gebhart/patrepeval huggingface dataset:
Cysteine endopeptidase activity levels in normal human tissues, colorectal adenomas and carcinomas (1991)

We have assayed cysteine endopeptidase activities in 17 types of normal human tissue and in matched sets of colorectal mucosa, adenoma and carcinoma samples. Our data indicate that cathepsin B enzyme levels vary 70-fold and cathepsin L enzyme levels vary 20-fold from one normal tissue to another. Cathepsin B specific activity in normal tissues fell into 3 categories. High activity, with a mean of 156.7 +/- 41.5 nmoles min-1 mg-1 protein, was measured in liver, thyroid, kidney and spleen; intermediate activity, with a mean of 60.2 +/- 8.3 nmoles min-1 mg-1 protein, was measured in heart, colon, adrenal and lung; and low activity, with a mean of 18.4 +/- 9.7 nmoles min-1 mg-1 protein, was measured in prostate, testis, nerve, stomach, pancreas, brain, skeletal muscle, skin and breast. Cathepsin L specific activity fell into 2 categories. High activity, with a mean of 51.1 +/- 4.9 nmoles min-1 mg-1 protein, was measured in thyroid, liver and kidney; and low activity, with a mean of 11.4 +/- 5.5 nmoles min-1 mg-1 protein, was measured in spleen, colon, heart, adrenal, lung, testis, brain, nerve, skin, stomach, pancreas, skeletal muscle, prostate and breast. Our characterization of these enzyme levels provides a reference standard for normal cathepsin B and L activities in human tissues that should enhance the detection of their deregulation in disease states. For example, in studies of colorectal carcinoma and normal mucosa, we observed a significant tumor-specific increase in cathepsin B and L activities with particularly high activity levels in earlier (Dukes' A and B) compared to later (Dukes' C and D) stages of colorectal cancer. In contrast, adenomas from colorectal cancer patients expressed normal levels of cathepsin B activity, providing evidence that the increase in expression of cathepsin B may be a sensitive marker for progression from the pre-malignant to the malignant state in the development of colorectal cancer.
Transforming growth factor beta 1 positively regulates its own expression in normal and transformed cells. (1988)

Transforming growth factor beta 1 (TGF-beta 1) regulates the growth, differentiation, or function of nearly all cell types. We now report that TGF-beta 1 increases steady-state levels of its own message in six different normal and transformed cells in culture. Accumulation of TGF-beta 1 mRNA can be detected by Northern blot analysis within 3 h of addition of the peptide to cells, and enhanced message levels persist as long as TGF-beta 1 is present in the culture medium. This autoinduction is half-maximal at approximately 10 PM TGF-beta 1, and maximal stimulation corresponds to a 2-3-fold increase in transcript levels. In normal rat kidney cells, the rise in TGF-beta 1 mRNA is actinomycin D-sensitive and is accompanied by a parallel (approximately 3-fold) increase in secretion of TGF-beta 1 protein in the culture medium of treated cells, as detected by immunoprecipitation of biosynthetically labeled 35S-labeled TGF-beta 1 using specific anti-TGF-beta 1 antibodies. Treatment of normal rat kidney cells with either epidermal growth factor or platelet-derived growth factor also results in an increase in TGF-beta 1 mRNA (2-3-fold), although epidermal growth factor and TGF-beta 1 appear to act via distinct mechanisms since their combined effects are greater than additive.
Multiple Recurrent Genomic Defects in Follicular Lymphoma (1987)

Several steps in the clinical evolution of human neoplasia are associated with a variety of recurrent chromosomal defects that could prove essential to the understanding of cancer. We found 15 types of nonrandom chromosomal abnormalities in a study of 71 patients with follicular lymphoma; 10 of the types appeared to influence the histopathological findings, clinical course, or response to treatment. A translocation, t(14;18), observed in 85 percent of all patients appeared to be the main determinant of a follicular pattern. Ten patients with a t(14;18) as a single defect had the histologic features of follicular small cleaved-cell lymphoma. Most did not require treatment for one to four years, because their tumors had an initial indolent course. In contrast, patients with follicular small cleaved-cell lymphoma with t(14;18) and deletion 13q32 acquired the hematologic features of leukemia and had an acceleration of the disease. A deletion 6q together with a complete or partial trisomy 7 or trisomy 12 (or both) was associated with the clinically more aggressive follicular mixed small- and large-cell or large-cell histologic type, which often evolves from follicular small-cell lymphoma. A complete or partial trisomy 3, 18, or 21 correlated almost exclusively with follicular large-cell lymphoma. In all follicular stages, a trisomy 2 or duplication 2p often accompanied an accelerated clinical course and a poor response to treatment. This study suggests that several discrete genomic defects may govern the evolution of a patient's malignant disease.
EVALUATION OF THE STREPTOCOCCAL DESOXYRIBO-NUCLEASE B AND DIPHOSPHOPYRIDINE NUCLEOTIDASE ANTIBODY TESTS IN ACUTE RHEUMATIC FEVER AND ACUTE GLOMERULONEPHRITIS (1962)

Antibody titers for two recently described streptococcal antigens, desoxyribonuclease B (DNase B) and diphosphopyridine nucleotidase (DPNase) have been compared with antistreptolysin O (ASO) titers in patients with acute rheumatic fever, in patients with acute nephritis, and in normal controls. Like the ASO, elevated titers for the two new antibodies are commonly found in patients with complications of streptococcal infections. The titers for anti-DPNase tend to be higher in acute nephritis than in acute rheumatic fever. These two new anti-body tests are particularly useful in providing evidence of a preceding streptococcal infection in those patients with manifestations of acute rheumatic fever or acute nephritis who fail to show an elevated ASO titer.
Control of Xanthan-Degrading Organisms in the Loudon Pilot: Approach, Methodology, and Results (1983)

Abstract An investigation of loss of mobility control in Exxon's Loudon micellar/polymer pilot test has confirmed that loss was caused by microbial degradation of the xanthan biopolymer used to viscosify the micro-emulsion and polymer drive banks. This paper describes techniques which were used to sample and culture bacteria from the Loudon pilot and demonstrate that these mixed cultures are able to degrade xanthan rapidly under reservoir conditions. Laboratory studies show that, under anaerobic conditions, bacteria cultured from the Loudon pilot can cause over 90% loss of xanthan viscosity in micellar/polymer fluids within seven days. To remedy this problem, an extensive laboratory screening program was conducted to identify biocides that are effective against the offending organisms. Complete kill of the organisms under repeated laboratory challenge tests was the chief screening criterion. Biocide compatibility (with biopolymer, formation rock, field brines, and microemulsion), cost effectiveness, and chemical stability were also judged key parameters for effectiveness in field applications. Of the biocides tested against the Loudon organisms, formaldehyde was found to be the most consistently effective, providing complete kill and persistence at levels of 500 to 2000 ppm. Formaldehyde was shown to reduce bacteria below detectable levels in the formation and permit propagation of xanthan in a follow-up test conducted within the highly contaminated pilot zone. Therefore, formaldehyde should be an effective biocide for future floods at Loudon.
Enhanced Anti-HIV Efficacy of Indinavir After Inclusion in CD4-Targeted Lipid Nanoparticles (2012)

We constructed CD4-targeted LNPs that provide selective binding and efficient delivery of indinavir to CD4-HIV host cells. Inclusion of polyethyleneglycol in LNPs would minimize immune recognition of peptides. The enhancement of anti-HIV effects is effective even under limited time exposure.
PP.12.09 (2015)

Objective: Patients with autonomic insufficiency syndromes accompanied by postural hypotension are commonly referred to hypertension experts, who are often expected to be skilled in low BP disorders also. One phenotype, pure autonomic failure (PAF), remains enigmatic. PAF is usually attributed to isolated degeneration of postganglionic sympathetic nerves, without CNS disease, as is conveyed in the name. Our results reported here suggest otherwise. Design and method: Nine patients with PAF and a reference group of 9 older healthy people aged 50–80 years were studied using novel molecular methods for studying sympathetic nerve proteins. As expected, the PAF patients had intractable postural hypotension without CNS disease, with diagnosis confirmed by presence of markedly reduced release of noradrenaline from sympathetic nerves, measured by isotope dilution (total noradrenaline spillover < 150 ng/min compared with 300–900 ng/min in health) and near-absence of sympathetic nerve firing recorded with microneurography. Results: When we tested for anticipated absence of specific sympathetic nerve proteins in biopsied subcutaneous forearm vein samples in PAF patients, veins being a rich source of sympathetic nerves, unexpectedly we found normal abundance of the noradrenaline transporter, NET and the vesicular transporter, VMAT2 (figure), unequivocal evidence that sympathetic nerves were present.Western blot analysis of sympathetic nerve proteins, accessed by forearm vein biopsy. The abundance of NET and VMAT2 was not reduced in PAF (P > 0.1 compared with normals). GAPDH served as a marker protein for protein loading of the gel. Conclusions: These results suggest that the abnormality in PAF, rather than being neurodegenerative, may be a sympathetic nerve membrane fault causing electrical silence so that, as we find here, microneurography registers no sympathetic nerve firing, electro-coupled noradrenaline release is nearly absent and neural postural circulatory homeostasis is severely compromised. The fault may be epigenetic, as PAF has onset in later life.
Centrifugal deposition of iron oxide magnetic nanorods for hyperthermia application (2015)

Centrifugal deposition of iron oxide was performed to manufacture magnetic nanorods in an aqueous solution. The nanorods were examined by electron microscopy. The diameter of the nanorods ranges from 10 to 20 nm. The length is about 150 nm. The nanorods were incorporated into a silicone polymer to simulate body tissues injected with magnetic nanomaterials. Then the magnetic nanorod-containing silicone samples were put into a microwave to examine the external electromagnetic field induced heating behavior. Dramatic increase in temperature was observed when the nanorods were exposed to the external electromagnetic field for 2 seconds. It is concluded that the nanorods generate intensive heating effect and they have the potential for hyperthermia application
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species (2005)

We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404).
Marginal decline in forced vital capacity is associated with a poor outcome in idiopathic pulmonary fibrosis (2009)

In therapeutic studies in idiopathic pulmonary fibrosis (IPF), the low prevalence of significant change in pulmonary functional tests (PFTs) has been a major constraint. The prognostic value of "marginal" changes in PFTs in IPF and fibrotic non-specific interstitial pneumonia (NSIP) was evaluated. In patients with biopsy-proven IPF (n = 84) and NSIP (n = 72), forced vital capacity (FVC) and diffusing capacity of the lung for carbon monoxide (D( L,CO)) trends at 6 months were categorised as "significant" (FVC >10%; D(L,CO) >15%) or "marginal" (FVC 5-10%; D(L,CO) 7.5-15%). Proportional hazards analysis and time-dependent receiver operating characteristic methodology were used to examine PFT trends against mortality. In IPF, reductions in FVC were significant in 22 cases (26%) and marginal in 19 cases (23%). Mortality was higher in patients with a significant decline in FVC (hazard ratio (HR) 2.80, 95% CI 1.54-5.06; p<0.001) and those with a marginal decline in FVC (HR 2.31, 95% CI 1.19-4.50; p = 0.01) than in those with stable disease. Progression-free survival was lower when the decline in FVC was marginal than in stable disease (HR 2.34, 95% CI 1.19-4.60; p = 0.01). Marginal changes in D(L,CO) in IPF and marginal changes in FVC and D (L,CO) in fibrotic NSIP did not provide useful prognostic information. Marginal change in FVC in IPF denotes a poor outcome. These findings are applicable to clinical practice and to the selection of patients with more progressive disease for therapeutic studies.
Building Phylogenetic Trees from Molecular Data with MEGA (2013)

Phylogenetic analysis is sometimes regarded as being an intimidating, complex process that requires expertise and years of experience. In fact, it is a fairly straightforward process that can be learned quickly and applied effectively. This Protocol describes the several steps required to produce a phylogenetic tree from molecular data for novices. In the example illustrated here, the program MEGA is used to implement all those steps, thereby eliminating the need to learn several programs, and to deal with multiple file formats from one step to another (Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739). The first step, identification of a set of homologous sequences and downloading those sequences, is implemented by MEGA's own browser built on top of the Google Chrome toolkit. For the second step, alignment of those sequences, MEGA offers two different algorithms: ClustalW and MUSCLE. For the third step, construction of a phylogenetic tree from the aligned sequences, MEGA offers many different methods. Here we illustrate the maximum likelihood method, beginning with MEGA's Models feature, which permits selecting the most suitable substitution model. Finally, MEGA provides a powerful and flexible interface for the final step, actually drawing the tree for publication. Here a step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence. MEGA is available for use on PCs and Macs from www.megasoftware.net.
Audiovisual speech enhancement: new advances using multi-layer perceptrons (2002)

This paper deals with the improvement of a noisy speech enhancement system based on the fusion of auditory and visual information. The system was presented in previous papers and implemented with a simple stimuli corrupted with white noise. Its principle consists of an analysis-enhancement-synthesis process based on a linear prediction (LP) model of the signal: the LP filter is enhanced thanks to associative tools that estimate the LP cleaned parameters from both noisy audio and lip shape information. The structure of the system is reviewed and we focus on the improvement that concerns the associators: multi-layers perceptrons are used instead of linear regression. It is shown that in the context of VCV transitions corrupted with white noise, the performances of the system are improved in terms of the intelligibility gain, distance measures and classification tests.
In Vitro Transcription and Translation Protocols (2007)

A highly anticipated update of the previous edition, In Vitro Transcription and Translation Protocols, Second Edition, provides molecular biology laboratories with the most powerful techniques for exploiting in vitro transcription and translation systems.In Section One: Technologies, authors discuss the use of alternative energy systems for ATP regeneration, the efficient in vitro production of integral membrane proteins, and the high-throughput production of protein libraries using the innovative single-molecule PRC-linked in vitro expression (SIMPLEX) technology. In Section Two: Applications, authors present in vitro translation of amplified protease gene from HIV patients to select proper anti-protease drug therapy, in vitro translation of genes from human patients to diagnose biologically relevant gene mutations, use of SIMPLEX technology to select enantioselective lipases from libraries of randomly produced lipase mutants, and the in vitro transcription and translation to identify proteins in 2D-maps
Characterization of a Nuclease Produced by Staphylococcus aureus (1967)

The conformational parameters of a nuclease produced by growing cultures of Staphylococcus aureus have been determined. This nuclease exhibits both ribonuclease and deoxyribonuclease activities. It has been shown to have a pH optimum of 9.2 and an absolute requirement for calcium ions. The experimental data are compatible with a compact globular protein of mol wt 17,000 and with a helical content of approximately 45%.
Spherical ensembles of gold nanoparticles on silica: electrostatic and size effects (2002)

Core-shell ensembles of citrate-stabilized gold nanoparticles (20-80 nm) on submicron silica cores (330-550 nm) have been prepared by electrostatic self-assembly with shell packing densities as high as phi = 0.55.
Absorption, metabolism, and transport of carotenoids (1996)

Carotenoids are currently under intense scrutiny regarding their potential to modulate chronic disease risk and prevent vitamin A deficiency, and renewed emphasis has been placed on achieving a better understanding of the metabolic fate of these compounds in humans. The development of new animal models, and use of human metabolic studies and stable tracer methods have greatly improved our knowledge of how carotenoids are absorbed, metabolized, and transported to tissues; however, many important issues remain unresolved. For example, intestinal uptake of carotenoids occurs by passive diffusion, but the lumenal or intracellular factors limiting this process are obscure. The intestinal mucosa plays a key role in the metabolism of provitamin A carotenoids such as beta-carotene, thus greatly influencing their bioavailability. Most recent evidence supports a central oxidation mechanism of cleavage of beta-carotene to retinal in the intestinal mucosa, but the extent and site(s) of postabsorptive metabolism in the human is unknown. While the human and other species clearly absorb non-provitamin A carotenoids, little is known of the extent and pathways of their metabolism and elimination. The metabolic fate of cis isomers of beta-carotene is a subject of recent interest, since 9-cis retinoic acid can apparently be formed from 9-cis beta-carotene in vitro and in vivo. Substantial cis-trans isomerization of at least small oral doses of 9-cis beta-carotene occurs in the human, although the site of isomerization is not yet known. Carotenoids are transported in plasma exclusively by lipoproteins, with the distribution among lipoprotein classes determined in large part by the physical properties of the carotenoid. The consequences of differential distribution in terms of tissue uptake and retention are not clear at present. Improved knowledge of the metabolic fate of carotenoids will assist in the development and testing of hypotheses regarding their potential to influence biological processes in the human.
Host-parasite relationship in murine leishmaniasis: pathophysiological and immunological changes (1982)

The host-parasite relationship in human visceral leishmaniasis remains poorly understood. In the present study, pathophysiological and immunological changes were examined in BALB/c mice infected with Leishmania donovani. These animals developed chronic infection with massive hepatosplenomegaly and hypergammaglobulinemia. In contrast to mice inoculated with 0.8 X 10(6) or 4 X 10(6) amastigotes, mice infected with 20 X 10(6) amastigotes failed to reduce liver parasite loads during 2 to 8 weeks of observation. At 8 weeks, liver size was increased by 26, 63, and 94%, respectively, in groups infected with 0.8 X 10(6), 4 X 10(6), or 20 X 10(6) amastigotes. Serum immunoglobulin G and M levels at 8 weeks in animals with the heaviest infection were increased by 53 and 80%, respectively, compared with controls. Specific antileishmanial antibodies were detected in the absence of antigen-specific delayed-type hypersensitivity or in vitro lymphocyte responses. Infection did not suppress the in vivo responses of mice to the non-parasite-related antigens sperm whale myoglobin or pneumococcal polysaccharide. Splenic mononuclear cell responses to phytohemagglutinin were suppressed as early as 2 weeks, and by 8 weeks, mice infected with 0.8 X 10(6), 4 X 10(6), or 20 X 10(6) amastigotes had phytohemagglutinin responses which were, respectively, 27.7, 13.9, and 15.8% of controls. Decreased phytohemagglutinin responses could not be related to reductions in splenic T cells; however, splenic B cells and macrophages were increased at 8 weeks of infection. The course of L. donovani infection and disease in BALB/c mice resembles events occurring in humans and should prove useful in defining mechanisms of immune alterations in visceral leishmaniasis.
Nerve growth factor-induced hyperalgesia in the neonatal and adult rat (1993)

Recently, we have shown that the interaction between NGF and sensory neurons in early postnatal periods is restricted to nociceptive afferents (Ritter et al., 1991; Lewin et al., 1992a; Ritter and Mendell, 1992). Here we show that administration of excess NGF to neonatal or mature animals can lead to a profound behavioral hyperalgesia. Neonatal NGF treatment (postnatal day 0-14) resulted in a profound mechanical hyperalgesia that persisted until the animals had reached maturity (6 weeks of age). This hyperalgesia could be explained by an NGF-mediated sensitization of A delta nociceptive afferents to mechanical stimuli. This peripheral sensitization wore off with a time course similar to that of the behavior hyperalgesia. Treatment of animals from the second postnatal week until 5 weeks of age (juveniles) led to a very similar behavioral hyperalgesia; however, there was no corresponding sensitization of A delta nociceptors to mechanical stimuli. Finally, one group of adult animals (5 weeks old) was treated daily with single injections of NGF for between 1 and 4 d. Within 24 hr after the first NGF injection these animals developed a mechanical hyperalgesia of the same magnitude seen after neonatal and juvenile NGF treatments. No sensitization of A delta nociceptive afferents was observed in these animals. In addition to the mechanical hyperalgesia, the animals also developed a heat hyperalgesia after one injection of NGF. The heat hyperalgesia was apparent within 15 min after the injection; however, signs of mechanical hyperalgesia were not seen until 6 hr after the injection. In conclusion, it appears that the NGF-induced mechanical hyperalgesia is brought about by different mechanisms in neonatal and adult rats. Furthermore, in adult animals the NGF-induced mechanical and heat hyperalgesia also appear to be attributable to two different mechanisms. The mechanical hyperalgesia may be due to central changes (see Lewin et al., 1992b), whereas the heat hyperalgesia is likely to result at least in part from the sensitization of peripheral receptors to heat.