gebhart/patrepeval huggingface dataset:
Hepatostat: Liver regeneration and normal liver tissue maintenance (2016)

In contrast to all other organs, liver-to-body-weight ratio needs to be maintained always at 100% of what is required for body homeostasis. Adjustment of liver size to 100% of what is required for homeostasis has been called "hepatostat." Removal of a portion of any other organ is followed with local regeneration of a limited degree, but it never attempts to reach 100% of the original size. The complex mechanisms involved in this uniquely hepatic process encompass a variety of regenerative pathways that are specific to different types of injury. The most studied form of liver regeneration (LR) is that occurring after loss of hepatocytes in a single acute injury, such as rodent LR after two-thirds partial hepatectomy or administration of damaging chemicals (CCl<sub>4</sub> , acetaminophen, etc.). Alternative regenerative pathways become activated when normal regeneration is thwarted and trigger the appearance of "progenitor" cells. Chronic loss of hepatocytes is associated with regenerative efforts characterized by continual hepatocyte proliferation and often has adverse consequences (development of cirrhosis or liver cancer). Even though a very few hepatocytes proliferate at any given time in normal liver, the mechanisms involved in the maintenance of liver weight by this slow process in the absence of liver injury are not as well understood. (Hepatology 2017;65:1384-1392).
Predicting Protein Disorder for N-, C-, and Internal Regions. (1999)

Logistic regression (LR), discriminant analysis (DA), and neural networks (NN) were used to predict ordered and disordered regions in proteins. Training data were from a set of non-redundant X-ray crystal structures, with the data being partitioned into N-terminal, C-terminal and internal (I) regions. The DA and LR methods gave almost identical 5-cross validation accuracies that averaged to the following values: 75.9 +/- 3.1% (N-regions), 70.7 +/- 1.5% (I-regions), and 74.6 +/- 4.4% (C-regions). NN predictions gave slightly higher scores: 78.8 +/- 1.2% (N-regions), 72.5 +/- 1.2% (I-regions), and 75.3 +/- 3.3% (C-regions). Predictions improved with length of the disordered regions. Averaged over the three methods, values ranged from 52% to 78% for length = 9-14 to >/= 21, respectively, for I-regions, from 72% to 81% for length = 5 to 12-15, respectively, for N-regions, and from 70% to 80% for length = 5 to 12-15, respectively, for C-regions. These data support the hypothesis that disorder is encoded by the amino acid sequence.
Memory after silent stroke (2011)

Both hippocampal volume and brain infarcts independently contribute to memory performance in elderly individuals without dementia. Given that age-associated neurodegenerative conditions, such as Alzheimer disease, are defined primarily by impairment in memory, these findings have clinical implications for prevention and for identification of pathogenic factors associated with disease symptomatology.
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites (2010)

Transcription of protein-coding genes in trypanosomes is polycistronic and gene expression is primarily regulated by post-transcriptional mechanisms. Sequence motifs in the untranslated regions regulate mRNA trans-splicing and RNA stability, yet where UTRs begin and end is known for very few genes. We used high-throughput RNA-sequencing to determine the genome-wide steady-state mRNA levels ('transcriptomes') for approximately 90% of the genome in two stages of the Trypanosoma brucei life cycle cultured in vitro. Almost 6% of genes were differentially expressed between the two life-cycle stages. We identified 5' splice-acceptor sites (SAS) and polyadenylation sites (PAS) for 6959 and 5948 genes, respectively. Most genes have between one and three alternative SAS, but PAS are more dispersed. For 488 genes, SAS were identified downstream of the originally assigned initiator ATG, so a subsequent in-frame ATG presumably designates the start of the true coding sequence. In some cases, alternative SAS would give rise to mRNAs encoding proteins with different N-terminal sequences. We could identify the introns in two genes known to contain them, but found no additional genes with introns. Our study demonstrates the usefulness of the RNA-seq technology to study the transcriptional landscape of an organism whose genome has not been fully annotated.
Whole-body Insulin Resistance in the Absence of Obesity in FVB Mice With Overexpression of Dgat1 in Adipose Tissue (2005)

Insulin resistance is often associated with obesity. We tested whether augmentation of triglyceride synthesis in adipose tissue by transgenic overexpression of the diacylglycerol aclytransferase-1 (Dgat1) gene causes obesity and/or alters insulin sensitivity. Male FVB mice expressing the aP2-Dgat1 had threefold more Dgat1 mRNA and twofold greater DGAT activity levels in adipose tissue. After 30 weeks of age, these mice had hyperglycemia, hyperinsulinemia, and glucose intolerance on a high-fat diet but were not more obese than wild-type littermates. Compared with control littermates, Dgat1 transgenic mice were both insulin and leptin resistant and had markedly elevated plasma free fatty acid levels. Adipocytes from Dgat1 transgenic mice displayed increased basal and isoproterenol-stimulated lipolysis rates and decreased gene expression for fatty acid uptake. Muscle triglyceride content was unaffected, but liver mass and triglyceride content were increased by 20 and 300%, respectively. Hepatic insulin signaling was suppressed, as evidenced by decreased phosphorylation of insulin receptor-beta (Tyr(1,131)/Tyr(1,146)) and protein kinase B (Ser473). Gene expression data suggest that the gluconeogenic enzymes, glucose-6-phosphatase and phosphoenolpyruvate carboxykinase, were upregulated. Thus, adipose overexpression of Dgat1 gene in FVB mice leads to diet-inducible insulin resistance, which is secondary to redistribution of fat from adipose tissue to the liver in the absence of obesity.
Compact explosive-driven generator of primary power based on a longitudinal shock wave demagnetization of hard ferri- and ferromagnets (2002)

A new type of compact explosive-driven generator of primary power, which utilizes phenomena of a shock wave demagnetization of hard ferri- and ferromagnets, was developed. The shock wave initiated by high explosive, as well as accelerated flyer plate, passes along the hard ferri- or ferromagnetic body, which serves as initial energy carrier. The shock wave demagnetizes the energy-carrying element, reducing the initial magnetic flux /spl Phi//sub 0/. In accordance with Faraday's law, this change of magnetic flux /spl Delta//spl Phi//sub 0/ generates an electromotive force in a coil wound on the energy carrier. Several types of compact generators with energy-carrying element of 10 cm/sup 3/ in volume were explored. High-voltage generators that utilize energy of BaFe/sub 12/O/sub 19/ hard ferrimagnets are capable of producing pulses of amplitude 5.5 kV with full width at half maximum (FWHM) of 1 /spl mu/s. The generators that utilize energy of Nd/sub 2/Fe/sub 14/B high-energy hard ferromagnets are capable of producing pulses with amplitude more than 10 kV and FWHM about 4 /spl mu/s. The high-current generators based on Nd/sub 2/Fe/sub 14/B produced pulses yielded 826 A and FWHM of 180 /spl mu/s. The developed generator can be used as the most reliable and effective source of primary power capable of seeding magnetocumulative generators.
Bioactivation of the anticancer agent CPT-11 to SN-38 by human hepatic microsomal carboxylesterases and the in vitro assessment of potential drug interactions. (1997)

Human hepatic microsomes were used to investigate the carboxylesterase-mediated bioactivation of CPT-11 to the active metabolite, SN-38. SN-38 formation velocity was determined by HPLC over a concentration range of 0.25-200 microM CPT-11. Biphasic Eadie Hofstee plots were observed in seven donors, suggesting that two isoforms catalyzed the reaction. Analysis by nonlinear least squares regression gave KM estimates of 129-164 microM with a Vmax of 5.3-17 pmol/mg/min for the low affinity isoform. The high affinity isoform had KM estimates of 1.4-3.9 microM with Vmax of 1.2-2.6 pmol/mg/min. The low KM carboxylesterase may be the main contributor to SN-38 formation at clinically relevant hepatic concentrations of CPT-11. Using standard incubation conditions, the effects of potential inhibitors of carboxylesterase-mediated CPT-11 hydrolysis were evaluated at concentrations >/= 21 microM. Positive controls bis-nitrophenylphosphate (BNPP) and physostigmine decreased CPT-11 hydrolysis to 1.3-3.3% and 23% of control values, respectively. Caffeine, acetylsalicylic acid, coumarin, cisplatin, ethanol, dexamethasone, 5-fluorouracil, loperamide, and prochlorperazine had no statistically significant effect on CPT-11 hydrolysis. Small decreases were observed with metoclopramide (91% of control), acetaminophen (93% of control), probenecid (87% of control), and fluoride (91% of control). Of the compounds tested above, based on these in vitro data, only the potent inhibitors of carboxylesterase (BNPP, physostigmine) have the potential to inhibit CPT-11 bioactivation if administered concurrently. The carboxylesterase-mediated hydrolysis of alpha-naphthyl acetate (alpha-NA) was used to determine whether CPT-11 was an inhibitor of hydrolysis of high turnover substrates of carboxylesterases. Inhibition of alpha-NA hydrolysis by CPT-11 was determined relative to positive controls BNPP and NaF. Incubation with microsomes pretreated with CPT-11 (80-440 microM) decreased alpha-naphthol formation to approximately 80% of control at alpha-NA concentrations of 50-800 microM. The inhibitors BNPP (360 microM) and NaF (500 microM) inhibited alpha-naphthol formation to 9-10% of control and to 14-20% of control, respectively. Therefore, CPT-11-sensitive carboxylesterase isoforms may account for only 20% of total alpha-NA hydrolases. Thus, CPT-11 is unlikely to significantly inhibit high turnover, nonselective substrates of carboxylesterases.
Sequence Determination of rRNA Genes of Pathogenic Vibrio Species and Whole-Cell Identification of Vibrio vulnificus with rRNA-Targeted Oligonucleotide Probes (1994)

A comparative analysis of seven new 16S rRNA gene sequences of pathogenic Vibrio species with previously published vibrio sequences confirmed that Vibrio vulnificus represents a group that is not closely related to the core organisms of the genus Vibrio. In addition, we found that V. vulnificus, Listonella (Vibrio) anguillarum and Vibrio diazotrophicus branch off separately from the core group. A comparison of the 16S rRNA gene sequences of V. vulnificus strains belonging to biotypes 1 and 2 revealed that the sequences of all but four biotype 1 strains were identical to each other but slightly different (17 bases) from the sequences of the rest of the V. vulnificus strains investigated. In addition, the sequences of variable regions of the 23S rRNA genes of Vibrio fluvialis, Vibrio furnissii, Vibrio harveyi, Vibrio cholerae, and V. vulnificus C7184 and TW1 were determined, aligned, and compared with all available bacterial 23S rRNA sequences in order to search for specific target sites. As a result, four oligonucleotide probes specific for V. vulnificus were synthesized, and the specificities of these probes were evaluated by dot blot hybridization to membrane-bound RNAs from 21 V. vulnificus strains, 13 strains belonging to other Vibrio species, 61 strains belonging to species that are members of the alpha, beta, and gamma subclasses of the Proteobacteria, and 3 eucaryotic microorganisms. Two probes hybridized with all of the V. vulnificus strains tested, and the other two probes distinguished V. vulnificus biotype 1 strains from all other organisms. In situ identification of V. vulnificus by using tetramethylrhodamine- or fluorescein-labelled oligonucleotides is now possible.
A germline transformation analysis reveals flexibility in the organization of beat shock consensus elements (1987)

Maximal expression of the Drosophila heat shock gene hsp70 can be activated by a pair of heat shock consensus elements (HSE's) positioned close to the transcription start site. In contrast, required HSE's of other heat shock genes (i.e., hsp26, 27, 23) are located several hundred base pairs (bp) farther upstream of their start sites. Using germline transformation, we analyzed the requirements for HSE organization in the hsp70 and hsp26 regulatory regions. A 51 bp fragment containing the two proximal hsp70 HSE's was sufficient to rescue the heat shock response of an hsp26-lacZ gene devoid of its HSE's. Heat inducibility was restored with either orientation of the fragment relative to the hsp26 transcription start. In hsp70 gene constructions, relocation of hsp70 HSE's to more remote positions by inserting 127 or 331 bp into the regulatory region failed to substantially reduce expression. Thus, in contrast to their native configurations, the hsp26 promoter can be activated by HSE's solely in a proximal position and the hsp70 promoter can be activated by remote HSE's. In addition, a simple and sensitive assay for quantitative measurement of beta-galactosidase activity in crude fly extracts is described.
Oligomeric binding of T3 receptor is required for maximal T3 response. (1991)

Receptors in the thyroid-steroid hormone superfamily bind preferentially as dimers to palindromic response elements containing two hexameric half-sites. The 23-base pair rat growth hormone (rGH) T3 response element (T3RE), however, contains three hexameric binding domains, all of which are required for maximal T3 response. We examined the binding of purified T3 receptor alpha (T3R alpha), overexpressed in Escherichia coli, to wild-type and up and down mutations of the rGH T3RE to evaluate whether transcriptional potency correlates with changes in T3R binding. T3R binds to the rGH T3RE as a monomer, dimer, or higher order oligomer. Cooperative T3R dimer binding was demonstrated to two hexameric domains of the rGH T3RE arranged as either direct or inverted repeats. Decreased binding was seen with point mutations in each domain as well as with mutations which altered hexamer orientation and spacing within the site. These results demonstrate that all three hexamers of the rGH T3RE are involved in binding T3R. Occupancy of all three hexamers by T3R in the gel shift assay was observed with functional up mutations of the T3RE, increasing receptor concentration or addition of nuclear extract. The transcriptional response potencies of T3RE up or down mutants in a transient transfection assay correlated closely with T3R binding. These results confirm our earlier hypothesis that all three hexamers of the rGH T3RE bind T3R in a novel binding arrangement and provide a model for the interaction of T3R and other nuclear proteins with the DNA sequences of thyroid hormone-regulated genes.
Carotid Body Tumor (1992)

To better define the management and behavior of carotid body tumors, a 34-year surgical experience with 33 tumors in 30 patients was reviewed. There were 20 women and 10 men with an age range of 20 to 78 years. All but one presented with a neck mass. Arteriography was performed on 21 patients and was diagnostic in every case. There was no surgical mortality. Complications occurred in eight patients (27%), and one long-term neurologic deficit occurred. Three of 33 tumors were malignant, and aggressive resection of all approachable disease with radiotherapy for unresectable metastases led to prolonged survival in each case. Carotid body tumors present with neck mass. Arteriography is diagnostic and surgery is indicated. Even for malignant tumors and metastases, aggressive resection and radiotherapy are indicated.
CVD Growth Kinetics of HfB2 Thin Films from the Single-Source Precursor Hf(BH4)4 (2006)

Thermal CVD from the single-source precursor Hf(BH4)4 affords stoichiometric, dense, and hard HfB2 films; this paper reports the growth kinetics in detail. The decomposition reaction starts at 200 °C; mass spectrometry of the material desorbing from the growth surface reveals that, for steady-state deposition at P ≤ 1 × 10-6 Torr, the reaction probability of the precursor is independent of flux and increases with temperature with an apparent activation energy of 0.43 eV. The precursor is less reactive on clean Si and SiO2 substrates than it is on the HfB2 growth surface. By analyzing the thickness profile of films grown on high-aspect-ratio trench structures, we find that the growth rate is proportional to P0.3 for 1 × 10-4 < P < 1 × 10-2 Torr at a substrate temperature of 250 °C. The reaction probability of the precursor decreases from ∼1 to 1 × 10-4 as the precursor pressure increases from 1 × 10-6 to 1 × 10-1 Torr. This behavior is consistent with a Langmuirian surface-reaction mechanism. The conformality and the surface morphology of the HfB2 film are functions of the reaction probability of the precursor molecule. Extremely conformal and smooth coatings on deep trenches (>20:1 aspect ratio) can be obtained at low growth temperatures (≤300 °C) and high precursor pressures (∼0.1 Torr) with high growth rates (>200 nm/min).
Shigella lipopolysaccharide antibodies in pediatric populations (1995)

Shigellosis is the most common cause of bacterial dysentery. To study the specific immunity to the two major groups causing shigellosis, we assayed antibodies to lipopolysaccharide (LPS) by enzyme-linked immunoadsorbent assay to both Shigella sonnei and Shigella flexneri 2a serotypes in the following populations: (1) women immediately after delivery and their infants to assess the transfer of passive immunity by placenta and the presence of secretory antibodies in breast milk; (2) children of different ages; and (3) the kinetics of antibody production in pediatric patients, who had culture-proved shigellosis. The sera of these women showed variable concentrations of antibodies of all three isotypes to LPS of S. sonnei and S. flexneri 2a. These serotype-specific antibodies were not cross-reactive. Transfer of IgG anti-LPS across the placenta was significantly correlated with concentration of the specific antibody in the mother (S. sonnei, r = 0.96; S. flexneri, r = 0.84). Varying concentrations of anti-LPS IgA were present in colostrum, which was correlated with serum anti-LPS IgA titers in the case of S. sonnei (r = 0.44; P < 0.05) but not S. flexneri (r = 0.17). Healthy children between the ages of 6 months and 4 years in our population had undetectable or relatively low titers of anti-S. sonnei IgG. More children had detectable antibody titers to S. flexneri 2a than to S. sonnei. The relatively high concentrations of these natural antibodies are particularly noteworthy because there is a far lower incidence (< 10% of patients) with S. flexneri than with S. sonnei disease in this population.(ABSTRACT TRUNCATED AT 250 WORDS)
Malignancies, Prothrombotic Mutations, and the Risk of Venous Thrombosis (2005)

Patients with cancer have a highly increased risk of venous thrombosis especially in the first few months after diagnosis and in the presence of distant metastases. Carriers of the factor V Leiden and prothrombin 20210A mutations appear to have an even higher risk.
An automated fitting procedure and software for dose-response curves with multiphasic features (2015)

In cancer pharmacology (and many other areas), most dose-response curves are satisfactorily described by a classical Hill equation (i.e. 4 parameters logistical). Nevertheless, there are instances where the marked presence of more than one point of inflection, or the presence of combined agonist and antagonist effects, prevents straight-forward modelling of the data via a standard Hill equation. Here we propose a modified model and automated fitting procedure to describe dose-response curves with multiphasic features. The resulting general model enables interpreting each phase of the dose-response as an independent dose-dependent process. We developed an algorithm which automatically generates and ranks dose-response models with varying degrees of multiphasic features. The algorithm was implemented in new freely available Dr Fit software (sourceforge.net/projects/drfit/). We show how our approach is successful in describing dose-response curves with multiphasic features. Additionally, we analysed a large cancer cell viability screen involving 11650 dose-response curves. Based on our algorithm, we found that 28% of cases were better described by a multiphasic model than by the Hill model. We thus provide a robust approach to fit dose-response curves with various degrees of complexity, which, together with the provided software implementation, should enable a wide audience to easily process their own data.
The role of tubular iron accumulation in the remnant kidney. (1994)

Iron has been implicated in the pathophysiology of several models of acute and chronic renal disease. In this study, energy-dispersive x-ray spectrometry was used to quantify and localize iron in rat remnant kidneys (RK) and normal kidneys (NK) and to determine its pathophysiologic significance. Substantial iron accumulation occurred in proximal tubular cell secondary lysosomes of RK (P < 0.001 versus NK) and reached a plateau at 8 wk after partial nephrectomy. In NK, minor increases of iron also occurred with aging (P < 0.02). Proximal tubular iron accumulation correlated independently with protein excretion (r = 0.90) and impairment of GFR (r = 0.70) and was associated with tubular damage and phosphate accumulation (both P < 0.001). Iron nitrilotriacetate (1 mg/kg ip) increased tubular lysosomal iron accumulation and tubular damage (P < 0.001 versus nitrilotriacetate) in NK, comparable to levels seen in untreated RK, and increased cortical cytosolic malondialdehyde, consistent with reactive oxygen species generation. The iron chelator deferoxamine (30 mg/kg per day ip) significantly reduced iron accumulation and tubular damage in RK at 4 wk, compared with deferoxamine chelated to iron and untreated RK. These results suggest that filtered iron enters the remnant tubular lysosomes across the brush border membrane by endocytosis and may produce tubular damage in chronic renal disease by the generation of reactive oxygen species.
Porcine Reproductive and Respiratory Syndrome Virus–Induced Immunosuppression Exacerbates the Inflammatory Response to Porcine Respiratory Coronavirus in Pigs (2010)

We performed a comprehensive analysis of innate and adaptive immune responses in dual-virus infected pigs to understand whether a pre-existing immunomodulatory respiratory viral infection affects the overall immunity to a subsequent porcine respiratory coronavirus (PRCV) infection in pigs. Pigs were either mock-infected or infected with porcine reproductive and respiratory syndrome virus (PRRSV), a virus known to cause immunosuppressive respiratory disease, and then pigs were co-infected with PRCV, which normally causes subclinical respiratory infection. We collected samples for six independent experiments from 178 pigs that were also used for pathological studies. We detected a significant reduction in innate NK-cell-mediated cytotoxic function in PRRSV-infected pigs, which was synergistically further decreased in pigs co-infected with PRCV. Subsequently, in association with clinical signs we observed elevated levels of proinflammatory (IL-6), Th-1 (IL-12), and regulatory (IL-10 and TGF-β) cytokines. Increased frequencies of CD4CD8 double-positive T lymphocytes and myeloid cells, in addition to the elevated Th-1 and proinflammatory cytokines in dual-infected pigs, contributed to the severity of lung disease in pigs. The results of our study clarify how each virus modulates the host innate and adaptive immune responses, leading to inflammatory reactions and lung pathology. Thus measurements of cytokines and frequencies of immune cells may serve as indicators of the progression of respiratory viral co-infections, and provide more definitive approaches for treatment.