gebhart/patrepeval huggingface dataset:
Hierarchical Bayesian clustering for automatic text classification (1995)

Text classification, the grouping of texts into several clusters, has been used as a means of improving both the efficiency and the effective-Dess of text retrieval/categorization In this paper we propose a hierarchical clustering algorithm that constructs a Bet of clusters having the maximum Bayesian posterior probability, the probability that the given texts are classified into clusters We call the algorithm Hierarchical Bayesian Clustering (HBC) The advantages of HBC are experimentally verified from several viewpoints (1) HBC can re-construct the original clusters more accurately than do other non probabilistic algorithms (2) When
168. Antitumoral Efficacy of Multiple Injection of JX-594 (Thymidine Kinase (TK) Deleted, Human GM-CSF Inserted Wyeth Strain) Via Tail Vein in N-Nitrosomorpholine (NNM) Treated Rats (2005)

Carcinogen-induced hepatoma in immunocompetent animal models has shown a progress similar to the clinical course of human hepatoma. Ultrasonography (U/S) was used for consecutive evaluation of the phenotypic changes in Sprague-Dawley rats exposed for 8 weeks to NNM (175 mg/L). Three distinctive US findings were ascites, coarseness (defined as small and heterogeneously widespread increased echogenecity), and nodularity (defined as a >0.6-cm-sized echogenic region and clearly showing a tumor-like mass). The gross and histological findings indicated that coarseness and nodularity shown in US reflected fibrosis and hepatocellular carcinoma or cholangiofibroma, respectively. U/S detectable tumor appeared on week 22 post NNM treatment (5>mm in diameter), and rats bearing HCC detected by U/S was injected by JX-594 via tail vein (four times every two weeks, 108 pfu/300 ml for each injection). Based on the similarity of progression of liver disease in NNM treated rat model to that of human liver disease, the clinical benefit of antitumoral efficacy by intravenous injection of JX-594, if it is, could be evaluated. U/S (every two weeks) monitoring showed that significantly decrease of tumor size after tail vein injection of JX-594. Q-PCR results showed indirect evidence of differential viral replication capacity in normal, tumor, and cirrhotic nodules, suggesting oncolytic capacity of JX-594. Eventually, quantification of cirrhosis, ascites and survival benefit could be measured between natural and JX-594 injected ones in NNM treated rats.
Separate cis sequences and trans factors direct metabolic and developmental regulation of a potato tuber storage protein gene (1994)

The expression of genes encoding patatin, a major tuber protein, is highly tissue-specific but is also modulated by exogenous sucrose. The patterns of transcription observed in potato plants could be due to mechanisms conferring tuber-specificity or they could reflect the concentrations of sucrose found in different tissues. To distinguish between these possibilities, a detailed examination was made of the function of a region of the promoter previously implicated in conferring tissue-specific and sucrose-inducible expression. Internal deletions of this region revealed three separate functional domains regulating expression. The B repeat region acted as a positive activator of transcription in the tuber and was also responsible for a degree of sucrose-inducibility. The distal region of the A repeat repressed transcription in leaf and tuber tissue, while the proximal region of the A repeat was able to confer sucrose-responsiveness. Each of these regions specifically bound nuclear proteins which may be putative transcription factors involved in conferring these responses. The region found to confer sucrose-inducible expression was conserved among some other genes that are also regulated by exogenous sucrose.
Premature small for gestational age infants fed an exclusive human milk-based diet achieve catch-up growth without metabolic consequences at 2 years of age (2018)

SGA premature infants who received an exclusive HM-based diet exhibited greater catch-up growth without increased adiposity or elevated insulin resistance compared with AGA at 2 years of age. An exclusive HM-based diet may improve long-term body composition and metabolic outcomes of premature infants with ≤1250 g birth weight, specifically SGA.
Improved system for helper-dependent adenoviral vector production (2003)

Helper-dependent adenoviral vectors (HDAds) are devoid of all viral coding sequences and have demonstrated tremendous potential for gene therapy by providing increased cloning capacity (up to 37 kb) and long-term, high-level transgene expression in vivo with negligible toxicity. Currently, the most widely used method of producing HDAds is the Cre/loxP system developed by Graham and co-workers. However, two major obstacles currently hinder progress of this promising technology: (1) the difficulty of large-scale vector production and (2) helper virus (HV) contamination. We have developed an improved producer cell line, HV, and protocols that have successfully addressed these problems. With this system, >1 x 10(13) viral particles (vp) can be easily produced from 3 liters of cells within 2 weeks of vector rescue, with specific yields of >10,000 vp/cell and with exceedingly low HV contamination of 0.4-0.1% without relying on density-based vector purification and 0.02-0.01% following CsCl purification. This new system represents a major improvement over the original method in terms of simplicity, speed, vector yield, and purity, and it will significantly improve our ability to assess this promising gene therapy technology, especially in large animal models and, ultimately, for clinical applications.
A phenylalanine in peptide substrates provides for selectivity between cGMP- and cAMP-dependent protein kinases. (1992)

Bovine lung cGMP-binding cGMP-specific phosphodiesterase (cG-BPDE) is a potent and relatively specific substrate for cGMP-dependent protein kinase (cGK) as compared to cAMP-dependent protein kinase (cAK) (Thomas, M. K., Francis, S. H., and Corbin, J. D. (1990) J. Biol. Chem. 265, 14971-14978). A synthetic peptide, RKISASEFDRPLR (BPDEtide), was synthesized corresponding to the sequence surrounding the phosphorylation site in cG-BPDE. BPDEtide retained the cGK/cAK kinase specificity demonstrated by native cG-BPDE: the apparent Km of BPDEtide for cGK was 5-fold lower than that for cAK (Km = 68 and 320 microM, respectively). Vmax values were 11 mumol/min/mg for cGK and 3.2 mumol/min/mg for cAK. The peptide was not phosphorylated to a measurable extent by protein kinase C or by calcium/calmodulin-dependent protein kinase II. Thus, the primary amino acid sequence of the peptide substrate was sufficient to confer kinase specificity. Studies in crude tissue extracts indicated that BPDEtide was the most selective peptide substrate documented for measuring cGK activity. Peptide analogs of BPDEtide were synthesized to determine the contribution of specific residues to cGK or cAK substrate specificity. Substitution of a Lys for the amino-terminal Arg did not reduce cGK/cAK specificity; neither did the exchange of an Ala for the non-phosphorylated Ser nor the removal of the 3 carboxyl-terminal residues. A truncated BPDEtide (RKISASE) served equally well as substrate (Km approximately 90 microM) for both kinases. However, restoration of the Phe, to yield RKISASEF, reproduced the original cGK/cAK specificity for BPDEtide (Km = 120 and 480 microM, respectively), primarily by decreasing the affinity of cAK. Addition of a carboxyl-terminal Phe to the peptide RKRSRAE (derived from the sequence of the cGK phosphorylation site in histone H2B) or to the peptide LRRASLG (derived from the sequence of the cAK phosphorylation site in pyruvate kinase) also improved the cGK/cAK specificity by decreasing the affinity of cAK. These data suggested that the Phe in each substrate tested is a negative determinant for cAK.
Left ventricular motion reconstruction from planar tagged MR images: a comparison (2000)

Through recent development of MR techniques, it is now possible to assess regional myocardial wall function in a non-invasive way. Using MR tagging, space is marked with planes which deform with the tissue, providing markers for tracking the local motion of the myocardium. Numerous methods to reconstruct the three-dimensional displacement field have been developed. The aim of this article is to provide a framework to quantitatively compare the performance of four methods the authors have developed. Five sets of experiments are described, and their results are reported. Instructions are also provided to perform similar tests on any method using the same data. The experiments show that some characteristic properties of the methods, such as sensitivity to noise or spatial resolution, can be quantitatively classified. Cross-comparison of performances show what range values for these properties can be considered acceptable.
Digital generation of RF signals for wireless communications with band-pass delta-sigma modulation (2002)

This paper demonstrates a high speed digital technique to produce binary (digital) signals that encode representative RF signals (with time varying envelope) as needed for wireless communications. Specifically, it shows that IS-95 format CDMA signals can be generated with a single bit digital data stream at 3.6 Gb/S. The technique uses band-pass delta-sigma modulation so that the quantization noise is shaped out of the frequency band of interest. This approach points the way to single-chip, DSP-based transmitters, used in conjunction with switching mode power amplifiers and simple analog filters, to implement all the functions of a wireless transmitter.
Pathogenesis of atherosclerosis and its complications: effects of antihypertensive drugs. (1989)

Since hypertension is an important risk factor for atherosclerosis, it is logical to assume that treatment to lower blood pressure will prevent atherosclerosis. However, the relationship between hypertension and atherosclerosis is indirect and complex. Drugs that lower pressure will prevent heart failure and arteriolar complications such as renal failure or strokes caused by lacunar infarction or brain haemorrhage due to rupture of microaneurysms. However, there is little evidence that atherosclerotic complications can be reduced by lowering pressure. It is important to understand the pathogenesis of atherosclerosis and its complications, which are related to lipoproteins and arterial flow disturbances, in order to develop an approach to selecting those antihypertensive drugs which may prevent atherosclerotic complications related not only to initiation and progression of atherosclerotic plaques, but to the embolisation of platelet clumps or atherosclerotic debris, or events such as intraplaque haemorrhages, that lead to myocardial or cerebral infarction. Antihypertensive drugs have different effects on lipoproteins and on arterial flow disturbances that may have important implications for prevention. Alpha-blockers and drugs with beta 2 agonist activity have beneficial effects on lipoprotein profiles, ACE inhibitors and calcium channel antagonists have some anti-atherosclerotic effects in animal models, while beta-blockers have beneficial effects on flow disturbances and are anti-atherosclerotic in animal models and man. Future studies to determine how to prevent atherosclerotic complications in hypertensive patients will require methods for noninvasive measurement of atherosclerosis.
Relationship between serum RANTES levels and radiological progression in rheumatoid arthritis patients treated with methotrexate. (1999)

We observed high levels of serum RANTES in a series of RA patients during the active stage of the disease. MTX treatment significantly lowered the serum levels of RANTES, GRO-alpha and MCP-1. High levels of serum RANTES or GRO-alpha after 6 months of MTX treatment seem to be predictive of radiological erosions after one year.
HPP1 : A transmembrane protein-encoding gene commonly methylated in colorectal polyps and cancers (2000)

Adenomas are the precursors of most colorectal cancers. Hyperplastic polyps have been linked to the subset of colorectal cancers showing DNA microsatellite instability, but little is known of their underlying genetic etiology. Using a strategy that isolates differentially methylated sequences from hyperplastic polyps and normal mucosa, we identified a 370-bp sequence containing the 5' untranslated region and the first exon of a gene that we have called HPP1. Rapid amplification of cDNA ends was used to isolate HPP1 from normal mucosa. Using reverse transcription-PCR, HPP1 was expressed in 28 of 30 (93%) normal colonic samples but in only seven of 30 (23%) colorectal cancers (P < 0.001). The 5' region of HPP1 included a CpG island containing 49 CpG sites, of which 96% were found to be methylated by bisulfite sequencing of DNA from colonic tumor samples. By COBRA analysis, methylation was detected in six of nine (66%) adenomas, 17 of 27 (63%) hyperplastic polyps, and 46 of 55 (84%) colorectal cancers. There was an inverse relationship between methylation level and mRNA expression in cancers (r = -0.67; P < 0.001), and 5-aza-2-deoxycytidine treatment restored HPP1 expression in two colorectal cancer cell lines. In situ hybridization of HPP1 indicated that expression occurs in epithelial and stromal elements in normal mucosa but is silenced in both cell types in early colonic neoplasia. HPP1 is predicted to encode a transmembrane protein containing follistatin and epidermal growth factor-like domains. Silencing of HPP1 by methylation may increase the probability of neoplastic transformation.
Molecular Dynamics Simulations of the Ala-Pro Dipeptide in Water:  Conformational Dynamics of Trans and Cis Isomers Using Different Water Models (2001)

Molecular dynamics simulations of a single dipeptide (Ala-Pro) molecule in water were carried out using different water models, the modified TIP3P (transferable intermolecular potential 3P), the refined SPC (simple point charge), and the original SPC/E (extended simple point charge). Both trans and cis isomers of the dipeptide were simulated, and conformations from simulations with the different water models were compared. Both isomers have several conformations, but the total conformational space is limited. Two experimentally obtained subconformations of the cis isomer were found in simulations with the different water models. The bioactive conformation, which is binding to Cyclophilin A, was the major cis conformation, and the conformation with an intramolecular hydrogen bond between the N-terminal and the C-terminal was found to exist as the minor cis conformation. The hydration of the dipeptide was found to depend both on its conformation and on the water model.
CARA: Collision-Aware Rate Adaptation for IEEE 802.11 WLANs (2006)

Today’s IEEE 802.11 WLANs (Wireless LANs) provide multiple transmission rates so that different rates can be exploited in an adaptive manner depending on the underlying channel condition in order to maximize the system performance. Many rate adaptation schemes have been proposed so far while most (if not all) of the commercial devices implement a simple open-loop rate adaptation scheme (i.e., without feedback from the receiver), called ARF (Automatic Rate Fallback) due to its simplicity. A key problem with such open-loop rate adaptation schemes is that they do not consider the collision effect, and hence, malfunction severely when many transmission failures are due to collisions. In this paper, we propose a novel rate-adaptation scheme, called CARA (Collision-Aware Rate Adaptation). The key idea of CARA is that the transmitter station combines adaptively the Request-to-Send/Clear-to-Send (RTS/CTS) exchange with the Clear Channel Assessment (CCA) functionality to differentiate frame collisions from frame transmission failures caused by channel errors. Therefore, compared with other open-loop rateadaptation schemes, CARA is more likely to make the correct rate adaptation decisions. Through extensive simulation runs, we evaluate our proposed scheme to show that our scheme yields significantly higher throughput performance than the existing schemes
Dehydroepiandrosterone Replacement in Women with Adrenal Insufficiency: Effects on Body Composition, Serum Leptin, Bone Turnover, and Exercise Capacity (2001)

Studies in animals and humans using supraphysiological doses of dehydroepiandrosterone (DHEA) reported significant changes in body composition and carbohydrate metabolism. To investigate the metabolic action of a physiological DHEA replacement dose, we studied 24 women with adrenal insufficiency (AI; mean +/- SD age, 42.3 +/- 9.3 yr; duration of disease, 9.2 +/- 8.4 yr; body mass index, 23.4 +/- 4.0 kg/m(2)) in a double blind, placebo-controlled, randomized, cross-over design. They received 50 mg DHEA/day and placebo orally for 4 months each, with a 1 -month washout period. Measurements included fasting serum glucose, insulin, leptin, bone markers, anthropometric parameters determined by bioimpedance analysis, and exercise capacity as assessed by an incremental cycling test. DHEA did not induce any change in body mass index (placebo vs. DHEA, 23.3 +/- 4.1 vs. 23.2 +/- 3.9 kg/m(2); P = 0.39), parameters of body composition, or exercise capacity. However, compared with placebo, DHEA replacement led to a significant decrease in serum leptin (absolute change after 4 months, DHEA vs. placebo, -5.3 +/- 8.0 vs. 1.1 +/- 5.7 ng/mL; P = 0.01). This is most likely the result of the DHEA-induced normalization of circulating androgens. DHEA had no effect on fasting glucose, insulin, or the glucose/insulin ratio. Compared with placebo, serum osteocalcin increased slightly, but significantly, during DHEA treatment (absolute change after 4 months DHEA vs. placebo, +1.6 +/- 5.3 vs. -1.2 +/- 6.2 ng/mL; P = 0.02). However, urinary cross-links excretion did not change. In conclusion, replacement of DHEA in a physiological dose in patients with pathological DHEA deficiency does not have a significant effect on carbohydrate metabolism, body composition, or exercise capacity. The biological relevance of the changes in leptin and osteocalcin levels remains to be determined.
Rapid, sensitive spectrophotometric method for quantitative determination of sulfatides (1968)

A rapid, sensitive spectrophotometric method for the analysis of sulfatides is described. The assay method is based upon the formation of a colored complex between the cationic dye azure A and (anionic) sulfolipids; the complex is extractable by a solution of chloroform-methanol 1:1. With the exception of some of the phospholipids, the reaction is specific for the sulfolipids. Cardiolipin was the most reactive of the non-sulfolipid compounds that were tested. Except for sphingosine and the mono- and dihexose derivatives of sphingosine, a wide variety of lipids did not interfere with the formation of color by standard sulfatides. Sulfur-containing amino acids, sugar sulfates, and sulfated polymers neither produced color nor interfered in its formation by sulfatide. Chloride and nitrate ions produced relatively little color. The method is much more sensitive (lower limit, about 0.002 micromole) than most methods currently employed for the analysis of sulfatides and has a high degree of precision. It is applicable to the analysis of sulfolipids in tissue extracts and gives values similar to those obtained by previously published procedures. The reliability of the method is increased when it is applied to partially purified lipid solutions. Sulfatides added to extracts of rabbit brain tissue were quantitatively accounted for by the assay. In addition, the method can be applied to samples obtained directly from thin-layer plates.
TSG-6, an Arthritis-Associated Hyaluronan Binding Protein, Forms a Stable Complex with the Serum Protein Inter-.alpha.-inhibitor (1994)

TSG-6 is a secreted 35-kDa glycoprotein, inducible by TNF and IL-1. The N-terminal portion of TSG-6 shows sequence homology to members of the cartilage link protein family of hyaluronan binding proteins. The C-terminal half of TSG-6 contains a so-called CUB domain, characteristic for developmentally regulated proteins. High levels of TSG-6 protein are found in the synovial fluid of patients with rheumatoid arthritis and some other arthritic diseases. Here we show that TSG-6 readily formed a complex with a protein present in human, bovine, rabbit, and mouse serum. This complex was stable during SDS-PAGE under reducing conditions, and in the presence of 8 M urea. The protein that binds TSG-6 was purified from human serum and identified as inter-alpha-inhibitor (I alpha I) by N-terminal microsequencing. Microsequencing of the complex itself revealed the presence of TSG-6 and two of the three polypeptide chains of I alpha I (bikunin and HC2). Experiments with recombinant TSG-6 and I alpha I purified from human serum showed that the TSG-6/I alpha I complex is rapidly formed even in the apparent absence of other proteins at 37 degrees C, but not at 4 degrees C. The TSG-6/I alpha I complex was cleaved by chondroitin sulfate ABC lyase, suggesting that cross-linking by chondroitin sulfate is required for the stability of the complex.(ABSTRACT TRUNCATED AT 250 WORDS)
Targeting Folate Receptor with Folate Linked to Extremities of Poly(ethylene glycol)-Grafted Liposomes:  In Vitro Studies (1999)

Conjugates of three components, folic acid-poly(ethylene glycol)-distearoylphosphatidylethanolamine (FA-PEG-DSPE), derived from PEG with molecular masses of 2000 and 3350 Da were synthesized by a carbodiimide-mediated coupling of FA to H2N-PEG-DSPE. The conjugates were characterized by 1H NMR, MALDI-TOF, and HPLC analysis of enzymatic cleavage with carboxypeptidase G. As a prototype of a folate receptor (FR)-targeted system, the conjugates were formulated at 0.5 mol % phospholipid in hydrogenated phosphatidylcholine/cholesterol liposomes with or without additional methoxyPEG2000-DSPE. In vitro binding studies were performed with sublines of M109 (murine lung carcinoma) and KB (human epidermal carcinoma) cells each containing high and low densities of FR. FA-PEG-DSPE significantly enhanced liposome binding to tumor cells. The best binding was observed when FA-PEG liposomes contained no additional mPEG-lipid. In fact, our experiments showed that the presence of mPEG on liposomal surfaces significantly inhibited FA-PEG-liposome binding to FR. Increasing the molecular mass of the PEG tether from 2000 to 3350 Da improved the FR binding, particularly in the case of mPEG-coated liposomes. The FA-PEG liposomes bound to M109-HiFR cells very avidly as demonstrated by the inability of free FA (used in a 700-fold excess either at the beginning or at the end of the incubation) to prevent the cell binding. This is in contrast to the 5-10-fold lower cell binding activity of mPEG-FA compared to that of free FA, and likely to be related to the multivalent nature of the liposome-bound FA. Only 22% of FA-PEG3350 and 32% of FA-PEG3350/mPEG cell-associated liposomes could be removed by exposure to pH 3, conditions that dissociate FA-FR, suggesting that more than two-thirds of the bound liposomes were internalized during incubation for 24 h at 37 degrees C. FA-targeted liposomes also show enhanced nonspecific binding to extracellular tissue culture components, a phenomenon especially relevant in short incubation time experiments.
Association of the PD‐1.3A allele of the PDCD1 gene in patients with rheumatoid arthritis negative for rheumatoid factor and the shared epitope (2004)

Patients negative for both RF and the SE alleles showed association with the same allele that we previously identified as being involved in susceptibility to SLE. These results provide the first evidence of the involvement of the human PDCD1 gene in arthritis.