached. Data on the M1 group showed encouraging preliminary objective responses (ORR) in 7 of 8 (86%) evaluable pts at 3 months. Safety: Drug was well tolerated by all tx groups. 94% of all adverse events (AE) were gr1 or 2 in severity. Most common < gr 2 AEs were GI (nausea, diarrhea), fatigue and pruritis with no mineralocorticoid excess (ME) or seizures. Conclusions: SDD Galeterone has shown significant biochemical activity and preliminary clinical activity and is well tolerated with no ME or seizures. These data support continued testing of this unique compound in pts with prostate cancer. Clinical trial information: NCT01709734.PSA response by tx group. Tx Group N Pts with >30% n (%) Pts with > 50% n (%) M0 TN 6* 5 (83) 4 (67) M1 TN 24* 22 (92) 20 (83) Abi-R 5** 2 (40) 0 (0) Enza-R 2 NA NA *N= # of pts completing 12 wks, reached PSA 50 or terminated early. **N= # of pts completing 12 wks.
High performance plasmonic crystal sensor formed by soft nanoimprint lithography (2005)

This paper describes a new type of plasmonic sensor fabricated by imprint lithography using a soft, elastomeric mold. Angle-dependent, zero-order transmission experiments demonstrate the sensing potential of this device, which uses a two dimensional plasmonic crystal. Full angle-dependent mapping shows that the sensitivity to surface chemical binding events reaches maxima near regions of the plasmonic Brillouin zone where the dispersion curves of multiple surface plasmon polariton modes converge. This behavior, together with the simple, low cost procedures for building the structures, suggests a potentially important role for these devices in high performance chemical and biological sensing.
Alteration of DSS-mediated immune cell redistribution in murine colitis by oral colostral immunoglobulin (2013)

These data demonstrated the potential of colostrum in disease recovery and epithelial homeostasis following intestinal injury. Colostral sIgA failed to improve acute disease activity but promoted weight gain and modulated immune cell responses that are involved in the genesis of colitis.
A phase I trial of DNA vaccination with a plasmid expressing prostate-specific antigen in patients with hormone-refractory prostate cancer (2004)

Prostate-specific antigen (PSA) is a serine protease secreted at low levels by normal luminal epithelial cells of the prostate and in significantly higher levels by prostate cancer cells. Therefore, PSA is a potential target for various immunotherapeutical approaches against prostate cancer. DNA vaccination has been investigated as immunotherapy for infectious diseases in patients and for specific treatment of cancer in certain animal models. In animal studies, we have demonstrated that vaccination with plasmid vector pVAX/PSA results in PSA-specific cellular response and protection against tumour challenge. The purpose of the trial was to evaluate the safety, feasibility and biological efficacy of pVAX/PSA vaccine in the clinic. A phase I trial of pVAX/PSA, together with cytokine granulocyte/macrophage-colony stimulating factor (GM-CSF) (Molgramostim) and IL-2 (Aldesleukin) as vaccine adjuvants, was carried out in patients with hormone-refractory prostate cancer. To evaluate the biologically active dose, the vaccine was administered during five cycles in doses of 100, 300 and 900 microg, with three patients in each cohort. Eight patients were evaluable. A PSA-specific cellular immune response, measured by IFN-gamma production against recombinant PSA protein, and a rise in anti-PSA IgG were detected in two of three patients after vaccination in the highest dose cohort. A decrease in the slope of PSA was observed in the two patients exhibiting IFN-gamma production to PSA. No adverse effects (WHO grade >2) were observed in any dose cohort. We demonstrate that DNA vaccination with a PSA-coding plasmid vector, given with GM-CSF and IL-2 to patients with prostate cancer, is safe and in doses of 900 microg the vaccine can induce cellular and humoral immune responses against PSA protein.
Hepatic MRI for Fat Quantitation (2005)

Hepatic MRI and ultrasound are both useful in identifying heavy fat accumulation associated with nonalcoholic fatty liver disease. MRI is superior to ultrasound in detecting and quantifying minor degrees of fatty metamorphosis in the liver.
A reconfigurable data-driven ALU for Xputers (2002)

A reconfigurable data-driven datapath architecture for ALUs is presented which may be used for custom computing machines (CCMs), Xputers (a class of CCMs) and other adaptable computer systems as well as for rapid prototyping of high speed datapaths. Fine grained parallelism is achieved by using simple reconfigurable processing elements which are called datapath units (DPUs). The word-oriented datapath simplifies the mapping of applications onto the architecture. Pipelining is supported by the architecture. The programming environment allows automatic mapping of the operators from high level descriptions. Two implementations, one by FPGAs and one with standard cells are shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antihypertensive activity of a new ACE-inhibitor, SCH 33844, during repeated administration in spontaneously hypertensive rats. (1987)

The antihypertensive activity of SCH 33844, a new angiotensin converting enzyme inhibitor, was investigated in conscious spontaneously hypertensive rats during a 3-week treatment regimen and for 1 week following drug withdrawal. SCH 33844 was given once daily at 2 dose levels (1 and 5 mg/kg orally) and its effects were compared with those of captopril (60 mg/kg orally). Systolic blood pressure was recorded twice weekly just before administration and at varying time intervals up to 6 hr after dosing; recordings were continued for 1 week after drug withdrawal. SCH 33844 was found to produce dose-related antihypertensive effects. Given at 1 mg/kg, the compound elicited small but significant blood pressure changes during the treatment. After drug withdrawal, systolic blood pressure returned to pre-drug levels within 1 week. SCH 33844 at 5 mg/kg, and captopril at 60 mg/kg, both reduced blood pressure markedly and to a similar extent. After each administration the effect was rapid in onset, lasted for over 6 hr and was not subject to tolerance. Drug withdrawal resulted in a gradual return of systolic blood pressure toward pre-treatment levels within 1 week, with no evidence of rebound phenomena. These results indicate that SCH 33844, like captopril, produces an effective antihypertensive action throughout a repeated dosing.