gebhart/patrepeval huggingface dataset:
The complete general secretory pathway in gram-negative bacteria (1993)

The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins.
[Renal tissue angiotensins during converting enzyme inhibition of angiotensin I in spontaneously hypertensive rat]. (1997)

To compare the effects of an angiotensin-converting enzyme inhibitor on circulating and tissue renin-angiotensin system, we measured different renin-angiotensin system parameters during the first day of treatment (Day 1) as well as after two weeks of treatment (Day 14). Ramipril was given orally once daily to adult male spontaneously hypertensive rats. Renin activity, angiotensin-converting enzyme activity and levels of angiotensin I and angiotensin II in the plasma, renal cortex and renal medullar were assessed at Day 1 and Day 14 of the treatment. In the plasma, both renin activity and angiotensin I increased 10 to 15 fold one to four hours after acute as well as at Day 14 of ramipril treatment and then returned to basal values within 24 hours. Plasma angiotensin II levels were not significantly decreased at Day 1 or Day 14. The decrease in the angiotensin II/angiotensin I ratio suggested a sustained inhibition of plasma angiotensin-converting enzyme at Day 14. In the renal cortex and medulla, a clearly different pattern was observed: in ramipril treated rats, renin activity in the renal cortex and medulla did not change at Day 1 but at Day 14 we observed a slight and sustained increase in renin activity. Despite very high basal levels of renin activity, angiotensin I levels in the renal cortex were comparable to those in the plasma. The angiotensin I level increased only one-fold one hour after ramipril intake at Day 1 and Day 14. This suggests that angiotensinogen may have a limiting role in the synthesis of angiotensin I in the kidney. Angiotensin II levels were slightly higher in the renal cortex and medulla than in the plasma suggesting local synthesis of the peptide. In the kidney, angiotensin II levels decreased one and four hours after the acute or prolonged ramipril treatment and the angiotensin II/angiotensin I ratio was reduced at the same time. Our results show that the responses of the plasma and kidney components of the renin-angiotensin system to angiotensin-converting enzyme inhibition are different in the plasma and the kidney suggesting that the circulating and tissue renin-angiotensin system are at least in part independent.
All-Optical Hydrogen-Sensing Materials Based on Tailored Palladium Alloy Thin Films (2004)

Optical reflectance measurements were performed to determine the hydrogen response characteristics of 20-nm-thick Pd-Au (Ag) films. The response characteristics displayed a strong dependence on alpha, mixed alpha/beta, and beta Pd-hydride phases formed in the films. The response time peaks in the alpha --> beta phase transition region (1625 s at 0.4% H(2) for Pd(0.94)Ag(0.06) and 405 s at 1% H(2) for Pd(0.94)Au(0.06)), consistent with critical slowing down phenomena. The alpha --> beta phase transition region was shifted and inhibited by changing the alloy element to Au and increasing its corresponding content to 40 atom %, respectively. Initial hydrogen uptake rate measurements determined that, due to the adsorption of ambient background gases, the rate-limiting step for alpha or beta phase PdH formation is dissociative chemisorption of hydrogen for each palladium alloy film. By tuning the alloy content and composition of the palladium films, the surface properties of the film become more receptive toward the rapid detection of hydrogen and a novel hydrogen-sensing material using Pd alloyed with 40 atom % Au is presented.
Hot Weather Volatility Requirements of European Passenger Cars (1978)

&lt;div class="htmlview paragraph"&gt;This paper reviews studies in Europe during the summer of 1977 to investigate the possibility of expanding gasoline supply through relaxation of existing Reid Vapor Pressure (RVP) volatility specifications. Performance parameters investigated included vehicle vapor lock and hot weather driveability under both controlled and consumer operation. Overall, it appears that some existing RVP specifications could be relaxed and still provide satisfactory consumer protection levels. This would permit more optimum utilization of available high volatility, high octane gasoline components and expand gasoline product yields while minimizing crude requirements.&lt;/div&gt;
An on-chip NBTI sensor for measuring PMOS threshold voltage degradation (2007)

Negative Bias Temperature Instability (NBTI) is one of the most critical device reliability issues facing scaled CMOS technology. In order to better understand the characteristics of this mechanism, accurate and efficient means of measuring its effects must be explored. In this work, we describe an on-chip NBTI degradation sensor using two delay-locked loops (DLL). The increase in PMOS transistor threshold due to NBTI stress is translated into the control voltage of a DLL for high sensing gain. Measurements from a 0.13μm test chip show a maximum gain of 16X in the operating range of interest, with microsecond order measurement times for minimal unwanted recovery. The proposed NBTI sensor also supports various DC and AC stress modes.
Inhibition of Amyloid β Protein Aggregation and Neurotoxicity by Rifampicin (1996)

Aggregation of physiologically produced soluble amyloid beta protein (Abeta) to insoluble, neurotoxic fibrils is a crucial step in the pathogenesis of Alzheimer's disease. Aggregation studies with synthetic Abeta1-40 peptide by the thioflavin T fluorescence assay and electron microscopy and cytotoxicity assays using rat pheochromocytoma PC12 cells showed that an antibiotic, rifampicin, and its derivatives, which possess a naphthohydroquinone or naphthoquinone structure, inhibited Abeta1-40 aggregation and neurotoxicity in a concentration-dependent manner. Hydroquinone, p-benzoquinone, and 1,4dihydroxynaphthalene, which represent partial structures of the aromatic chromophore of rifampicin derivatives, also inhibited A beta1 40 aggregation and neurotoxicity at comparable molar concentrations to rifampicin. Electron spin resonance spectrometric analysis revealed that the inhibitory activities of those agents correlated with their radical-scavenging ability on hydroxyl free radical, which was shown to be generated in cell-free incubation of Abeta1-40 peptide. These results suggest that at least one mechanism of rifampicin-mediated inhibition of A beta aggregation and neurotoxicity involves scavenging of free radicals and that rifampicin and/or appropriate hydroxyl radical scavengers may have therapeutic potential for Alzheimer's disease.
The yeast VAS1 gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. (1988)

S1 mapping on the VAS1 structural gene indicates the existence of two classes of transcripts initiating at distinct in-frame translation start codons. The longer class of VAS1 transcripts initiates upstream of both ATG codons located 138 base pairs away and the shorter class downstream of the first ATG. A mutation that destroys the first AUG on the long message results in respiratory deficiency but does not affect viability. Mutation of the ATG at position 139 leads to lethality because the initiating methionine codon of the essential cytoplasmic valyl-tRNA synthetase has been destroyed. N-terminal protein sequence data further confirm translation initiation at ATG-139 for the cytoplasmic valyl-tRNA synthetase. From these results, we conclude that the VAS1 single gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. The presequence of the mitochondrial valyl-tRNA synthetase shows amino acid composition but not the amphiphilic character of imported mitochondrial proteins. From mutagenesis of the ATG-139 we conclude that the presequence specifically targets the cytoplasmically synthesized mitochondrial valyl-tRNA synthetase to the mitochondrial outer membrane and prevents binding of the enzyme core to cytoplasmic tRNAVal.
Cell expansion of human articular chondrocytes on macroporous gelatine scaffolds—impact of microcarrier selection on cell proliferation (2011)

This study investigates human chondrocyte expansion on four macroporous gelatine microcarriers (CultiSpher) differing with respect to two manufacturing processes-the amount of emulsifier used during initial preparation and the gelatine cross-linking medium. Monolayer-expanded articular chondrocytes from three donors were seeded onto the microcarriers and cultured in spinner flask systems for a total of 15 days. Samples were extracted every other day to monitor cell viability and establish cell counts, which were analysed using analysis of variance and piecewise linear regression. Chondrocyte densities increased according to a linear pattern for all microcarriers, indicating an ongoing, though limited, cell proliferation. A strong chondrocyte donor effect was seen during the initial expansion phase. The final cell yield differed significantly between the microcarriers and our results indicate that manufacturing differences affected chondrocyte densities at this point. Remaining cells stained positive for chondrogenic markers SOX-9 and S-100 but extracellular matrix formation was modest to undetectable. In conclusion, the four gelatine microcarriers supported chondrocyte adhesion and proliferation over a two week period. The best yield was observed for microcarriers produced with low emulsifier content and cross-linked in water and acetone. These results add to the identification of optimal biomaterial parameters for specific cellular processes and populations.
A Hands-Free Unit with Noise Reduction by Using Adaptive Beamformer (2008)

This paper presents an implementation of adaptive beamformer in a hands-free unit. The proposed adaptive beamformer suppresses stationary noise and interference sound. The adaptive beamformer and acoustic echo canceller were implemented in a compact hands-free unit with a low-cost DSP. The experimental results demonstrate the noise reduction performance of the hands-free unit.
NITROGEN FIXATION AND ITS IMPROVEMENT THROUGH GENETIC ENGINEERING (2013)

The process of conversion of nitrogen to a combined form is catalyzed by a complex metalloenzyme nitrogenase. It catalyzes the reduction of dinitrogen to ammonia in an ATPdependent manner. Recently, though in limited extent, evidences have been found regarding the nitrogen fixation in non leguminous crops. The total understanding of both leguminous and non-leguminous nitrogen fixation in the crops and the cause of limited nitrogen fixation is reviewed here. The various achievements in manipulating the host plant and the microorganism to improve the yield of nitrogen fixation are also discussed in this review.
Protocol conversion (1988)

The problem of achieving communication between two processes across a network or an internetwork is considered. The notion of logical connectivity between processes in a protocol is formalized. The problem of constructing a protocol converter to achieve interoperability between processes that implement different protocols is addressed. A formal model is presented, based on the theory of protocol projection, for reasoning about the semantics of different protocols and conversions between them. Two kinds of converters are presented: memoryless converters and finite-state converters. The construction of some finite-state converters is illustrated, and examples are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fine-Tuning of ENA ® Gapmers as Antisense Oligonucleotides for Sequence-Specific Inhibition (2007)

For gene validation and the development of oligonucleotide agents, 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) antisense gapmers are widely available. An in vitro Escherichia coli RNase H reaction analysis using ENA gapmers and an RNA oligonucleotide with mouse peptidylarginine deiminase 4 (PADI4) gene sequences revealed that the RNA oligonucleotide was specifically cleaved in the only reported case of the use of an ENA gapmer with an antisense sequence. On the other hand, duplexes of the full-length transcripts of PADI4 mRNA and ENA gapmers with a wide DNA window were cleaved not only at the target site, but also at nontarget sites by RNase H derived from partial base-pairing between the transcript and the ENA gapmer. When the DNA window region of the ENA gapmer was shortened to 5 or 6 nucleotides, the nontarget cleavage was effectively diminished. Moreover, the specific inhibition of PADI4 mRNA expression was observed in the cotransfection of PADI4 cDNA and ENA gapmers containing a short DNA region into NIH3T3 cells. These results demonstrated that ENA gapmers with a short DNA region improved the sequence-specificity of mRNA downregulation. These optimized ENA gapmers could reduce the "off-target" effect and be applicable to gene validation and oligonucleotide therapeutics.
Immunological and Molecular Correlates of Disease Recurrence after Liver Resection for Hepatocellular Carcinoma (2012)

The definition of the risk of hepatocellular carcinoma (HCC) recurrence after resection represents a central issue to improve the clinical management of patients. In this study we examined the prognostic relevance of infiltrating immune cell subsets in the tumor (TIL) and in nontumorous (NT) liver (LIL), and the expression of immune-related and lineage-specific mRNAs in HCC and NT liver derived from 42 patients. The phenotype of infiltrating cells was analyzed by flow cytometry, and mRNA expression in liver tissue was examined by real-time reverse transcription (RT)-PCR. The tumor immune microenvironment was enriched in inhibitory and dysfunctional cell subsets. Enrichment in CD4+ T-cells and in particular CD4 and CD8+ memory subsets within TIL was predictive of better overall survival (OS) and time to recurrence (TTR). Increased programmed death ligand 1 (PDL1) mRNA content and higher prevalence of invariant NKT (iNKT) cells were associated with shorter OS and TTR, respectively. By combined evaluation of infiltrating cell subsets along with mRNA profiling of immune and tumor related genes, we identified the intratumoral frequency of memory T-cells and iNKT-cells as well as PDL1 expression as the best predictors of clinical outcome. HCC infiltrate is characterized by the expression of molecules with negative regulatory function that may favor tumor recurrence and poor survival.
Centromeric Localization and Adaptive Evolution of an Arabidopsis Histone H3 Variant (2002)

Centromeric H3-like histones, which replace histone H3 in the centromeric chromatin of animals and fungi, have not been reported in plants. We identified a histone H3 variant from Arabidopsis thaliana that encodes a centromere-identifying protein designated HTR12. By immunological detection, HTR12 localized at centromeres in both mitotic and meiotic cells. HTR12 signal revealed tissue- and stage-specific differences in centromere morphology, including a distended bead-like structure in interphase root tip cells. The anti-HTR12 antibody also detected spherical organelles in meiotic cells. Although the antibody does not label centromeres in the closely related species Arabidopsis arenosa, HTR12 signal was found on all centromeres in allopolyploids of these two species. Comparison of the HTR12 genes of A. thaliana and A. arenosa revealed striking adaptive evolution in the N-terminal tail of the protein, similar to the pattern seen in its counterpart in Drosophila. This finding suggests that the same evolutionary forces shape centromeric chromatin in both animals and plants.
Use of polyclonal immunoglobulins as adjunctive therapy for sepsis or septic shock * (2007)

Objective: There is ongoing debate about the efficacy of polyvalent immunoglobulins as adjunctive therapy for sepsis or septic shock. Two meta-analyses by the Cochrane collaboration calculated a significant reduction in mortality. However, data of the largest study were missing in one, and a subset of four high-quality studies failed to show an effect in the other. To broaden the database, we performed a meta-analysis of all randomized controlled studies published so far. Data Source: MEDLINE, EMBASE, Cochrane Library of randomized trials, and personal files. Study Selection: Meta-analysis of all published randomized controlled studies published on polyvalent immunoglobulins (Ig) for treatment of sepsis or septic shock in adults, children, or neonates. Data Extraction: Twenty-seven trials with a total of 2,202 patients fulfilled the inclusion criteria. Data Synthesis: As the immunologic state of neonates is different than that of adults or older children, data were evaluated separately for each group. Fifteen trials on 1,492 adults could be included. The pooled effect on mortality was a relative risk of death (RR) of 0.79 (95% confidence interval [CI] 0.69–0.90,p<= .0003). There was a strong trend in favor of an immunoglobulin preparation enriched with IgA and IgM (IgGAM) (RR = 0.66, 95% CI 0.51–0.84,p<= .0009) compared with preparations containing only IgG (RR = 0.85, 95% CI 0.73–0.99,p<= .04). In 12 trials on 710 neonates, the pooled effect on mortality was 0.56 (95% CI 0.42–0.74,p<= .0001). There was also a positive although less pronounced trend favoring the effect of IgGAM (RR = 0.50, 95% CI 0.34–0.73,p<= .0003) compared with IgG (RR = 0.63, 95% CI 0.42–0.96,p<= .03). A sensitivity analysis selecting eight trials in adults and ten in neonates of highest methodological quality confirmed these results. Conclusions: Polyvalent immunoglobulins exert a significant effect on mortality in sepsis and septic shock, with a trend in favor of IgGAM.
Hepatic Adverse Effects of Fructose Consumption Independent of Overweight/Obesity (2013)

The chronic intake of fructose has been linked to insulin resistance, obesity, dyslipidemia and nonalcoholic fatty liver disease (NAFLD), which in turn, may progress to nonalcoholic steatohepatitis (NASH). We aimed to evaluate the magnitude of the effects of the chronic consumption of high-fructose (HFr) and high fat (HF) alone or combined. Four groups of male mice were fed different diets for 16 weeks: standard chow (9% fat: SC), HF diet (42% fat), HFr diet (34% fructose) and HF/HFr diet (42% fat, 34% fructose). The food intake was not different among the groups, and the body mass was not greater in the HFr group than in the SC group. The homeostasis model assessment for insulin resistance (HOMA-IR), as well as plasmatic total cholesterol and triglycerides were greater in the groups HF, HFr, and HF/HFr group than in the SC group. We observed in the groups HF, HFr and HF/HFr, compared to the group SC, nonalcoholic fatty liver disease (NAFLD) with a predominance of lipogenesis mediated by SREBP-1c and PPAR-γ, and a reduction of the oxidation mediated by PPAR-α. We also observed an increase in gluconeogenesis mediated by the GLUT-2 and the PEPCK. Importantly, we identified areas of necroinflammation indicating a transition from NAFLD to nonalcoholic steatohepatitis in the HFr and HF/HFr groups. This study is relevant in demonstrating that fructose consumption, even in the absence of obesity, causes serious and deleterious changes in the liver with the presence of the dyslipidemia, insulin resistance (IR), and NAFLD with areas of necroinflammation. These conditions are associated with a poor prognosis.
Mapping the evolution of regional atrophy in Alzheimer's disease: Unbiased analysis of fluid-registered serial MRI (2002)

Alzheimer's disease (AD) is characterized by progressive cerebral atrophy, which may be assessed by using volumetric MRI. We describe a voxel-based analysis of nonlinear-registered serial MRI to demonstrate the most statistically significant (P < 0.001) regions of change at different stages of the disease. We compared presymptomatic (n = 4), mild (n = 10), and moderately affected (n = 12) patients with early- and late-onset AD, with age- and sex-matched controls, and demonstrated increasing global atrophy with advancing disease. Significantly increased rates of hippocampal atrophy were seen in presymptomatic and mildly affected patients. There was a shift in the distribution of temporal lobe atrophy with advancing disease; the inferolateral regions of the temporal lobes showed the most significantly increased rates of atrophy by the time the patients were mildly or moderately affected. Significantly increased rates of medial parietal lobe atrophy were seen at all stages, with frontal lobe involvement occurring later in the disease. Our results suggest that the sites showing the most significant rates of atrophy alter as the disease advances, and that regional atrophy is already occurring before the onset of symptoms. This technique provides insights into the natural history of AD, and may be a valuable tool in assessing the efficacy of disease-modifying treatments, especially if these treatments were to have region-specific effects.
Altering Genes in Animals by Gene Targeting (1992)

It is possible to create mice in which a planned alteration has been introduced at a specific locus in the genome. The planned alteration is first introduced into the genome of mouse embryonic stem (ES) cells in tissue culture. This is accomplished by homologous recombination between the targeted genomic locus and DNA introduced into the ES cells. Cells containing the desired alteration are injected into recipient blastocysts for return to pseudo-pregnant foster mothers, where they can develop into chimeric pups. ES cells that contribute to the germline of the resulting chimeric mice allow the altered ES cell genome to be transmitted to future generations. This technique provides a powerful tool for exploring the mechanisms underlying the development and function of the immune system in vivo.