gebhart/patrepeval huggingface dataset:
Behavioral Deficits Following Experimental Subarachnoid Hemorrhage in the Rat (1994)

To characterize some of the short-term and long-term functional consequences of subarachnoid hemorrhage (SAH) in rats, we employed a battery of well-characterized tests for assessment of acute and chronic behavioral and neurologic performances. Three groups of 10 rats (blood injected, mock CSF injected and sham-operated controls) were studied. During the acute stage, simple nonpostural somatomotor reflexes (pinna and corneal reflexes), simple postural responses (paw flexion, tail flexion, and head support), startle response, and postural functions (righting reflex) did not differ significantly between the experimental groups. Assessments of body weight, beam walking ability, and beam balancing revealed significant disturbances in blood-injected rats. This work demonstrates that this single-hemorrhage rodent model of SAH is associated with the induction of enduring neurologic and behavioral deficits. Because of the significant interspecies difference, a direct extrapolation of our results to humans may not be appropriate. However, we suggest that the observed behavioral and neurologic changes may parallel those seen in humans after SAH. Results reported here further confirm the rat model of SAH as a viable laboratory instrument for the study of the pathophysiology of SAH and provide normative values for the evaluation of new treatment modalities.
Towards a Structure for a TSG-6·Hyaluronan Complex by Modeling and NMR Spectroscopy (2005)

The Link module from human TSG-6, a hyaladherin with roles in ovulation and inflammation, has a hyaluronan (HA)-binding groove containing two adjacent tyrosine residues that are likely to form CH-pi stacking interactions with sequential rings in the sugar. We have used this observation to construct a model of a protein.HA complex, which was then tested against existing experimental information and by acquisition of new NMR data sets of [(13)C, (15)N]HA (8-mer) complexed with unlabeled protein. A major finding of this analysis was that acetamido side chains of two GlcNAc rings fit into hydrophobic pockets on either side of the adjacent tyrosines, providing a selectivity mechanism of HA over other polysaccharides. Furthermore, two basic residues have a separation that matches that of glucuronic acids in the sugar, consistent with the formation of salt bridges; NMR experiments at a range of pH values identified protein groups that titrate due to their proximity to a free carboxylate in HA. Sequence alignment and construction of homology models for all human Link modules in their HA-bound states revealed that many of these features are conserved across the superfamily, thus allowing the prediction of functionally important residues. In the case of cartilage link protein, its two Link modules were docked together (using bound HA as a guide), identifying hydrophobic residues likely to form an intra-Link module interface as well as amino acids that could be involved in supporting intermolecular interactions between link proteins and chondroitin sulfate proteoglycans. Here, we propose a mechanism for ternary complex formation that generates higher order helical structures, as may exist in cartilage aggregates.
Recombinant plasmid obtained from two different, compatible staphylococcal plasmids (1975)

From two different, compatible staphylococcal plasmids that determine streptomycin and chloramphenicol resistance, respectively, a recombinant plasmid was obtained. This plasmid can be transduced with a rather high frequency (10(-4)/plaque-forming unit) to plasmid-negative strains, the linkage of the two markers being 100%. The maintenance of the recombinant plasmid in the host cell seems to be controlled by the chloramphenicol resistance plasmid. The recombinant plasmid proved to be incompatible with both parental plasmids, which are unrelated. The relationship between the chloramphenicol resistance plasmid and the recombinant plasmid was the same as the between genetically marked derivatives of the recombinant plasmid, whereas the relationship of the streptomycin resistance plasmid to the recombinant plasmid was of a different, asymmetrical type.
Comprehensive Computational Assessment of ADME Properties Using Mapping Techniques (2005)

One strategy to potentially improve the success of drug discovery is to apply computational approaches early in the process to select molecules and scaffolds with ideal binding and physicochemical properties. Numerous algorithms and different molecular descriptors have been used for modeling ligand-protein interactions as well as absorption, distribution, metabolism and excretion (ADME) properties. In most cases a single data set has been evaluated with one approach or multiple algorithms that have been compared for a single dataset. These models have been primarily evaluated by leave-one out analysis or boot strapping with groups representing 25-50% of the training set left out of the final model. In a very few examples a test set of molecules not included in the model has been used for an external evaluation. In the present study we have applied Sammon non-linear maps, Support Vector Machines and Kohonen Self Organizing Maps to modeling numerous datasets for ADME properties including human intestinal absorption, blood brain barrier permeability, cytochrome P450 binding, plasma protein binding, P-gp inhibition, volume of distribution and plasma half life.
Human Renal Carcinoma Line Transfected With Interleukin-2 and/or Interferon Gene(s): Implications for Live Cancer Vaccines (1993)

Continuous local delivery of cytokines via transfer of cytokine genes into tumor cells for use as live cancer vaccines is a novel strategy for manipulation of host-mediated antitumor immune response in patients with advanced RCC.
Abnormal liver tests in people aged 75 and above: prevalence and association with mortality (2011)

Abnormal liver tests occur commonly in elderly people and are associated with a modest increase in all-cause mortality. There was a strong association with liver disease; however, the majority of deaths were not due to this cause.
Pyrimidoindole derivatives are agonists of human hematopoietic stem cell self-renewal (2014)

The small number of hematopoietic stem and progenitor cells in cord blood units limits their widespread use in human transplant protocols. We identified a family of chemically related small molecules that stimulates the expansion ex vivo of human cord blood cells capable of reconstituting human hematopoiesis for at least 6 months in immunocompromised mice. The potent activity of these newly identified compounds, UM171 being the prototype, is independent of suppression of the aryl hydrocarbon receptor, which targets cells with more-limited regenerative potential. The properties of UM171 make it a potential candidate for hematopoietic stem cell transplantation and gene therapy.
Immunohistochemical expression of androgen receptor and prostate-specific antigen in breast cancer. (2006)

AR (androgen receptor) and PSA (prostate-specific antigen) are involved in the pathogenesis of breast cancer, but their role is not clearly defined. The purpose of this study was to analyze by immunohistochemistry the AR and PSA (prostate-specific antigen) expression in 156 female breast carcinomas and to correlate the results with some histopathological parameters, like ER (estrogen receptor), PR (progesterone receptor), HER2/neu, nodal and metastasis status, histological type and grade. ARs and PSA were expressed in 112/156 (72%) and respectively in 61/156 (39%) of cases and we found a positive correlation between AR and PSA expression in breast carcinomas (p<0.0002). We also found an association between the histological type of the tumor and AR (p<0.001), respectively PSA (p=0.01) and between AR and the grade of differentiation (p=0.007) and the nodal status (p=0.02). No correlations were found between the metastasis status and AR or PSA. 47.3% (53/112) of AR-positive cases and 46% (28/61) of PSA-positive cases were ER-negative. High frequency of AR (87.5%) and PSA (75%) expression was found in medullary carcinomas and 53% of lobular invasive carcinomas co-expressed AR and PSA. We found an inverse correlation between HER2/neu and PSA (p=0.05). Although most of the PSA-positive carcinomas were lymph node-negative, well and moderately differentiated, we did not find any statistically significant correlations between these parameters and PSA expression. Our study confirms that ARs are commonly expressed in breast cancer and the expression of PSA and AR are highly correlated. Moreover, all the lobular carcinomas and the majority of medullary carcinomas co-expressed AR and PSA, the majority of AR-positive carcinomas were lymph node-negative, well and moderately differentiated, and large number of ER-negative carcinomas expressed AR and PSA.
Headphone simulation of free-field listening. II: Psychophysical validation (1989)

Listeners reported the apparent spatial positions of wideband noise bursts that were presented either by loudspeakers in free field or by headphones. The headphone stimuli were digitally processed with the aim of duplicating, at a listener's eardrums, the waveforms that were produced by the free-field stimuli. The processing algorithms were based on each subject's free-field-to-eardrum transfer functions that had been measured at 144 free-field source locations. The headphone stimuli were localized by eight subjects in virtually the same positions as the corresponding free-field stimuli. However, with headphone stimuli, there were more front-back confusions, and source elevation seemed slightly less well defined. One subject's difficulty with elevation judgments, which was observed both with free-field and with headphone stimuli, was traced to distorted features of the free-field-to-eardrum transfer function.
Dynamic regulation of mitochondrial fission through modification of the dynamin‐related protein Drp1 (2010)

Mitochondria in cells comprise a tubulovesicular network shaped continuously by complementary fission and fusion events. The mammalian Drp1 protein plays a key role in fission, while Mfn1, Mfn2, and OPA1 are required for fusion. Shifts in the balance between these opposing processes can occur rapidly, indicating that modifications to these proteins may regulate mitochondrial membrane dynamics. We highlight posttranslational modifications of the mitochondrial fission protein Drp1, for which these regulatory mechanisms are best characterized. This dynamin-related GTPase undergoes a number of steps to mediate mitochondrial fission, including translocation from cytoplasm to the mitochondrial outer membrane, higher-order assembly into spirals, GTP hydrolysis associated with a conformational change and membrane deformation, and ultimately disassembly. Many of these steps may be influenced by covalent modification of Drp1. We discuss the dynamic nature of Drp1 modifications and how they contribute not only to the normal regulation of mitochondrial division, but also to neuropathologic processes.
Monitoring Healthy Metabolic Trajectories with Nutritional Metabonomics (2009)

Metabonomics is a well established analytical approach for the analysis of physiological regulatory processes via the metabolic profiling of biofluids and tissues in living organisms. Its potential is fully exploited in the field of "nutrimetabonomics" that aims at assessing the metabolic effects of active ingredients and foods in individuals. Yet, one of the greatest challenges in nutrition research is to decipher the critical interactions between mammalian organisms and environmental factors, including the gut microbiota. "Nutrimetabonomics" is today foreseen as a powerful approach for future nutritional programs tailored at health maintenance and disease prevention.
111-Gb/s PolMux-Quadrature Duobinary for Robust and Bandwidth Efficient Transmission (2010)

We investigate, by means of simulations, polarization-multiplexed (PolMux) quadrature duobinary (QDB) as a modulation format for transmitting 111-Gb/s signals with high spectral efficiency (SE) and acceptable system complexity. We show that PolMux-QDB can be used to transmit 111-Gb/s signals with an SE of 4-b/s/Hz, but at the same time has a higher tolerance to nonlinear transmission effects and local oscillator laser linewidth compared to PolMux-16QAM at the same data rate and SE.
CCR5 Expression Levels Influence NFAT Translocation, IL-2 Production, and Subsequent Signaling Events during T Lymphocyte Activation (2009)

Ligands of CCR5, the major coreceptor of HIV-1, costimulate T lymphocyte activation. However, the full impact of CCR5 expression on T cell responses remains unknown. Here, we show that compared with CCR5(+/+), T cells from CCR5(-/-) mice secrete lower amounts of IL-2, and a similar phenotype is observed in humans who lack CCR5 expression (CCR5-Delta32/Delta32 homozygotes) as well as after Ab-mediated blockade of CCR5 in human T cells genetically intact for CCR5 expression. Conversely, overexpression of CCR5 in human T cells results in enhanced IL-2 production. CCR5 surface levels correlate positively with IL-2 protein and mRNA abundance, suggesting that CCR5 affects IL-2 gene regulation. Signaling via CCR5 resulted in NFAT transactivation in T cells that was blocked by Abs against CCR5 agonists, suggesting a link between CCR5 and downstream pathways that influence IL-2 expression. Furthermore, murine T cells lacking CCR5 had reduced levels of intranuclear NFAT following activation. Accordingly, CCR5 expression also promoted IL-2-dependent events, including CD25 expression, STAT5 phosphorylation, and T cell proliferation. We therefore suggest that by influencing a NFAT-mediated pathway that regulates IL-2 production and IL-2-dependent events, CCR5 may play a critical role in T cell responses. In accord with our prior inferences from genetic-epidemiologic studies, such CCR5-dependent responses might constitute a viral entry-independent mechanism by which CCR5 may influence HIV-AIDS pathogenesis.
Increased resistance of crosslinked cornea against enzymatic digestion (2004)

Photochemical crosslinking of the cornea using riboflavin and UVA results in a markedly increased resistance versus collagen digesting enzymes. The findings support the use of the new method in the treatment of corneal ulcers.
Determining the initial states in forward-backward filtering (1996)

Forward-backward filtering is a common tool in off-line filtering for implementing noncausal filters. Filtering first forward and then backward or the other way around does not generally give the same result. Here, we propose a method to choose the initial state to obtain uniqueness and to remove transients at both ends.
Immunoregulation in the gut: success and failures in human disease (2002)

In normal conditions, human gut mucosa is infiltrated with a large number of mononuclear cells. This is a reflection of the fact that human intestine is continuously subjected to a massive stimulation by luminal antigens. This state of "physiological" inflammation is a tightly controlled phenomenon, as several mucosal cells interact to generate and maintain an appropriate local immune response. Changes in cell type number and/or function, including the release of soluble mediators, have been associated with the development of chronic inflammatory diseases, such as Crohn's disease (CD) and ulcerative colitis (UC), the two major forms of inflammatory bowel disease. Evidence also indicates that the type of inflammatory response occurring in the intestine of patients with CD differs from that in UC, and this probably reflects distinct pathways of immune activation. In CD mucosa, a Th1 response with high IL-12 and IFNgamma production prevails, while in UC a humoral immunity appears to be predominant. Despite this, CD and UC share downstream inflammatory events, characterised by high levels of inflammatory cytokines, free radicals, matrix-degrading enzymes and growth factors.
The Isolation and Properties of Some Soluble Proteins From Wool II. the Preferential Extraction of High-Sulphur Proteins (1962)

A study has been made of the preferential extraction of high· sulphur protein components from wool by alkaline solutions of potassium thioglycollate. It was found that in general the high. sulphur proteins were extracted in quantity at lower values of pH, temperature, and time than the low· sulphur proteins. The extraction of low· sulphur proteins was repressed by small increases in salt concentration and by the addition of divalent cations such as zinc and calcium, whereas the solubility of the high. sulphur proteins was much less affected by these additions.
Genetic association of cutaneous neonatal lupus with HLA class II and tumor necrosis factor α: Implications for pathogenesis (2004)

Taken together, the finding of a genetic predisposition to generate increased levels of TNFalpha following tissue injury and the histologic demonstration of TNFalpha in the target organ support the notion that this inflammatory cytokine plays a role in the pathogenesis of cutaneous neonatal lupus. Furthermore, the results of these studies provide evidence of a biologic link between neonatal lupus and the rash of SCLE.
Nucleosides. Part LV. Efficient synthesis of arabinoguanosine building blocks (1994)

Abstract From guanosine ( 1 ) as starting molecule, protected arabinoguanosine derivatives such as phosphoramidite precursors and arabinoguanosine ( 18 ) itself were prepared in high yields. Inversion of the configuration at C(2′) was achieved by introduction of the (trifluoromethyl)sulfonyl residue and subsequent displacement by nucleophiles like acetate, bromide, and azide. The guanine moiety was protected at the amide function by the 2‐(4‐nitrophenyl)ethyl (npe) group on O 6 and at the NH 2 function by the 2‐(4‐nitrophenyl)ethoxycarbonyl (npeoc) group.
Irisin mRNA and circulating levels in relation to other myokines in healthy and morbidly obese humans (2013)

The newly identified myokine irisin may be positively associated with FST at both the mRNA and circulating protein level.
Inhibition of Hypoxia Inducible Factor Hydroxylases Protects Against Renal Ischemia-Reperfusion Injury (2008)

Acute renal failure resulting from hypoperfusion and hypoxia is a significant clinical problem. Hypoxia activates the heterodimeric transcription factor hypoxia inducible factor (HIF), leading to changes in gene expression that promote tissue adaptation and survival. To determine whether HIF may protect the kidney from ischemia-reperfusion injury, we subjected hif1a(+/-) and hif2a(+/-) mice to renal ischemia-reperfusion injury. Injury was substantially more severe in hif(+/-) than in littermate controls, consistent with a protective role for HIF. Because wild-type mice exhibited submaximal HIF accumulation in response to no-flow ischemia, we tested compounds that might augment the protective HIF response following ischemia-reperfusion in these animals. We found that l-mimosine and dimethyloxalylglycine, two small molecules that activate HIF by inhibiting HIF hydroxylases, protected mouse kidneys from ischemia-reperfusion injury. Therefore, pharmacological activation of HIF may offer an effective strategy to protect the kidney from ischemic injury.
Subcolloidal Fe/Ag Particles for Reductive Dehalogenation of Chlorinated Benzenes (2000)

Subcolloidal (<0.1 μm) iron−silver (1% Ag) particles were synthesized for the transformation of chlorinated benzenes in aqueous solution. Hexachlorobenzene (HCB) (4 mg/L) was dechlorinated to tetra-, tri-, and dichlorobenzenes (TeCB, TCB, and DCB, respectively) within 24 h at a metal loading of 25 g/L. Principal degradation products included 1,2,4,5-TeCB, 1,2,4-TCB, and 1,4-DCB. Continuous dechlorination was observed during a 57-day experiment. The rate of dechlorination was positively correlated to the silver loading of the bimetallic particles. The bimetallic particles also effectively degraded penta- and tetrachlorobenzenes (PCB and TeCB, respectively). The Fe/Ag particles could become a cost-effective alternative to the previously reported Pd/Fe particles. The subcolloidal bimetallic particles may be applied in slurry reactors, in situ applications, and in combination with biological treatment for the complete degradation of chlorinated benzenes and PCBs.
Digital Control of Single-Inductor Dual-Output DC-DC Converters in Continuous-Conduction Mode (2006)

This paper investigates the application of digital control for non-isolated single-inductor dual-output step-down dc-dc converters operating in continuous-conduction mode (CCM). The accurate and independent control of each output requires sophisticated digital control architecture so as to minimize cross-regulation problem. The adopted control includes a separate regulation of common-mode and differential-mode output voltages. Moreover, variable gain of the differential-mode regulator and a non-linear evaluation of the common-mode voltage have been investigated in order to improve the system dynamic response at different load conditions. Experimental investigation has been performed using discrete components, implementing the digital control in a field programmable gate array (FPGA). Simulation and experimental results on dual output converters (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in </sub> =2.5/5 V, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o1</sub> =V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o2</sub> =0.9/1.5 V, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o1</sub> =I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o2</sub> =0/0.6 A) confirm the proposed analysis
Contributory role of VEGF overexpression in endothelin-1-induced cardiomyocyte hypertrophy (2007)

Although endothelin-1 (ET-1) stimulates vascular endothelial growth factor (VEGF) expression in a variety of cells, including endothelial cells and vascular smooth muscle cells, the effects of ET-1 on expression of VEGF and its receptors in cardiomyocytes are unknown. In the present study, we found that treatment of neonatal rat cardiomyocytes with ET-1 for 24 h resulted in upregulation of VEGF and its two principal receptors, fetal liver kinase 1 and fms-like tyrosine kinase 1, in a concentration-dependent manner (10(-12) to 10(-6) M). ET-1 treatment also caused significant cardiomyocyte hypertrophy, as indicated by increases in cell surface area and [(14)C]leucine uptake by cardiomyocytes. Treatment with TA-0201 (10(-6) M), an ET(A)-selective blocker, eliminated ET-1-induced overexpression of VEGF and its receptors as well as cardiomyocyte hypertrophy. Treatment with VEGF neutralizing peptides (5-10 mug/ml) partially but significantly inhibited ET-1-induced cardiomyocyte hypertrophy. These results suggest that ET-1 treatment of cardiomyocytes promotes overexpression of VEGF and its receptors via activation of ET(A) receptors, and consequently the upregulated VEGF signaling system appears to contribute, at least in part, to ET-1-induced cardiomyocyte hypertrophy.
α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers (2015)

Short α-peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non-peptide helical foldamers to stabilize α-helices when fused to short α-peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C- or N-termini of α-peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α-helical conformation in the fused peptide segment. The remarkable compatibility of α-peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non-peptide backbones as a means to further control the behavior of α-peptides.