gebhart/patrepeval huggingface dataset:
A single-chip biosensing platform integrating FBAR sensor with digital microfluidic device (2014)

Although digital microfluidic system has shown great potential in a wide range of applications, a single-chip platform integrating biochemical sensors with digital microfluidic devices is still lacking. In this paper, film bulk acoustic resonator (FBAR) sensors and electrowetting-on-dielectric (EWOD) actuator are integrated on a single silicon chip, where the EWOD actuator manipulates digital droplets and the FBAR sensor detects analyte in the droplets. Thin aluminum nitride (AlN) film is a critical material as both the FBAR piezoelectric layer and the EWOD dielectric layer, which facilitates the compact integration of the two devices on a chip. A preliminary demonstration of Hg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> droplet transportation and detection is conducted on the platform. The integrated platform is expected to play an important role in many complex lab-on-a-chip applications in chemistry, biology and medicine.
Canola and high erucic rapeseed oil as substitutes for diesel fuel: Preliminary tests (1983)

Abstract A cooperative project using the facilities of the POS Pilot Plant Corporation, the Saskatchewan Research Council and the Agricultural Engineering Department, University of Saskatchewan, and funded by Agriculture Canada, was initiated in 1980 to investigate the feasibility of using canola and high erucic rapeseed oil as a replacement/extender to diesel fuel in direct‐injection diesel engines. Work carried out included the documented production and refining of canola and R500 (high erucic) vegetable oils, preparation of methyl ester and of blends of all these fuels with methanol and ethanol. These fuels were evaluated by ASTM and improvised tests to determine their usefulness as diesel fuel. Engine tests involved a 2‐cylinder Petter diesel and a 6‐cylinder John Deere turbocharged diesel. Results were similar for both engines in short‐term performance tests, and indicated that: (a) maximal power was essentially the same when burning canola oil as when burning diesel fuel; (b) specific fuel consumption was ca. 6% higher when burning canola oil, but because canola oil has a heating value 14% less than diesel fuel, the thermal efficiency is somewhat higher when operating on canola oil; (c) there were no starting problems down to 10 C; (d) there were fewer particulates in the exhaust when burning canola oil; and (e) there was generally less combustion noise when burning canola oil. The high viscosity of canola oil (ca. 35 times that of disel fuel at 20 C) poses a major problem in using the oil at low temperature. Blending with diesel fuel and the creation of a methyl ester from the canola oil both proved effective in reducing viscosity, but neither lowered the pour point apprecibly. Efforts on reduction of pour points and further work on blends and on heating the fuel are described.
Biological models and genes of tumor reversion: Cellular reprogramming through tpt1 /TCTP and SIAH-1 (2002)

Tumor reversion is the process by which some cancer cells lose their malignant phenotype. This study was aimed at defining some of the molecular and phenotypic properties of this process. Biological models of tumor reversion were isolated from human leukemia and breast cancer cell lines by using the H-1 parvovirus as a selective agent. Differential gene expression analysis was performed between the parental malignant cells and their revertants or alternatively between these parental cells and their SIAH-1 transfectant counterparts. These SIAH-1 transfectants have a suppressed malignant phenotype and were used as a control for a viral-free system. Two hundred sixty-three genes were found to be either activated or inhibited during the reversion process, as confirmed by Northern blot analysis or quantitative PCR. Of these, 32% were differentially expressed in all systems, irrespective of whether parvovirus-selected, SIAH-1 overexpressing, or p53 mutant or wild-type cell lines were used, suggesting the existence of a universal mechanism underlying tumor reversion. Translationally Controlled Tumor Protein (tpt1/TCTP) has the strongest differential expression, down-regulated in the reversion of U937- and SIAH-1-overexpressing cells. Inhibition of TCTP expression by anti-sense cDNA or small interfering RNA molecules results in suppression of the malignant phenotype and in cellular reorganization, similar to the effect of SIAH-1. Hence, tumor reversion can be defined at the molecular level, not just as the reversal of malignant transformation, but as a biological process in its own right involving a cellular reprogramming mechanism, overriding genetic changes in cancer, by triggering an alternative pathway leading to suppression of tumorigenicity.
High-performance liquid chromatography of mycolic acids as a tool in the identification of Corynebacterium, Nocardia, Rhodococcus, and Mycobacterium species (1986)

High-performance liquid chromatography of bromophenacyl esters of mycolic acid was used as an aid to assign a particular organism to one of four mycolic acid-containing genera. A gradient elution system, with methanol and chloroform, was used to distinguish representative mycolic acid patterns for the genera Corynebacterium, Rhodococcus, Nocardia, and Mycobacterium.
The Structure of Mineralized Collagen Fibrils (1989)

A new model for the structure of mineralized bone collagen is presented which is compatible with neutron diffraction, electromicroscopic, crosslinking, and composition-density data. Mineralized collagen fibrils are comprised of azimuthally oriented, flexible molecules laterally arranged on a superlattice. Four nearest neighbors are longitudinally staggered by 67 nm and two neighbors by 2* 67 nm. In early stages of mineralization the molecules are parallel to the fibril axis with an average interaxis distance of 1.8 nm. In later stages they become flexed away from the fibril axis by an anisotropic lateral compression of molecules to an interaxis distance of 1.3 nm. Three quarters of the mineral in bone is disposed within the fibrils with a symmetry and habit reflecting the above organization of the collagen molecules.
Ligand Bonding and Dynamics on Colloidal Nanocrystals at Room Temperature: The Case of Alkylamines on CdSe Nanocrystals (2008)

With CdSe nanocrystals stabilized with very weak ligands (pyridine) as the starting materials, NMR techniques were applied to distinguish the bonded and free alkylamine ligands in an equilibrated adsorption/desorption system for the CdSe-amine nanocrystal-ligand pair. NMR and photoluminescence (PL) measurements were further correlated to identify the linear relationship between PL intensity and the surface ligand coverage of the amine-coated CdSe nanocrystals. For 3.5 nm CdSe nanocrystals and octylamine ligands, the chemical equilibrium constant (K) of the CdSe-amine nanocrystal-ligand adsorption/desorption process was found to be around 50-100, and the corresponding Delta(r)G(o) was calculated as 9.8-11.5 kJ/mol. With a proposed mathematic method, the corresponding chemical kinetic constants for the desorption (kd) and adsorption (ka) processes were measured to be 0.01 s(-1) and 0.5 L mol(-1) s(-1), respectively. K, kd, and ka obtained here are generally 2-4 magnitudes different from those estimated in literature. Analysis indicates that these constants are well consistent with the existing experimental observations.
ATM Influences the Efficiency of TCRβ Rearrangement, Subsequent TCRβ-Dependent T Cell Development, and Generation of the Pre-Selection TCRβ CDR3 Repertoire (2013)

Generation and resolution of DNA double-strand breaks is required to assemble antigen-specific receptors from the genes encoding V, D, and J gene segments during recombination. The present report investigates the requirement for ataxia telangiectasia-mutated (ATM) kinase, a component of DNA double-strand break repair, during TCRβ recombination and in subsequent TCRβ-dependent repertoire generation and thymocyte development. CD4(-)CD8(-) double negative stage 2/3 thymocytes from ATM-deficient mice have both an increased frequency of cells with DNA break foci at TCRβ loci and reduced Vβ-DJβ rearrangement. Sequencing of TCRβ complementarity-determining region 3 demonstrates that ATM-deficient CD4(+)CD8(+) double positive thymocytes and peripheral T cells have altered processing of coding ends for both in-frame and out-of-frame TCRβ rearrangements, providing the unique demonstration that ATM deficiency alters the expressed TCRβ repertoire by a selection-independent mechanism. ATMKO thymi exhibit a partial developmental block in DN cells as they negotiate the β-selection checkpoint to become double negative stage 4 and CD4(+)CD8(+) thymocytes, resulting in reduced numbers of CD4(+)CD8(+) cells. Importantly, expression of a rearranged TCRβ transgene substantially reverses this defect in CD4(+)CD8(+) cells, directly linking a requirement for ATM during endogenous TCRβ rearrangement to subsequent TCRβ-dependent stages of development. These results demonstrate that ATM plays an important role in TCRβ rearrangement, generation of the TCRβ CDR3 repertoire, and efficient TCRβ-dependent T cell development.
Structure of the HMG box motif in the B-domain of HMG1. (1993)

The conserved, abundant chromosomal protein HMG1 consists of two highly homologous, folded, basic DNA-binding domains, each of approximately 80 amino acid residues, and an acidic C-terminal tail. Each folded domain represents an 'HMG box', a sequence motif recently recognized in certain sequence-specific DNA-binding proteins and which also occurs in abundant HMG1-like proteins that bind to DNA without sequence specificity. The HMG box is defined by a set of highly conserved residues (most distinctively aromatic and basic) and appears to define a novel DNA-binding structural motif. We have expressed the HMG box region of the B-domain of rat HMG1 (residues 88-164 of the intact protein) in Escherichia coli and we describe here the determination of its structure by 2D 1H-NMR spectroscopy. There are three alpha-helices (residues 13-29, 34-48 and 50-74), which together account for approximately 75% of the total residues and contain many of the conserved basic and aromatic residues. Strikingly, the molecule is L-shaped, the angle of approximately 80 degrees between the two arms being defined by a cluster of conserved, predominantly aromatic, residues. The distinctive shape of the HMG box motif, which is distinct from hitherto characterized DNA-binding motifs, may be significant in relation to its recognition of four-way DNA junctions.
Effects of Pinacidil and Cromakalim (BRL 34915) On Bladder Function in Rats with Detrusor Instability (1989)

Normal rats as well as rats with bladder hypertrophy secondary to outflow obstruction were investigated cystometrically before and after administration of the potassium channel openers pinacidil or cromakalim one mg./kg. orally. In normal rats cromakalim decreased micturition pressure by 15 +/- 6%. A diminished micturition pressure was also seen after pinacidil (by 18 +/- 8%) but this did not achieve statistical significance. Further, no clear-cut effects on bladder capacity, residual volume, basal bladder pressure, threshold pressure, bladder compliance or on bladder wall tension were seen in this group of rats neither in the presence of pinacidil nor cromakalim. Rats with bladder hypertrophy exhibited a significant bladder instability during cystometrical investigations. The mean amplitude of the spontaneous bladder contraction exceeded 20 cm. H2O prior to micturition. Administration of pinacidil and cromakalin decreased the spontaneous contractions to 26 +/- 12% and 22 +/- 7%, respectively, of that seen in the absence of the drugs. Furthermore, pinacidil decreased micturition pressure by 61 +/- 12%. Also cromakalim decreased micturition pressure (by 27 +/- 13%) but this effect did not achieve statistical significance. After both pinacidil and cromakalim these rats tended to develop residual urine. In accordance with the results in normal rats pinacidil and cromakalim showed no effects on bladder capacity, basal bladder pressure, threshold pressure, bladder compliance or on bladder wall tension in rats with bladder hypertrophy. The findings of an almost complete disappearance of spontaneous bladder contractions in rats with bladder instability and a remaining voiding ability after administration of pinacidil or cromakalim suggest that potassium channel openers may be a therapeutic alternative in the treatment of bladder instability associated with outflow obstruction.
Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence. (1994)

A novel highly repetitive retrotransposable element was cloned based on a limited sequence homology to the human T-cell leukemia virus and a related endogenous retroviral sequence, HRES-1. This repetitive element was found to constitute an integral part of the coding sequence of the human gene for transaldolase. In comparison with the intronless yeast gene, structural analysis of the human transaldolase genomic locus revealed that the human gene is comprised of five exons, second and third of which uniquely developed by insertion of a retrotransposable element. The 1329-base pair full-length cDNA, clone 4/2-4/1, contains an open reading frame coding for a protein of 336 amino acids with a predicted molecular mass of 38 kDa. This protein shows a 58% overall sequence homology with the 37-kDa yeast transaldolase. Antibodies raised against a 22-kDa recombinant polypeptide expressed from a 474-base pair 5' fragment of clone 4/2-4/1, containing repetitive exons 2 and 3, cross-reacted with yeast transaldolase and recognized the 38-kDa native human protein. Detection of a retrotransposon in the coding sequence of the human transaldolase gene demonstrates the importance of these repetitive elements in evolution of the eukaryotic genome.
Mammaglobin and DOG‐1 expression in polymorphous low‐grade adenocarcinoma: an appraisal of its origin and morphology (2016)

Polymorphous low-grade adenocarcinoma has been confirmed to originate from the intercalated duct and to feature high expression of mammaglobin in its lobular pattern resembling that of mammary secretory analogue carcinoma, except for the ETV6 gene rearrangement.
Intrathecal topotecan in adult patients with neoplastic meningitis (2006)

Intrathecal topotecan appeared to be effective and safe in adult patients with NM.
Paclitaxel plus Bevacizumab versus Paclitaxel Alone for Metastatic Breast Cancer (2007)

Initial therapy of metastatic breast cancer with paclitaxel plus bevacizumab prolongs progression-free survival, but not overall survival, as compared with paclitaxel alone. (ClinicalTrials.gov number, NCT00028990 [ClinicalTrials.gov].).
A novel zinc finger gene on human chromosome 1qter that is alternatively spliced in human tissues and cell lines. (1993)

DNA-binding proteins that share the conserved C2-H2 zinc finger motif have been shown to have important roles as transcriptional regulators of gene expression and have been implicated in several hereditary human diseases. In order to define potential candidate genes for inherited disorders characterized by aberrant gene expression, we utilized Kruppel-related sequences to isolate zinc finger-containing cDNAs. We isolated and characterized two novel zinc finger-encoding cDNAs from a human hepatoblastoma cell line, which demonstrate DNA sequence homology to a recently described human Kruppel-related gene HZF-3 and appear to be derived from a single gene by alternate mRNA splicing. This gene, denoted "HZF-16," give rise to at least two gene products. One cDNA (i.e., HZF-16.2) has nine zinc finger domains, while alternative splicing of the message gives rise to a smaller product (i.e., HZF-16.1) that has four domains. Despite the internal splicing event, both the 5'- and 3'-untranslated sequences in both cDNAs are identical, as are the first three domains. In the HZF-16.1 cDNA, the fourth zinc finger domain is a fusion product of domains four and nine of HZF-16.2 and could potentially give rise to a new DNA-binding specificity. These alternatively spliced transcripts are differentially regulated in human tissues and transformed cell lines and show a different distribution of expression between human cell lines and normal human tissue. This novel gene was mapped to human chromosome 1q44 by chromosomal in situ suppression hybridization and thus represents a candidate gene for trisomy 1q syndrome and for several other disorders.
Uracil-DNA Glycosylase Inhibitor Gene of Bacteriophage PBS2 Encodes a Binding Protein Specific for Uracil-DNA Glycosylase (1989)

The uracil-DNA glycosylase inhibitor gene (ugi) of the Bacillus subtilis bacteriophage PBS2 has been subcloned to a 720-base pair DNA fragment contained in pZW2-0.7 and its nucleotide sequence determined. Using nucleotide deletion analysis, we have located the cloned ugi gene along with potential regulatory elements. A promoter-like region (-10 and -35 consensus sequences) similar to other B. subtilis genes and the Shine-Dalgarno sequence characteristic of Gram-positive bacteria were both identified upstream from the initiator AUG codon. A 17-nucleotide exact inverted repeat followed by runs of adenine and thymine residues was positioned almost immediately downstream of the ochre codon. The ugi gene product was identified on sodium dodecyl sulfate-polyacrylamide gels using Escherichia coli minicells containing pZW2-0.7 and by recovering uracil-DNA glycosylase inhibitor activity following electrophoresis. The ugi gene codes for an acidic polypeptide of 9,477 molecular weight (84 amino acids) whose electrophoretic mobility was greater than predicted for a protein of this size. The mode of inhibition did not appear to involve a catalytic process nor did it directly involve inhibitor-DNA interaction. Rather, the inhibitor protein was shown to bind physically to the E. coli uracil-DNA glycosylase, forming a 36,000 molecular weight complex. This complex seems to be reversible, since inhibitor activity was recovered after heat treatment of the complex. In addition, we demonstrated that the inhibitor protein is active against uracil-DNA glycosylases isolated from several diverse biological sources but inactive against E. coli deoxyuridine triphosphatase, DNA polymerase I, and DNA polymerase alpha, beta, and gamma.
Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer‐Scale Wells Embedded in DNA Origami Assembly (2009)

A new punched DNA origami assembly with periodic nanometer-scale wells has been successfully designed and constructed. Through the attachment of two biotins at the two edges of each well, just one streptavidin (SA) tetramer (d = 5 nm) was size-selectively captured in each 6.8 x 12 x 2.0 nm well; this allowed formation of a 28 nm-period SA nanoarray of individual molecules. The position of SA capture can be fully controlled by placement of biotins in the nanoarray well. Moreover, construction of a 2D nanoarray of individual SA tetramers through selective positioning of SA tetramers in any desired wells in a complex of such punched origami motifs is also possible. The stability of the SA captured by this fixation strategy (DNA wells and two biotin linkers) was directly compared on the same molecule with the stability of SA captured with other possible strategies that do not employ wells or two linkers. In this way, the robustness of this means of fixation was clearly established.
Found: a cellular activating ligand for NKp44 (2013)

In this issue of Blood, Baychelier et al identify a ligand for a major natural killer (NK) cell receptor that mediates natural cytotoxicity toward tumor cells, thus ending a search that lasted well over a decade.
The Actinic (Solar) Keratosis (2003)

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The Endophthalmitis Vitrectomy Study (1991)

Endophthalmitis after cataract surgery can be a disastrous complication that may result in functional loss of an eye. All patients with this problem should receive direct injection of intravitreal antibiotics. The roles of initial vitrectomy and of intravenous antibiotics in treating this condition are controversial. Through a prospective, randomized, clinical trial, these issues can be assessed. We encourage ophthalmologists close to each clinical center to refer patients with postoperative endophthalmitis to these clinics. Questions concerning the Endophthalmitis Vitrectomy Study can be addressed to the principal investigator at the nearest clinical trial center.
Predicting the orientation of eukaryotic membrane-spanning proteins. (1989)

We have developed a rule to predict the orientation of the first internal signal-anchor sequence in eukaryotic transmembrane proteins synthesized on the rough endoplasmic reticulum. The difference in the charges of the 15 residues flanking the first internal signal-anchor determines its orientation, with the more positive portion facing the cytosol. In proteins that span the membrane more than once, the orientation of all subsequent transmembrane segments would be determined by that of the most N-terminal one.
Novel Therapeutic Targets for Acute Pancreatitis and Associated Multiple Organ Dysfunction Syndrome (2002)

Acute pancreatitis is a common clinical condition. The exact mechanisms by which diverse etiological factors induce an attack are unclear but once the disease process is initiated, common inflammatory and repair pathways are invoked. Acinar cell injury early in acute pancreatitis leads to a local inflammatory reaction; if marked, this leads to a systemic inflammatory response syndrome (SIRS). An excessive SIRS leads to distant organ damage and multiple organ dysfunction syndrome (MODS). MODS associated with acute pancreatitis is the primary cause of morbidity and mortality in this condition. The systemic effects of acute pancreatitis have many similarities to those of other conditions such as septicemia, severe burns and trauma. Potentially, there is a therapeutic window between symptom onset and the development of distant organ damage in acute pancreatitis, when anti-inflammatory therapy may be of use. Recent studies conducted by us and other investigators have established the critical role played by inflammatory mediators such as TNF-alpha, IL-1beta, IL-6, IL-8, CINC/GRO-alpha, MCP-1, PAF, IL-10, CD40L, C5a, ICAM-1, and Substance P in acute pancreatitis and the resultant MODS. It is reasonable to speculate that elucidation of the key mediators in acute pancreatitis coupled with the discovery of specific inhibitors will make it possible to develop a clinically effective anti-inflammatory therapy.