gebhart/patrepeval huggingface dataset:
Molecular cloning and expression of GalNAc alpha 2,6-sialyltransferase. (1994)

cDNA clones encoding GalNAc alpha 2,6-sialyltransferase (EC 2.4.99.3) have been isolated from chick embryo cDNA libraries using sequence information obtained from the conserved amino acid sequence of the previously cloned enzymes. The cDNA sequence included an open reading frame coding for 566 amino acids, and the deduced amino acid sequence showed 12% identity with that of Gal beta 1,4GlcNAc alpha 2,6-sialyltransferase from chick embryo. The primary structure of this enzyme suggested a putative domain structure, like that in other glycosyltransferases, consisting of a short NH2-terminal cytoplasmic domain, a signal-membrane anchor domain, a proteolytically sensitive stem region, and a large COOH-terminal active domain. The identity of this enzyme was confirmed by the construction of a recombinant sialyltransferase in which the NH2-terminal part (232 amino acid residues) was replaced with the immunoglobulin signal sequence. The expression of this recombinant in COS-7 cells resulted in secretion of a catalytically active and soluble form of the enzyme into the medium. The expressed enzyme exhibited activity toward only asialomucin and (asialo)fetuin, no significant activity being detected toward the other glycoprotein and glycolipid substrates tested. 14C-Sialylated glycols obtained from asialomucin re-sialylated with this enzyme were identical to NeuAc alpha 2,6-GalNAc-ol and GlcNAc beta 1,3(NeuAc alpha 2,6) GalNAc-ol. Synthetic GalNAc-SerNAc also served as an acceptor for alpha 2,6-sialylation. These results clearly showed that the expressed enzyme is GalNAc alpha 2,6-sialyltransferase.
On the Use of Soft-Decision Error-Correction Codes in nand Flash Memory (2010)

As technology continues to scale down, NAND Flash memory has been increasingly relying on error-correction codes (ECCs) to ensure the overall data storage integrity. Although advanced ECCs such as low-density parity-check (LDPC) codes can provide significantly stronger error-correction capability over BCH codes being used in current practice, their decoding requires soft-decision log-likelihood ratio (LLR) information. This results in two critical issues. First, accurate calculation of LLR demands fine-grained memory-cell sensing, which nevertheless tends to incur implementation overhead and access latency penalty. Hence, it is critical to minimize the fine-grained memory sensing precision. Second, accurate calculation of LLR also demands the availability of a memory-cell threshold-voltage distribution model. As the major source for memory-cell threshold-voltage distribution distortion, cell-to-cell interference must be carefully incorporated into the model. However, these two critical issues have not been ever addressed in the open literature. This paper attempts to address these open issues. We derive mathematical formulations to approximately model the threshold-voltage distribution of memory cells in the presence of cell-to-cell interference, based on which the calculation of LLRs is mathematically formulated. This paper also proposes a nonuniform memory sensing strategy to reduce the memory sensing precision and, thus, sensing latency while still maintaining good error-correction performance. In addition, we investigate these design issues under the scenario when we can also sense interfering cells and hence explicitly estimate cell-to-cell interference strength. We carry out extensive computer simulations to demonstrate the effectiveness and involved tradeoffs, assuming the use of LDPC codes in 2-bits/cell NAND Flash memory.
Silicone Nanofilaments and Their Application as Superhydrophobic Coatings (2006)

Silicone nanofilaments (see figure) are grown by a simple chemical vapor deposition method on different substrate materials. The filaments are flexible, and have lengths of up to several micrometers and diameters of up to 150 nm. The dense and entangled arrangement of these filaments yields a superhydrophobic coating that is also optically transparent and antireflective.
MINIREVIEW: Estrogen Receptor Variants in Clinical Breast Cancer (1991)

We have used the screening techniques of chemical mismatch cleavage, single stranded conformational polymorphism, and gel retardation to discover a number of estrogen receptor RNA variants in clinical breast cancer tissues. We have found basepair insertions, transitions, and deletions as well as alternative splicing, yielding deletions of exon 3, 5, or 7. Using a yeast transactivation assay we have discovered receptors with outlaw function, including both a dominant-positive receptor, which is transcriptionally active in the absence of estrogen, and a dominant-negative receptor, which is itself transcriptionally inactive, but prevents the action of normal estrogen receptor. These variants could have clinical significance, helping to explain breast tumor behavior and patient outcome.
Immunological properties of a type C retrovirus isolated from cultured human T-lymphoma cells and comparison to other mammalian retroviruses (1981)

HTLV strain CR (HTLVCR) is a retrovirus which was isolated from a human T-cell lymphoma cell line. A protein of molecular weight 24,000 p24, was purified from this virus. Several results indicate that this p24 is an internal core protein of HTLVCR. (i) The p24 copurified with viral cores. (ii) It was labeled with 125I after disruption of the virus, but not when undisrupted virus was iodinated. (iii) The amount of p24 was directly proportional to the amount of HTLVCR. (iv) In chromatographic properties, the HTLVCR p24 behaved similarly to the major structural protein (24,000- to 30,000-molecular-weight protein) of other retroviruses. A rabbit antiserum raised against disrupted HTLVCR precipitated the labeled p24, and the precipitation was competed for by unlabeled HTLVCR and by cytoplasmic proteins from cells producing HTLVCR, but not by proteins from normal human cells, including normal growing human T-cells, and several cultured human cutaneous T-cell lymphoma lines. Proteins from several mammalian type B, type C, and type D viruses also failed to compete in this precipitation. Moreover, HTLVCR did not react in homologous and interspecies assays for p30 antigens of several mammalian type C and type D viruses. These observations agree with immunological comparisons between reverse transcriptase of HTLVCR and other retroviruses and nucleic acid sequence homology studies which indicate that the various HTLVCR isolates represent new retroviruses found in some human T-cell neoplasias.
Micronuclei as an index of cytogenetic damage: Past, present, and future (1991)

The workshop was designed to present what is known about the production of micronuclei, what protocols are now accepted or proposed internationally, what new results have been obtained, and what new methods and protocols are likely to be forthcoming. This report is designed to convey the flavour of the workshop and to provide the essence of the new information. After the workshop an effort was made to determine what single protocol would satisfy the requirements set for the micronucleus test by as many regulatory agencies as possible. The result, reported here, includes the requirements of six regulatory authorities in Canada, the European Economic Community, the Organization for Economic Co-operation and Development, Japan, and the United States.
Optical sectioning of microbial biofilms (1991)

Scanning confocal laser microscopy (SCLM) was used to visualize fully hydrated microbial biofilms. The improved rejection of out-of-focus haze and the increased resolution of SCLM made it preferable to conventional phase microscopy for the analysis of living biofilms. The extent of image improvement was dependent on the characteristics of individual biofilms and was most apparent when films were dispersed in three dimensions, when they were thick, and when they contained a high number of cells. SCLM optical sections were amenable to quantitative computer-enhanced microscopy analyses, with minimal interference originating from overlying or underlying cell material. By using SCLM in conjunction with viable negative fluorescence staining techniques, horizontal (xy) and sagittal (xz) sections of intact biofilms of Pseudomonas aeruginosa, Pseudomonas fluorescens, and Vibrio parahaemolyticus were obtained. These optical sections were then analyzed by image-processing techniques to assess the distribution of cellular and noncellular areas within the biofilm matrices. The Pseudomonas biofilms were most cell dense at their attachment surfaces and became increasingly diffuse near their outer regions, whereas the Vibrio biofilms exhibited the opposite trend. Biofilms consisting of different species exhibited distinctive arrangements of the major biofilm structural components (cellular and extracellular materials and space). In general, biofilms were found to be highly hydrated, open structures composed of 73 to 98% extracellular materials and space. The use of xz sectioning revealed more detail of biofilm structure, including the presence of large void spaces within the Vibrio biofilms. In addition, three-dimensional reconstructions of biofilms were constructed and were displayed as stereo pairs. Application of the concepts of architectural analysis to mixed- or pure-species biofilms will allow detailed examination of the relationships among biofilm structure, adaptation, and response to stress.
Concerning nonnegative matrices and doubly stochastic matrices (1967)

This paper is concerned with the condition for the convergence to a doubly stochastic limit of a sequence of matrices obtained from a nonnegative matrix A by alternately scaling the rows and columns of A and with the condition for the existence of diagonal matrices A and D2 with positive main diagonals such that ΏγAΏ2 is doubly stochastic. The result is the following. The sequence of matrices converges to a doubly stochastic limit if and only if the matrix A contains at least one positive diagonal. A necessary and sufficient condition that there exist diagonal matrices A and D2 with positive main diagonals such that D1AD2 is both doubly stochastic and the limit of the iteration is that AφO and each positive entry of A is contained in a positive diagonal. The form DιAD2 is unique, and A and D2 are unique up to a positive scalar multiple if and only if A is fully indecomposable.
Jasmonate-Inducible Genes Are Activated in Rice by Pathogen Attack without a Concomitant Increase in Endogenous Jasmonic Acid Levels (1997)

The possible role of the octadecanoid signaling pathway with jasmonic acid (JA) as the central component in defense-gene regulation of pathogen-attacked rice was studied. Rice (Oryza sativa L.) seedlings were treated with JA or inoculated with the rice blast fungus Magnaporthe grisea (Hebert) Barr., and gene-expression patterns were compared between the two treatments. JA application induced the accumulation of a number of pathogenesis-related (PR) gene products at the mRNA and protein levels, but pathogen attack did not enhance the levels of (-)-JA during the time required for PR gene expression. Pathogen-induced accumulation of PR1-like proteins was reduced in plants treated with tetcyclacis, a novel inhibitor of jasmonate biosynthesis. There was an additive and negative interaction between JA and an elicitor from M. grisea with respect to induction of PR1-like proteins and of an abundant JA-and wound-induced protein of 26 kD, respectively. Finally, activation of the octadecanoid signaling pathway and induction of a number of PR genes by exogenous application of JA did not confer local acquired resistance to rice. The data suggest that accumulation of nonconjugated (-)-JA is not necessary for induction of PR genes and that JA does not orchestrate localized defense responses in pathogen-attacked rice. Instead, JA appears to be embedded in a signaling network with another pathogen-induced pathway(s) and may be required at a certain minimal level for induction of some PR genes.
Modified HIV-1 Based Lentiviral Vectors Have an Effect on Viral Transduction Efficiency and Gene Expression in Vitro and in Vivo (2001)

Gene transfer using lentiviral vectors has been recently shown to be enhanced with cis-acting elements in a cell-type-dependent manner in vivo. For this reason, the study reported here was designed to modify lentiviral vectors that express lacZ, human factor IX (FIX), or human alpha1-anti-trypsin (AAT) to study the effect of different cis DNA elements on transduction efficiencies. We found that incorporation of the central polypurine tract sequence (cppt) increased transduction efficiency in vitro while increasing the transduction of non-cell-cycling hepatocytes in vivo. C57Bl/6 scid mice that were administered lentiviral vectors devoid of the cppt (2 x 10(8) transducing units (T.U.)/mouse) had 81% of their lacZ-transduced hepatocytes colabeled with the cell cycle marker 5'-bromo-2'-deoxyuridine (BrdU). In contrast, inclusion of the cppt reduced the colabeling in mouse hepatocytes by 50%. Further modifications in the lentiviral vectors were performed to enhance viral titer and gene expression. We found that the inclusion of a matrix attachment region (MAR) from immunoglobulin-kappa (Igkappa) significantly increased the transduction efficiency, as measured by transgene protein expression and proviral DNA copy number, compared with vectors without Igkappa MAR. In vitro studies using human hepatoma cells demonstrated a significant increase (two- to fourfold) in human AAT and human FIX production when the Igkappa MAR was incorporated. In vivo transduction of partially hepatectomized C57Bl/6 mice given an optimized lentiviral vector containing the cppt and Igkappa MAR (2 x 10(8) T.U./mouse) resulted in sustained therapeutic levels of serum FIX (approximately 65 ng/ml). Our study demonstrates the importance of cis-acting elements to enhancing the transduction ability of lentiviral vectors and the expression of vector transgenes.
Spectroscopic Quantitative Analysis of Strongly Interacting Systems: Human Plasma Protein Mixtures (1988)

Blood plasma protein infrared spectra, while qualitatively very similar, display subtle differences in the frequencies and intensities of absorption bands. These small differences are sufficient to permit an accurate quantitative analysis of mixtures of these proteins. In this paper we examine the performance of some alternative methods of spectroscopic quantitative analysis in determining the concentrations of proteins in aqueous solutions. The widely-used K matrix method, using sloping baselines and intercept functions, was found to be inadequate for these determinations. In contrast, a method based on the little-known Q matrix approach, augmented by a robust equation solver, yielded results with a sufficient degree of accuracy to make it a viable tool for use in the study of proteins at solid interfaces and for more general applications in the field of protein chemistry.
High Resolution Computed Tomography Scoring Systems for Evaluating Interstitial Lung Disease in Systemic Sclerosis Patients (2012)

Interstitial lung disease commonly develops in patients with Systemic sclerosis (SSc). High resolution computed tomography (HRCT) has become the gold standard for detection and evaluation of lung involvement in SSc. Several HRCT scoring methods have been described and used to characterize and quantify the disease. This article reviews the different scoring systems and how they have been validated clinically and applied to prognosticate patients, assess disease progression and evaluate response to treatment.
Tradeoffs in instruction format design for horizontal architectures (1989)

With recent improvements in software techniques and the enhanced level of fine grain parallelism made available by such techniques, there has been an increased interest in horizontal architectures and large instruction words that are capable of issuing more that one operation per instruction. This paper investigates some issues in the design of such instruction formats. We study how the choice of an instruction format is influenced by factors such as the degree of pipelining and the instruction's view of the register file. Our results suggest that very large instruction words capable of issuing one operation to each functional unit resource in a horizontal architecture may be overkill. Restricted instruction formats with limited operation issuing capabilities are capable of providing similar performance (measured by the total number of time steps) with significantly less hardware in many cases.
[Sexually transmitted diseases and the HIV/AIDS epidemic]. (1996)

Studies on sexually transmitted diseases (STD) during the previous years in Mexico are discussed. The information sources were: a) Surveys among commercial sex workers. Since 1990, 1,386 women have been studied in four federal states through structured questionnaires and laboratory tests. Prevalence of different STD's has been significant (syphilis (VDRL, FTA-abs) 23.7%; chlamydiosis (Ag IF) 12.9%; gonorrhea (Ag, ELISA) 11.5%; anti-HBs 11.0%; herpes 1,2 (IgM) 9.3%, HBsAg 5.7%. Frequency of HIV (ELISA, Western blot) has been low; 0.5%. In 1994, 662 women were studied in Mexico City, with different laboratory techniques for chlamydiosis and gonorrhea (culture), hepatitis B (anticore antibodies) and herpes (total antibodies) with the following results: syphilis 1.5-12%; chlamydiosis 10.8-11.7%; gonorrhea 0-5.9%; hepatitis B 0-7.1%; herpes 44.7-78%; and HIV 0-1.4%. b) Surveys among men with homosexual and bisexual practices. 325 subjects have been studied in three federal states using methods similar to those of the 1990 survey. Contrasting with results among women, HIV prevalence was found to be high; (18.8%), and considerable for other STD's: anti-HBsAg 28.6%, syphilis 34.9%, recent herpes 10.9%, HBsAg 5.0%, chlamydiosis (Ag, IF) 4.3%, herpes simplex 1,2 (Ag, IF) 4.7%, gonorrhea (Ag, ELISA) 2.8%. c) Patient clinical studies. The clinical interrelationship between different STD and HIV infection has been studied; clinical differences are described between patients with condylomata or syphilis depending on HIV serostatus. Implications of the interrelationship between different STD's and HIV infection for the prevention and control of these diseases are discussed.
Physicians and the Pharmaceutical Industry: Is a Gift Ever Just a Gift? (2000)

Physicians have frequent contact with pharmaceutical firms and their sales personnel, who spend substantial sums in the form of gifts, free meals and travel, and sponsored educational programs. The implications of these practices and attitudes about the physician-industry relationship were examined by conducting a MEDLINE search for English-language articles published since 1994. An internet database also was searched, and five key informants were interviewed. Of 538 articles providing relevant data, 29 that were published in peer-reviewed journals were analyzed. Sixteen of them dealt with the extent of physician-industry interactions. The same number of articles identified physician attitudes, and 16 of the articles examined the effect of the interaction on the practitioners. A majority of studies used a self-reporting cross-sectional survey design. Response rates ranged from 30 percent to 100 percent. Interactions began as early as medical school. Most physicians met with pharmaceutical company representatives approximately four times a month starting in the residency years. As physicians left residency and began practicing, industry-sponsored meals and samples were replaced to some extent by honoraria, conference travel, and research funding. Both residents and physicians believe that the representatives provide accurate drug information, but they also reported believing that they place product promotion ahead of patient welfare and are likely to use unethical practices. Most physicians deny that gifts might influence their behavior. They see drug samples, continuing medical education, and conference travel funding as having more influence than promotional materials. Interactions with pharmaceutical representatives seemed to influence the prescribing practices of residents and physicians. Those accepting gifts professed to believe that the representatives have no effect on their prescribing behavior. Samples, in general, were associated with positive attitudes toward industry. Accepting funds to attend a symposium correlated with increased requests for the sponsor’s drug. Physicians participating in sponsored continuing medical education programs changed their prescribing practices in favor of the sponsor’s drug. Accepting an honorarium to present information on a new treatment and receiving research support correlated with requests for the sponsor’s drug but also for any drug. This survey suggests that interactions between resident and postresident physicians and the pharmaceutical industry do influence prescribing behavior. These issues should be addressed at both the educational and policy-making levels. JAMA 2000;283:373–380
<title>Nanoscale modification of DLC film surfaces with femtosecond laser pulses</title> (2004)

Surface modification of thin diamond-like carbon (DLC) films deposited on stainless steel has been studied by irradiating linearly and circularly polarized femtosecond (fs), 800- and 267-nm Ti:sapphire laser pulses at laser fluence around the ablation threshold. The morphology of the DLC surfaces was observed and characterized with a field-emission scanning electron microscope and a scanning probe microscope. The linearly polarized light produced arrays of fine slender granular structure on the ablated surface, while the circularly polarized light formed a fine dot-like periodic structure. The mean spacing of these fine structures was 1/10 - 1/5 of the laser wavelength used. With an increase in the laser fluence, the size of structure was observed to increase, while the surface roughness decreased. We have analyzed the modified DLC surfaces by observing Raman spectra and found that the nanoscale modification of the DLC films is accompanied with a structural change into glassy carbon. This structural change depended on the fs laser fluence and little on the laser polarization and wavelength.
Pharmacokinetics of Interferon in Blood, Cerebrospinal Fluid, and Brain after Administration of Modified Polyriboinosinic-Polyribocytidylic Acid and Amphotericin B (1982)

Polyriboinosinic-polyribocytidylic acid (with a sedimentation coefficient of 9S) prepared in a complex with poly-L-lysine and carboxymethylcellulose (poly ICLC) was given intravenously to rabbits in a priming technique with two infusions 4 hr apart; and with low-dose amphotericin B (AmB, 0.5 mg) to trace the transfer of interferon (IFN) in serum to cerebrospinal fluid (CSF) and brain. Peak titers of IFN in serum were at 4 hr, but peak titers of IFN in CSF and brain occurred at 8 hr. At 4 hr, CSF IFN was 0.6%-2.7% of serum titers but at 8 hr had increased to 11.7%-51.1%. IFN was uniformly distributed to all areas of the brain and spinal cord at 8 hr. Titers of IFN in the brain were independent of CSF values, and varied from 5.9%-44.1% of the serum titers. When two injections of poly ICLC were given 4 hr apart, IFN titers in serum, CSF, and brain were significantly raised. Poly ICLC together with AmB increased serum IFN.
Effects of a high-voltage electrical impulse and an anticancer drug on in vivo growing tumors. (1987)

Application of a high-voltage electrical impulse (5 kV/cm, 2 msec) after bleomycin administration resulted in a significant size decrease of subcutaneously inoculated AH-109A hepatocellular carcinoma in Donryu rats. The tumor size decreased to an average of 17% of the initial mass 4 days after the treatment. Neither the high-voltage electrical impulse nor bleomycin administration alone showed an inhibitory effect on the tumor growth. It was concluded that the concomitant use of a high-voltage electrical impulse and an anticancer drug has the potential to be applicable for cancer treatment.