gebhart/patrepeval huggingface dataset:
Heterozygote and mutation detection by direct automated fluorescent DNA sequencing using a mutant Taq DNA polymerase. (1996)

We describe a method for direct cycle sequencing of PCR fragments amplified from genomic DNA or cDNA. DNA sequencing template is amplified using PCR and oligonucleotide primers flanking the region of interest. The amplified fragment is directly cycle sequenced using fluorescent sequencing primers, Sanger dideoxy sequencing chemistry and an enzyme mixture of a mutant Taq DNA polymerase and thermostable pyrophosphatase. The sequence ladders produced are analyzed on a real-time, automated four-color sequencing system. The method produces sequence ladders from unpurified PCR fragments of sufficiently high quality such that heterozygotes can be reproducibly detected and identified by software that recognizes signal-strength patterns indicative of mixed-base positions.
Bent Structure and Dynamic Stereochemistry of Chiral Acridinium Cations (2003)

Chiral acridinium cations, easily prepared by reaction of enantiopure primary amines and tris(2,6-dimethoxy)trityl cation, display restricted rotations around the C(sp(3))-N(sp(2)) bond. A bending of the aromatic backbone and "out-of-plane" displacements of C(9) and N(10) atoms are enforced if bulky amines are introduced.
Evaluation of Protein A and a Commercial Bacterin as Vaccines Against Staphylococcus aureus Mastitis by Experimental Challenge (1985)

Protein A and a commercial staphylococcal bacterin were evaluated by experimental challenge with Staphylococcus aureus (ATCC 29740). Thirty cows in first lactation were in three treatment groups, protein A, bacterin, and nonvaccinated controls. Studies were through three lactations and included bacteriological and cytological analyses of quarter milk samples. Rate of intramammary infection with Staphylococcus aureus was similar for vaccinated and unvaccinated cows. Rates of spontaneous cure within each lactation were significantly higher for vaccinated cows. For all three lactations, spontaneous cure rates were 83, 73, and 47% for protein A, bacterin, and control cows. Somatic cell counts were significantly lower for vaccinated cows for quarters infected with Staphylococcus aureus, but no differences were demonstrated for milk production by lactation. Incidence of clinical mastitis was higher in unvaccinated cows, but too few developed for a valid comparison.
The genome of herpes simplex virus: structure, replication and evolution (1987)

The objectives of this paper are to discuss the structure and genetic content of the genome of herpes simplex virus type 1 (HSV-1), the nature of virus DNA replicative processes, and aspects of the evolution of the virus DNA, in particular those bearing on DNA replication. We are in the late stages of determining the complete sequence of the DNA of HSV-1, which contains about 155,000 base pairs, and thus the treatment is primarily from a viewpoint of DNA sequence and organization. The genome possesses around 75 genes, generally densely arranged and without long range ordering. Introns are present in only a few genes. Protein coding sequences have been predicted, and the functions of the proteins are being pursued by various means, including use of existing genetic and biochemical data, computer based analyses, expression of isolated genes and use of oligopeptide antisera. Many proteins are known to be virion structural components, or to have regulatory roles, or to function in synthesis of virus DNA. Many, however, still lack an assigned function. Two classes of genetic entities necessary for virus DNA replication have been characterized: cis-acting sequences, which include origins of replication and packaging signals, and genes encoding proteins involved in replication. Aside from enzymes of nucleotide metabolism, the latter include DNA polymerase, DNA binding proteins, and five species detected by genetic assays, but of presently unknown functions. Complete genome sequences are now known for the related alphaherpesvirus varicella-zoster virus and for the very distinct gammaherpesvirus Epstein-Barr virus. Comparisons between the three sequences show various homologies, and also several types of divergence and rearrangement, and so allow models to be proposed for possible events in the evolution of present day herpesvirus genomes. Another aspect of genome evolution is seen in the wide range of overall base compositions found in present day herpesvirus DNAs. Finally, certain herpesvirus genes are homologous to non-herpesvirus genes, giving a glimpse of more remote relationships.
Cancer antigen 125, human epididymis 4, kallikrein 6, osteopontin and soluble mesothelin-related peptide immunocomplexed with immunoglobulin M in epithelial ovarian cancer diagnosis (2013)

This study confirms the diagnostic role of CA125, HE4, KLK6, OPN and SMRP, and for the first time showed that CA125, HE4, KLK6, OPN and SMRP immunocomplexed with IgM are not a potential tool for EOC diagnosis.
Optical properties of normal and diseased human breast tissues in the visible and near infrared (1990)

The optical absorption and scattering coefficients have been determined for specimens of normal and diseased human breast tissues over the range of wavelengths from 500 to 1100 nm. Total attenuation coefficients were measured for thin slices of tissue cut on a microtome. The diffuse reflectance and transmittance were measured for 1.0 mm thick samples of these tissues, using standard integrating sphere techniques. Monte Carlo simulations were performed to derive the scattering and absorption coefficients, as well as the mean cosine of the scattering angle. The results indicate that scatter exceeds absorption by at least two orders of magnitude. Absorption is most significant at wavelengths below 600 nm. The scattering coefficients lie in the range 30-90 mm-1 at 500 nm, and fall smoothly with increasing wavelength to between 10 and 50 mm-1 at 1100 nm. The scattering coefficient for adipose tissue differs, in that it is invariant with wavelength over this spectral range. For all tissues examined, the scattered light is highly forward peaked, with the mean cosine of the scattering angle in the range 0.945-0.985. Systematic differences between the optical properties of some tissue types are demonstrated.
Identification of glycoprotein IV (CD36) as a primary receptor for platelet-collagen adhesion (1989)

The role of glycoprotein IV (GPIV) in platelet activation processes has been examined by several different approaches: (i) Fab fragments of a monospecific polyclonal antibody to purified platelet GPIV (approximately 20 micrograms/ml) completely inhibited platelet shape change, aggregation, and secretion induced by collagen. Aggregation and secretion by ADP (but not shape change) and by epinephrine were also inhibited, but there was no effect on platelet activation induced by thrombin, arachidonate, or ionophore A23187. (ii) Purified GPIV was able to compete completely with membrane-bound GPIV to inhibit platelet activation induced by collagen, including shape change, but not in activation induced by any of the other platelet agonists. 50% inhibition of collagen-induced activation and secretion were obtained at GPIV concentrations of approximately 10 nM (1 micrograms/ml). (iii) Purified GPIV bound rapidly and reversibly to collagen Type I fibrils, and binding was not inhibited by adhesive proteins such as denatured collagen, fibronectin, fibrinogen, or von Willebrand factor. The direct binding of purified GPIV to collagen Type I fibrils fit best to a single site model with Kd 0.34 +/- 0.10 nM. (iv) Using a microtiter assay, platelet adhesion to collagen was shown to be inhibited by Fab fragments of monospecific polyclonal anti-GPIV antibodies, but adhesion to other adhesive proteins was unaffected. (v) When anti-GPIV was added at various times during adhesion the time dependence of inhibition was seen to be biphasic. Anti-GP antibody was able to reverse adhesion that occurred within the first 5-8 min and to inhibit adhesion occurring thereafter. These results demonstrate that GPIV mediates the early stages of platelet recognition by and attachment to collagen but that there may be a second GPIV-independent mechanism that mediates the subsequent anchorage of these adherent platelets.
[The prevalence of Th17 cells in patients with acute myeloid leukemia]. (2010)

Th17 cells might be negatively correlated with the AML development. The overexpression of TGF-β1 in AML patients might suppress the differentiation of Th17 cells.
Purification and characterization of an inducible L‐lysine: 2‐oxoglutarate 6‐aminotransferase from Candida utilis (1992)

L-Lysine:2-oxoglutarate 6-aminotransferase (EC 2.1.6.36) was purified 202-fold from the yeast Candida utilis. The subunit Mr estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis was 40 kDa. The Mr of the native enzyme was estimated to be 83 kDa by gel filtration, suggesting a dimeric structure. The enzyme exhibits absorption maxima at 280, 340 and 420 nm, and binds 2 mol pyridoxal-5-phosphate/mol of the native enzyme. The aminotransferase has a maximum activity at pH 8.5 and at 4 degrees C. 2-Oxoglutarate is the best amino acceptor with L-lysine as amino donor. Lower activity is observed with oxaloacetate (38%), pyruvate (19%) and 2-oxoadipate (7%) as acceptor or with L-thialysine (13%) as donor. The Km values are 2.5 mM for L-lysine, 3.8 mM for 2-oxoglutarate and 0.015 mM for pyridoxal-5-phosphate. The enzyme activity is induced in cells grown in the presence of L-lysine.
<i>neu</i>(c-erbB-2/HER2) and the Epidermal Growth Factor Receptor (EGFR) in Breast Cancer (1993)

One hundred and eighty thousand new cases of invasive breast cancer were diagnosed in 1992 within the United States. This disease affects approximately 1 out of 8 women in the US. Chemotherapy and/or hormonal therapy have shown some improved disease-free and/or overall survival rates. Unfortunately, this type of therapy is not directed specifically to the malignant cells, and systemic toxicities are observed. In order to develop site-specific treatment, the biology of the disease must be understood such that certain genes or their products which are involved in the pathogenesis of the disease can be targeted. Two structurally related tyrosine kinase growth factors, the epidermal growth factor receptor (EGFR) and c-erbB-2 (neu) have been identified in human breast cancer tissue and, in many instances, may function as oncogenes. The clinical data related to these two growth factor receptors as prognostic factors for the disease have been critically evaluated. Several problems with the critical studies were identified, and solutions were proposed to clarify the conflicting results reported in the studies which have attempted to examine whether c-erbB-2 (neu), in particular, is a prognostic indicator for breast cancer. In addition, data related to the structure of, ligands for and interaction between the proteins have been reviewed and presented with respect to their role in breast cancer development. A more thorough understanding of the genetic changes which contribute to the development of breast cancer will lead to more specific and less toxic treatment for this disease.
ECG beat detection using filter banks (1999)

We have designed a multirate digital signal processing algorithm to detect heart beats in the electrocardiogram (ECG). The algorithm incorporates a filter bank (FB) which decomposes the ECG into subbands with uniform frequency bandwidths. The FB-based algorithm enables independent time and frequency analysis to be performed on a signal. Features computed from a set of the subbands and a heuristic detection strategy are used to fuse decisions from multiple one-channel beat detection algorithms. The overall beat detection algorithm has a sensitivity of 99.59% and a positive predictivity of 99.56% against the MIT/BIH database. Furthermore this is a real-time algorithm since its beat detection latency is minimal. The FB-based beat detection algorithm also inherently lends itself to a computationally efficient structure since the detection logic operates at the subband rate. The FB-based structure is potentially useful for performing multiple ECG processing tasks using one set of preprocessing filters.
Enhancement of stimulated Raman scattering of acetone and the generation of three-color laser by using fluorescence dye RB (2005)

The enhancement of stimulated Raman scattering (SRS) of acetone (C3H6O) and the generation of three-color lasers in lasing dye rhodamine B (RB) were reported. The first-order Stokes wave (629.9 nm) of SRS of C3H6O was amplified by 2.83 times than that of pure C3H6O. At the same time, a dye laser of RB at the wavelength from 575 to 598 nm can be generated in a suitable concentration of RB between 3*10^(-5) and 2*10^(-4) mol/L. Thus the green pump laser, yellow dye laser, and red Stokes wave concurred.
A single-molecule barcoding system using nanoslits for DNA analysis (2007)

Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.
1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid. A novel cyclic amino acid from halophilic phototrophic bacteria of the genus Ectothiorhodospira (1985)

A novel cyclic amino acid was detected in and subsequently isolated from extremely halophilic species of the bacterial genus Ectothiorhodospira. The structure of this new compound was elucidated by a combination of nuclear magnetic resonance (NMR) techniques and mass spectrometry. 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid is only accumulated within the cytoplasm under certain growth conditions and seems to serve an osmoregulatory function. There is no previous reference to this molecule in the chemical literature and we, therefore, propose to use the trivial name 'ectoine', due to its discovery in members of the bacterial genus Ectothiorhodospira. (formula: see text).
Tryptophan deprivation sensitizes activated T cells to apoptosis prior to cell division (2002)

Cells expressing indoleamine 2,3-dioxygenase (IDO), an enzyme which catabolizes tryptophan, prevent T-cell proliferation in vitro, suppress maternal antifetal immunity during pregnancy and inhibit T-cell-mediated responses to tumour-associated antigens. To examine the mechanistic basis of these phenomena we activated naïve murine T cells in chemically defined tryptophan-free media. Under these conditions T cells expressed CD25 and CD69 and progressed through the first 12 hr of G0/G1 phase but did not express CD71, cyclin D3, cdk4, begin DNA synthesis, or differentiate into cytotoxic effector cells. In addition, activated T cells with their growth arrested by tryptophan deprivation exhibited enhanced tendencies to die via apoptosis when exposed to anti-Fas antibodies. Apoptosis was inhibited by caspase inhibitor and was not observed when T cells originated from Fas-deficient mice. These findings suggest that T cells activated in the absence of free tryptophan entered the cell cycle but cell cycle progression ceased in mid-G1 phase and T cells became susceptible to death via apoptosis, in part though Fas-mediated signalling. Thus, mature antigen-presenting cells expressing IDO and Fas-ligand may induce antigen-specific T-cell tolerance by blocking T-cell cycle progression and by rapid induction of T-cell activation induced cell death in local tissue microenvironments.
Path delay fault simulation algorithms for sequential circuits (2003)

The authors present a differential algorithm for concurrent simulation of path delay faults in sequential circuits. The simulator determines all three conditions, namely, initialization, signal transition propagation through the path, and fault effect observation at a primary output, by analyzing vector-pairs and the hazard states occurring between vectors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional and Topological Analysis of Yeast Acyl-CoA:Diacylglycerol Acyltransferase 2, an Endoplasmic Reticulum Enzyme Essential for Triacylglycerol Biosynthesis (2011)

Acyl-CoA:diacylglycerol acyltransferase (EC 2.3.1.20) is a membrane protein present mainly in the endoplasmic reticulum. It catalyzes the final and committed step in the biosynthesis of triacylglycerol, which is the principal repository of fatty acids for energy utilization and membrane formation. Two distinct family members of acyl-CoA:diacylglycerol acyltransferase, known as DGAT1 and DGAT2, have been characterized in different organisms, including mammals, fungi, and plants. In this study, we characterized the functional role and topological orientation of signature motifs in yeast (Saccharomyces cerevisiae) DGAT2 using mutagenesis in conjunction with chemical modification. Our data provide evidence that both the N and C termini are oriented toward the cytosol and have different catalytic roles. A highly conserved motif, (129)YFP(131), and a hydrophilic segment exclusive to yeast DGAT2 reside in a long endoplasmic reticulum luminal loop following the first transmembrane domain and play an essential role in enzyme catalysis. In addition, the strongly conserved His(195) within the motif HPHG, which may play a role in the active site of DGAT2, is likely embedded in the membrane. These results indicate some similarities to the topology model of murine DGAT2 but also reveal striking differences suggesting that the topological organization of DGAT2 is not ubiquitously conserved.
Clinical benefit of a precision medicine based approach for guiding treatment of refractory cancers (2016)

Patients with refractory metastatic cancer who receive genomically guided therapy have improved PFS ratios and longer median PFS compared to patients who do not receive genomically guided therapy.
A standard burn model using rats (1999)

Experimental burn models are always needed, being essential for burn research. In the present study, we describe a standard Fischer F-344 rat burn model, in which burns are produced with a heated brass bar. The animals were anesthetized with ketamine (90 mg/kg). After the burns, they were resuscitated with saline. Burns ranging from 26% to 30% of total body surface area resulted in a 62.5 % mortality rate after 25 days. This model is an additional option for those interested in burn research.
Analysis of p53 antibodies in patients with various cancers define B-cell epitopes of human p53: distribution on primary structure and exposure on protein surface. (1993)

p53 antibodies have been found in sera of patients with breast and lung carcinomas and in children with B-lymphomas. We report here the presence of p53 antibodies in sera of patients with 11 different types of cancer. The frequency of seropositives for p53 varied among the different types of cancer, but a correlation with the frequency of p53 gene alteration was established. Using a powerful peptide enzyme-linked immunosorbent assay, we demonstrated that the immune response of patients with p53 antibodies was restricted to a small subset of peptides localized in the amino and carboxy termini of p53, whatever the type of cancer. Given the similarities of the patterns of immune responses in patients with p53 antibodies and animals hyperimmunized with human p53, we propose that the p53 humoral response is the result of a self-immunization process which is itself the consequence of p53 protein accumulation in tumor cells.
NDRG2 expression and mutation in human liver and pancreatic cancers (2004)

NDRG2 gene might express differently between normal tissues and cancer tissues, and might play an important role in the development of pancreatic cancer and liver cancer. Low expression of NDRG2 might be unrelated to the mutation of coding region of NDRG2.
Design of peptidomimetic .delta. opioid receptor antagonists using the message-address concept (1990)

Highly selective nonpeptide ligands with potent delta opioid receptor antagonist activity have been developed using the message-address concept. This approach envisaged the delta opioid receptor to contain two major recognition subsites; a message subsite which recognizes the pharmacophore, and an address subsite that is unique for the delta receptor type and confers selectivity. The message and address components of the delta-selective enkephalins were postulated to be Tyr1 and Phe4, respectively, with Gly2-Gly3 functioning as a spacer. The message component of the target compounds in this study was derived from naltrexone and related structures. An indole system was fused to the C ring of naltrexone as a mimic of the address component. The benzene moiety of indole was viewed as the delta address component, mimicking the phenyl group of Phe4, and the pyrrole portion was used as a rigid spacer. Members of the series (1-23) were evaluated for opioid antagonist activity on the guinea pig ileum (GPI) and mouse vas deferens (MVD) preparations. Naltrindole (NTI, 1) was the most potent member of the series, with Ke values of approximately 0.1 nM at delta receptors. The antagonism by NTI was approximately 220- and 350-fold greater at delta than at mu and kappa opioid receptors. The binding of NTI and selected members of the series to guinea pig brain membranes was qualitatively consistent with their pharmacologic antagonist activity profiles in the MVD and GPI, but the Ki values were not in the same rank order. The selectivity of NTI arises mainly as a consequence of increased affinity at delta receptors. Thus, the Ke and Ki values of NTI were 1/530 and 1/90 that of the delta antagonist enkephalin analogue, ICI 174864. In contrast to NTI, ICI174864 derives its selectivity through greatly decreased recognition at mu and kappa receptors. The implications of the high affinity and selectivity of NTI as a consequence of its conformational rigidity are discussed. It is suggested that any attempt to model a receptor-bound conformation of an opioid peptide should consider affinity and potency at multiple receptor sites rather than selectivity alone.
Wasserstein GAN (2017)

We introduce a new algorithm named WGAN, an alternative to traditional GAN
training. In this new model, we show that we can improve the stability of
learning, get rid of problems like mode collapse, and provide meaningful
learning curves useful for debugging and hyperparameter searches. Furthermore,
we show that the corresponding optimization problem is sound, and provide
extensive theoretical work highlighting the deep connections to other distances
between distributions.