gebhart/patrepeval huggingface dataset:
Development of 1480 nm Photothermal High-Speed Real-Time Polymerase Chain Reaction System for Rapid Nucleotide Recognition (2008)

The polymerase chain reaction (PCR) is a key technology used in genome-based biological analysis; however, requests have been made to shorten the operation time for emergency tests such as medical diagnostics, and countermeasures against bioterrorism. We have developed a novel rapid real-time PCR system using the direct absorption of an IR laser beam by water droplets as the heating device. The advantage of this system is that only the target water droplet was heated photothermally without transmitting any heat to the surroundings, which is important for the production of fast thermal cycle intervals. The system consists of a fluorescent microscope, an oil chamber with a set of water droplets lined up at the bottom, a 1480 nm IR laser unit, which is absorbed by water and can be focused on the droplets on the stage of the microscope, and an image intensifier to quantify the PCR reaction within a water droplet by measuring the change of fluorescent intensity. Using the system, we examined the PCR procedure under the following conditions: initial heating to 95 °C, maintaining this temperature for 10 s, and the suggested here and in similar places throughout 50 cycles of 1 s at 95 °C for denaturation and 3 s at 60 °C for annealing/extension. The temperature increase and decrease between the two temperatures 95 and 60 °C, were within 1 and 0.8 s respectively, i.e., 32 K/s, which is 1.5 times faster than the conventional heat conduction-based system. Rapid PCR amplification was observed successfully by the rise change in the sigmoidal curvature of fluorescent intensity, and the procedure was accomplished within 3.5 min, including the initial heating and complete 50 PCR cycles. The results indicate that the direct absorption-based heating of water droplets photothermally could give us a faster temperature chnage than the conventional heat-conduction-based systems such as Peltier heating/cooling.
Retroviral Vector-Mediated Gene Transfer into Human Hematopoietic Progenitor Cells (1985)

The transfer of the human gene for hypoxanthine phosphoribosyltransferase (HPRT) into human bone marrow cells was accomplished by use of a retroviral vector. The cells were infected in vitro with a replication-incompetent murine retroviral vector that carried and expressed a mutant HPRT complementary DNA. The infected cells were superinfected with a helper virus and maintained in long-term culture. The production of progeny HPRT virus by the bone marrow cells was demonstrated with a colony formation assay on cultured HPRT-deficient, ouabain-resistant murine fibroblasts. Hematopoietic progenitor cells able to form colonies of granulocytes or macrophages (or both) in semisolid medium in the presence of colony stimulating factor were present in the nonadherent cell population. Colony forming units cloned in agar and subsequently cultured in liquid medium produced progeny HPRT virus, indicating infection of this class of hematopoietic progenitor cell.
Multiple tandemly repeated binding sites for cellular nuclear factor 1 that surround the major immediate-early promoters of simian and human cytomegalovirus (1987)

We show that the large DNA genomes of human and simian cytomegaloviruses (HCMV and SCMV, respectively) each contain multiple binding sites for purified cellular nuclear factor 1 (NF1) protein. Examination of the major immediate-early (IE) gene region in the HindIII H fragment of SCMV (Colburn) by filter binding assays showed that it competed 45-fold better than the single adenovirus type 2 binding site for NF1 protein and that it contained at least two distinct binding loci. Direct DNase I footprinting analyses of the 5' upstream locus detected at least 20 adjacent NF1-binding sites located between positions -600 and -1300 relative to the IE94 mRNA start site. DNA sequence analysis of the region revealed a conserved consensus NF1 recognition element (T)TGG(C/A)N5GCCAA embedded within each of 23 highly diverged 30-base-pair tandem repeats, together with a second downstream cluster of five consensus NF1-binding sites between positions +470 and +570 in the large first intron. Two separate NF1-binding loci were also found in the equivalent IE68 gene of HCMV(Towne) DNA, but in this case the DNA sequence and competition filter binding experiments indicated a maximum of only four to five consensus binding sites encompassing the promoter-enhancer region. In transient expression assays, neither the isolated upstream IE94 tandem repeats nor a synthetic single-copy consensus NF1-binding site acted as transcriptional cis activators or enhancers when placed adjacent to the simian virus 40 minimal early region promoter. We conclude that the large and complex 5' upstream promoter-regulatory region for the SCMV IE94 gene comprises two distinct domains. The previously described four sets of 13- to 18-base-pair interspersed repeat elements between -55 and -580 provide most of the high basal transcriptional strength, whereas the arrangement of further upstream tandemly repeated NF1-binding sites may contribute significantly to the expanded biological host range for expression of SCMV IE94 compared with HCMV IE68.
Increased susceptibility of cytoplasmic over nuclear polyglutamine aggregates to autophagic degradation (2005)

CNS neurons are endowed with the ability to recover from cytotoxic insults associated with the accumulation of proteinaceous aggregates in mouse models of polyglutamine disease, but the cellular mechanism underlying this phenomenon is unknown. Here, we show that autophagy is essential for the elimination of aggregated forms of mutant huntingtin and ataxin-1 from the cytoplasmic but not nuclear compartments. Human orthologs of yeast autophagy genes, molecular determinants of autophagic vacuole formation, are recruited to cytoplasmic but not nuclear inclusion bodies in vitro and in vivo. These data indicate that autophagy is a critical component of the cellular clearance of toxic protein aggregates and may help to explain why protein aggregates are more toxic when directed to the nucleus.
Differential In Vivo Persistence of Two Subsets of Memory Phenotype CD8 T Cells Defined by CD44 and CD122 Expression Levels (2002)

The existence of distinct subsets of memory CD8 T cells with different characteristics is now well established. In this work, we describe two subsets of mouse CD8 T cells with memory characteristics that coexist in primed thymectomized TCR-transgenic F5 mice and that share some properties with the human central and effector memory cells. The first subset corresponds to CD8 T cells generated following nucleoprotein 68 peptide priming which are CD44(int)CD122(-)nucleoprotein 68/H-2D(b) tetramer(+) and express high levels of CCR7 mRNA. In contrast, CD8 T cells in the second subset are CD44(high)CD122(+), are heterogeneous in terms of Ag specificity, and express low levels of CCR7 mRNA. We have studied the functional characteristics and the persistence of these two subsets in thymectomized mice. CD44(int) CD8 T cells persist like naive cells; i.e., they are slowly lost with time. However, surviving cells maintain their phenotype and memory characteristics for the entire life span of the animal. In contrast, CD44(high) CD8 T cells are persistent and accumulate in thymectomized but not euthymic mice. This is correlated with an increased in vivo proliferative and survival potential of these cells. These results show that acquisition of enhanced functional characteristics and long-term persistence by memory T cells are independent. This may have important consequences for the design of specific vaccine.
Serum-, TPA-, and Ras-induced expression from Ap-1/Ets-driven promoters requires Raf-1 kinase. (1992)

Raf-1 serine-threonine protein kinase has the hallmarks of a critical switch that connects growth factor receptor activation at the cell membrane with transcriptional events in the nucleus. We show by use of Raf-1 dominant-negative mutants that Raf-1 is required for serum-, TPA-, and Ras-induced expression from the oncogene-responsive element in the polyomavirus enhancer. The minimal region of Raf-1 that displays this dominant-negative phenotype (Raf-C4) contains a cysteine finger motif. Raf-C4 appears to function by titrating out a Raf-1-activating factor that is induced by Ras following serum or TPA treatment of NIH-3T3 cells. In addition, we show that Raf-1 and Ras cooperate in trans-activation through the oncogene-responsive element and that the cysteine-rich region is necessary for this effect.
Apolipoprotein C-III: understanding an emerging cardiovascular risk factor (2008)

The concurrence of visceral obesity, insulin resistance and dyslipidaemia comprises the concept of the metabolic syndrome. The metabolic syndrome is an escalating problem in developed and developing societies that tracks with the obesity epidemic. Dyslipidaemia in the metabolic syndrome is potently atherogenic and, hence, is a major risk factor for CVD (cardiovascular disease) in these subjects. It is globally characterized by hypertriglyceridaemia, near normal LDL (low-density lipoprotein)-cholesterol and low plasma HDL (high-density lipoprotein)-cholesterol. ApoC-III (apolipoprotein C-III), an important regulator of lipoprotein metabolism, is strongly associated with hypertriglyceridaemia and the progression of CVD. ApoC-III impairs the lipolysis of TRLs [triacylglycerol (triglyceride)-rich lipoproteins] by inhibiting lipoprotein lipase and the hepatic uptake of TRLs by remnant receptors. In the circulation, apoC-III is associated with TRLs and HDL, and freely exchanges among these lipoprotein particle systems. However, to fully understand the complex physiology and pathophysiology requires the application of tracer methodology and mathematical modelling. In addition, experimental evidence shows that apoC-III may also have a direct role in atherosclerosis. In the metabolic syndrome, increased apoC-III concentration, resulting from hepatic overproduction of VLDL (very-LDL) apoC-III, is strongly associated with delayed catabolism of triacylglycerols and TRLs. Several therapies pertinent to the metabolic syndrome, such as PPAR (peroxisome-proliferator-activated receptor) agonists and statins, can regulate apoC-III transport in the metabolic syndrome. Regulating apoC-III metabolism may be an important new therapeutic approach to managing dyslipidaemia and CVD risk in the metabolic syndrome.
Regression analysis of extended vectors to obtain coefficients for use in probabilistic information retrieval systems (1987)

Previous work by Fox has extended the vector space model of information retrieval and its implementation in the SMART system so different types of information about documents can be separately handled as multiple subvectors, each for a different concept type. We hypothesized that relevance of a document could be best predicted if proper coefficients are obtained to reflect the importance of the query-document similarity for each subvector when computing an overall similarity value. Two different research collections, CACM and ISI, each split into halves, were used to generate data for the regression studies to obtain coefficients. Most of the variance in relevance could be accounted for by only four of the subvectors (authors, Computing Review descriptors, links, and terms) for the CACM1 collection. In the ISI1 collection, two of the vectors (terms and cocitations) accounted for most of the variance. Log transformed data and samples of the records gave the best RSQ's; .6654 was the highest RSQ (binary relevance). The regression runs provided coefficients which were used in subsequent feedback runs in SMART. Having ranked relevance did not improve the regression model over binary relevance. The coefficients in the feedback runs with SMART proved to be of limited usefulness since improvements in precision were in the 1-5% range. Although log data and samples of the records gave the best RSQ's, coefficients from log values of all data improved precision the most. The findings of this study support previous work of Fox, that additional information improves retrieval. Regression coefficients improved precision slightly when used as subvector weights. Log transforming the data values for the concept types modestly helped both the regression analyses and the retrieval in SMART.
Bacteremia in Patients on Chronic Hemodialysis (1993)

A prospective epidemiologic survey of bacterial infections in chronic hemodialysis patients was conducted from September 1, 1989 to February 28, 1990 in 27 dialysis units. Of the 1,455 patients enrolled in the study, 55 presented 63 episodes of bacteremia (incidence of 0.7 bacteremia per 100 patient-months). The portal of entry of sepsis was the vascular access in 50.8% of the episodes. The causative microorganisms were most often gram-positive cocci (69.8%). 23% of the teremic patients had a serum ferritin > 1,000 micrograms/l versus 7% of the nonbacteremic infected patients (p = 0.005). 39.7% of the patients had undergone a surgical operation during the month preceding the bacteremia. Eight patients had a recurrence during the study period and 8 had a metastatic localization: spondylodiscitis 2, septic pulmonary embolus 2, endocarditis 1, arthritis 1, liver abscess 1 and endophthalmia 1. 66% of the episodes required a hospitalization that lasted an average of 20 days. Mortality rate was 6.3%. This prospective study showed a trend towards a reduction in incidence and mortality of bacteremia in patients on chronic hemodialysis.
A formal approach to recovery by compensating transactions (1990)

Compensating transactions are intended to handle situ-ations where it is required to undo either committed or uncommitted transactions that affect other trans-actions, without resorting to cascading aborts. This stands in sharp contrast to the standard approach to transaction recovery where cascading aborts are avoided by requiring transactions to read only committed data, and where committed transactions are treated as per-manent and irreversible. We argue that this standard approach to recovery is not suitable for a wide range of advanced database applications, in particular those applications that incorporate long-duration or nested transactions. We show how compensating transactions can be effectively used to handle these types of appli-cations. We present a model that allows the definition of a variety of types of correct compensation. These types of compensation range from traditional undo, at one extreme, to application-dependent, special-purpose compensating transactions, at the other extreme, 1
Fluorine‐Directed Glycosylation (2010)

Everything's under control: A stabilizing fluorine electrostatic interaction has been exploited to control oxonium ion conformation in 2-fluoropyranose derivatives (see scheme). When matched with the inductive nature of the protecting groups, the glycosyl donors were found to be highly selective (2-FGluc/benzyl → β; 2-FManno/pivaloyl → α) leading to fluoro-glycostructures with excellent control over the anomeric configuration. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
DARWIN: A program for docking flexible molecules (2000)

A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM to make the energy calculations. A second important feature is its parallel interface, which allows simultaneous use of multiple stand-alone copies of CHARMM to rapidly evaluate large numbers of potential solutions. This permits an "accuracy first" approach to docking, which avoids many of the common assumptions and shortcuts often made to reduce computation time. The method was applied to three protein-carbohydrate complexes: the crystallographically determined structures of Concanavalin A and Fab Se155-4; and a model structure for Fab ME36.1. Conformations close to the crystal structures were obtained with this approach, but some "false positive" solutions were also selected. Many of these could be eliminated by introducing different methods for simulating solvent effects. An effective screening method for docking a database of compounds to a single target enzyme using DARWIN is also presented.
Chemotherapy for advanced non-small-cell lung cancer: how much benefit is enough? (1993)

Chemotherapy is effective in the treatment of advanced NSCLC, but its impact on the length of survival is limited. Future RCTs should still include an untreated control group and should measure quality of life in addition to survival.
Modulation of anti-pathogenic activity in canine-derived Lactobacillus species by carbohydrate growth substrate (2004)

Knowledge of the effect that the carbon source has on the production of antimicrobial compounds by gut-associated lactobacilli allows the rational design of prebiotic/probiotic combinations to combat gastrointestinal pathogens.
The Relationships Between Age, Sex, and the Incidence of Dementia and Alzheimer Disease (1998)

Prevalence studies on dementia and Alzheimer disease (AD) have reported a positive association with age. However, the trend of the association in the oldest-old categories has been the subject of discussion. The relationship between sex and AD has been inconsistent with these studies. Prevalence rates are influenced by the survival and disease incidence. Incidence rates provide a better measure of disease risk.English-language articles identified through a MEDLINE search on "incidence dementia" and "incidence Alzheimer's disease" were examined and references from identified articles were reviewed. Population-based studies using personal interviews, standard clinical diagnosis criteria (DSM-III for dementia, National Institute of Neurological and Communicative Disorders and Stroke-Alzheimer's Disease and Related Disorder Association for AD) and reporting age-specific incidence rates were included in the meta-analysis. Data from the selected studies were extracted and verified. Mixed-effect models were used in the meta-analysis to accommodate the heterogeneity of the studies.Incident dementia and AD are associated with a significant quadratic age effect indicating that the increase in incidence rates slows down with the increase in age, although there is no sign of a decline in the incidence rates themselves. The odds ratios for women to develop incidence of dementia and AD relative to men are 1.18 (95% confidence interval, 0.95-1.46) and 1.56 (95% confidence interval, 1.16-2.10), respectively.The acceleration of incidence rates for AD and dementia slows down with the increase in age, although we find no evidence of a rate decline. Women are at higher risk of developing AD than men.
Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA (2018)

Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
Increased content of Type V Collagen in desmoplasia of human breast carcinoma. (1982)

Type V (AB) collagen is present in increased amounts in desmoplasia of human breast carcinoma. Type V collagen occurs as linear deposits in the interstitium (desmoplastic stroma surrounding the tumor), as demonstrated by immunofluorescence and immunoperoxidase techniques utilizing antibodies to Type V collagen. In contrast, no demonstratable Type V occurs in the interstitium of fibroadenoma, fibrocystic disease, or normal breast tissue. As identified and quantitated by pepsin extraction, salt fractionation, and polyacrylamide gel electrophoresis, Type V constitutes 10% +/- 5% of all interstitial collagens (Types I, III, and V) in desmoplasia, compared with 1.5% +/- 0.5% in fibroadenoma and less than 0.1% in all types of fibrocystic disease, including sclerosing adenosis, and less than 0.1% in normal breast tissue. For infiltrating ductal carcinoma, Type V collagen is not secreted by the invasive carcinoma cells, nor is it present in an extracellular basement membrane location. By immunohistologic methods, Type V collagen can be seen exclusively in the desmoplastic stroma. The authors propose that desmoplasia of human breast carcinoma manifests a characteristic collagen profile and that the increased Type V may be produced by specialized cells such as myofibroblasts in the interstitium, which are recruited in response to invasive carcinoma.
Energy Metabolic Profile of Mice after Chronic Activation of Central NPY Y1, Y2, or Y5 Receptors** (2005)

Central activation of both Y1 and Y5 receptors increases RQ and adiposity, whereas only Y5 receptor activation reduces energy expended per energy ingested. Selective activation of Y2 autoreceptors leads to hypophagia and transient weight loss, with little effect on total EE. Our study indicates that all three NPY receptor subtypes may play a role in regulating energy homeostasis in mice.
The Cross-Search Algorithm for Motion Estimation (1990)

Abstract-A fast block matching algorithm for motion estimation is presented. It is based on a logarithmic step where in each search step only 4 locations are tested. For a motion displacement of w pels/frame, this technique requires 5 + 4 1og2w computations to locate the best match. Using sequences of CIF standard pictures, the interframe motion compensated prediction error with this technique is compared to the other fast methods. The computational complexity of this algorithm is also compared against those methods. I.
Agonistic Anti-CD137 Monoclonal Antibody Treatment Induces CD11b+Gr-1+Myeloid-derived Suppressor Cells (2010)

CD137 (4-1BB/tnfrsf9) has been shown to co-stimulate T cells. However, agonistic anti-CD137 monoclonal antibody (mAb) treatment can suppress CD4(+) T cells, ameliorating autoimmune diseases, whereas it induces activation of CD8(+) T cells, resulting in diverse therapeutic activity in cancer, viral infection. To investigate the CD137-mediated T cell suppression mechanism, we examined whether anti-CD137 mAb treatment could affect CD11b(+)Gr-1(+) myeloid-derived suppressor cells (MDSCs). Intriguingly, anti-CD137 mAb injection significantly increased CD11b(+)Gr-1(+) cells, peaking at days 5 to 10 and continuing for at least 25 days. Furthermore, this cell population could suppress both CD8(+) T cells and CD4(+) T cells. Thus, this study demonstrated that, for the first time, anti-CD137 mAb treatment could induce CD11b(+)Gr-1(+) MDSCs under normal conditions, suggesting a possible relationship between myeloid cell induction and CD137-mediated immune suppression.