gebhart/patrepeval huggingface dataset:
An Inhibition of Urinary Albumin Excretion by Protease Inhibitor in Streptozotocin-Diabetic Rats (1996)

To evaluate the protecting effect of camostat mesylate, N,N-dimethylcarbamoylmethyl-p-(p-guanidinobenzoyloxy)phenylacetate methanesulfonate, one of the synthetic trypsin inhibitors, on diabetic nephropathy, urinary albumin excretion was measured in streptozotocin-induced (50 mg/kg, i.p.) diabetic rats treated with oral camostat mesylate for 12 weeks. The rats were divided into three groups: (1) nondiabetic control rats; (2) diabetic rats, and (3) diabetic rats received rat chow containing 0.1% camostat mesylate (PI rats). After induction of diabetes, the ratio of kidney weight to body weight and urinary albumin excretion (UAE) were significantly increased. However, the ratio of kidney weight to body weight in PI rats was significantly lower than that in diabetic rats, and UAE in PI rats was also significantly lower than that in diabetic rats at 4, 8 and 12 weeks. Kidney tissue insulin-like growth factor I (IGF-I) contents were significantly reduced in diabetic rats, and there were no significant differences in kidney tissue IGF-I contents between diabetic and PI rats. These results suggest that camostat mesylate reduces the UAE probably through an inhibitory effect on initial diabetic renal hypertrophy and that camostat mesylate is available for diabetic nephropathy.
Classification of all putative permeases and other membrane plurispanners of the major facilitator superfamily encoded by the complete genome of Saccharomyces cerevisiae (2006)

On the basis of the complete genome sequence of the budding yeast Saccharomyces cerevisiae, a computer-aided analysis was carried out of all members of the major facilitator superfamily (MFS), which typically consists of permeases with 12 transmembrane spans. Analysis of all 5885 predicted open reading frames identified 186 potential MFS proteins. Binary sequence comparison made it possible to cluster 149 of them into 23 families. Putative permease functions could be assigned to 12 families, the largest including sugar, amino acid, and multidrug transport. Phylogenetic clustering of proteins allowed us to predict a possible permease function for a total of 119 proteins. Multiple sequence alignments were made for all families, and evolutionary trees were constructed for families with at least four members. The latter resulted in the identification of 21 subclusters with presumably tightly related permease function. No functional clues were predicted for a total of 41 clustered or unclustered proteins.
Shape Effects of Nanoparticles Conjugated with Cell-Penetrating Peptides (HIV Tat PTD) on CHO Cell Uptake (2008)

In order to probe the nanoparticle shape/size effect on cellular uptake, a spherical and two cylindrical nanoparticles, whose lengths were distinctively varied, were constructed by the selective cross-linking of amphiphilic block copolymer micelles. Herein, we demonstrate that, when the nanoparticles were functionalized with the protein transduction domain of human immunodeficiency virus type 1 Tat protein (HIV Tat PTD), the smaller, spherical nanoparticles had a higher rate of cell entry into Chinese hamster ovary (CHO) cells than did the larger, cylindrical nanoparticles. It was also found that nanoparticles were released after internalization and that the rate of cell exit was dependent on both the nanoparticle shape and the amount of surface-bound PTD.
Nucleic Acids in Innate Immunity (2008)

Until recently, innate immunity was regarded as a relatively nonspecific system designed to engulf and destroy pathogens. However, new studies show that the innate immune system is highly developed in its ability to discriminate between self and foreign entities. Understanding this mechanism can lead to therapeutic strategies based on manipulation
MD Simulations of Homomorphous PNA, DNA, and RNA Single Strands:  Characterization and Comparison of Conformations and Dynamics (2001)

MD simulations of homomorphous single-stranded PNA, DNA, and RNA with the same base sequence have been performed in aqueous solvent. For each strand two separate simulations were performed starting from a (i) helical conformation and (ii) random coiled state. Comparisons of the simulations with the single-stranded helices (case i) show that the differences in the covalent nature of the backbones cause significant differences in the structural and dynamical properties of the strands. It is found that the PNA strand maintains its nice base-stacked initial helical structure throughout the 1.5-ns MD simulation at 300 K, while DNA/RNA show relatively larger fluctuations in the structures with a few local unstacking events during -ns MD simulation each. It seems that the weak physical coupling between the bases and the backbone in PNA causes a loss of correlation between the dynamics of the bases and the backbone compared to the DNA/RNA and helps maintain the base-stacked helical conformation. The global flexibility of a single-stranded PNA helix was also found to be lowest, while RNA appears to be the most flexible single-stranded helix. The sugar pucker of several nucleotides in single-stranded DNA and RNA was found to adopt both C2'-endo and C3'-endo conformations for significant times. This effect is more pronounced for single strands in completely coiled states. The simulations with single-stranded coils as the initial structure also indicate that a PNA can adopt a more compact globular structure, while DNA/RNA of the same size adopts a more extended coil structure. This allows even a short PNA in the coiled state to form a significantly stable nonsequentially base-stacked globular structure in solution. Due to the hydrophobic nature of the PNA backbone, it interacts with surrounding water rather weakly compared to DNA/RNA.
Memory trace replay: the shaping of memory consolidation by neuromodulation (2015)

The consolidation of memories for places and events is thought to rely, at the network level, on the replay of spatially tuned neuronal firing patterns representing discrete places and spatial trajectories. This occurs in the hippocampal-entorhinal circuit during sharp wave ripple events (SWRs) that occur during sleep or rest. Here, we review theoretical models of lingering place cell excitability and behaviorally induced synaptic plasticity within cell assemblies to explain which sequences or places are replayed. We further provide new insights into how fluctuations in cholinergic tone during different behavioral states might shape the direction of replay and how dopaminergic release in response to novelty or reward can modulate which cell assemblies are replayed.
Pharmacokinetic and Pharmacodynamic Profile of Oral and Intravenous Meta-Chlorophenylpiperazine in Healthy Volunteers (1998)

meta-Chlorophenylpiperazine (mCPP) is a compound that is frequently used in challenge tests of the serotonergic system. Its human pharmacology is largely unexplored. The objective of this study was to investigate the pharmacokinetic and pharmacodynamic profile of mCPP. Eight female and six male healthy volunteers were included in a randomized, double-blind, double-dummy, three-way crossover design of single-dose intravenous (0.1 mg/kg), oral (0.5 mg/kg), and placebo treatment, with 24-hour follow-up. mCPP showed a large variability in clearance (11-92 mL/hr) and bioavailability (14-108%). Two female subjects dropped out because of headache and dysphoria. During the 27 occasions in which mCPP was administered, autonomic physical symptoms were observed in 23 subjects and disturbances of mood in 6 subjects. Oral and intravenous mCPP caused sudden increases in cortisol levels, prolactin levels, and total scores of the Body Sensation Questionnaire. Administration of mCPP also led to concentration-dependent increases of saccadic peak velocity and adaptive tracking performance and to a decrease of electroencephalographic occipital theta activity. No clinically relevant effects on electrocardiogram, temperature, and blood pressure were found. In conclusion, it is doubtful whether mCPP is a useful compound for challenge tests in view of the large pharmacokinetic variability after intravenous and oral administration. The effects of mCPP are consistent with disinhibition of the central nervous system.
Prostate Cancer: Cell and Molecular Mechanisms in Diagnosis and Treatment (1991)

With the aim of developing diagnostic techniques that can identify which, if any, of detected prostate cancers have progressed to a clinical stage, researchers report their findings on the role of various genetic changes in prostatic carcinogenesis; and on cellular factors, focusing on the roles of
Severe Lung Lesions Caused by Salmonella Are Prevented by Inhibition of the Contact System (2000)

Vascular damage induced by trauma, inflammation, or infection results in an alteration of the endothelium from a nonactivated to a procoagulant, vasoconstrictive, and proinflammatory state, and can lead to life-threatening complications. Here we report that activation of the contact system by Salmonella leads to massive infiltration of red blood cells and fibrin deposition in the lungs of infected rats. These pulmonary lesions were prevented when the infected animals were treated with H-D-Pro-Phe-Arg-chloromethylketone, an inhibitor of coagulation factor XII and plasma kallikrein, suggesting that inhibition of contact system activation could be used therapeutically in severe infectious disease.
Double-stage phase-diversity (DSPD) experiment using 100 Mbit/s FSK coherent optical communication system (1989)

An experimental 100 Mbit/s FSK coherent optical communication system employing a double-stage phase-diversity (DSPD) scheme has been constructed, and the bit error rate (BER) has been measured. A heterodyne-like second IF signal can be obtained as expected. A sensitivity 0.6 dB worse than that of heterodyne is achieved.
InGaN nanopillars grown on silicon substrate using plasma assisted molecular beam epitaxy (2009)

Single crystalline and single phase In(x)Ga(1-x)N nanopillars were grown spontaneously on (111) silicon substrate by plasma assisted molecular beam epitaxy. The surface morphology, structural quality, and optoelectronic properties of InGaN nanopillars were analyzed using scanning electron microscopy (SEM), energy dispersive x-ray (EDXA) analysis, high resolution x-ray diffraction (HR-XRD), and both room and low temperature photoluminescence spectra. The EDXA results showed that these nanopillars were composed of InGaN and the amount of indium incorporation in In(x)Ga(1-x)N NPs could be controlled by changing the growth temperature. The room temperature and low temperature PL spectra revealed that the emission wavelength could be tuned from a blue to green luminescent region depending on the growth temperature. The wavelength tuning was attributed to a higher amount of In incorporation at a lower growth temperature which was consistent with the EDXA and HR-XRD results.
Imaging mammalian tissues and organs using laser collimated transillumination (1984)

Images of mammalian organs were built up using a Laser collimated transillumination device equipped with a bidirectional scanning setup. A microcomputer was used to run the scanning process, acquisition of detected signals and images restitution. The images featured a satisfactory resolution of optical discontinuities on both sample surfaces. Light scattering within biological tissues restricted the spatial discrimination encountered with geometrical selection approach. By combining space and time resolution at various wavelengths, the production of an efficient tomospectroscopy could be envisaged.
Ribonucleic Acid Polymerase II Binding Subunit 3 (Rpb3), a Potential Nuclear Target of Insulin-Like Growth Factor Binding Protein-3 (2006)

IGF-binding protein (IGFBP)-3 has intrinsic antiproliferative and proapoptotic functions that are independent of IGF binding and may involve nuclear localization. We determined that exogenous IGFBP-3 rapidly translocates to myoblast nuclei and that a 22-residue peptide containing the metal binding domain (MBD) and nuclear localization sequence (NLS) can similarly direct chimeric GFP into myoblast nuclei. Furthermore, a non-IGF-binding IGFBP-3 mutant inhibited myoblast proliferation without stimulating apoptosis. These results suggest that IGFBP-3 inhibits muscle cell growth in an IGF-independent manner that may be influenced by its rapid nuclear localization. We therefore identified IGFBP-3 interacting proteins by screening a rat L6 myoblast cDNA library using the yeast two-hybrid assay and two N-terminal deletion mutants as bait: BP3/231 (231 residues, L61 to K291) and BP3/111 (K181-K291). Proteins previously known to interact with IGFBP-3 as well as several novel proteins were identified, including RNA polymerase II binding subunit 3 (Rpb3). The domain necessary for Rpb3 binding was subsequently identified using different IGFBP-3 deletion mutants and was localized to the MBD/NLS epitope. Rpb3/IGFBP-3 binding was confirmed by coimmunoprecipitation assays with specific antisera, whereas a NLS mutant IGFBP-3 did not associate with Rpb3, suggesting that a functional NLS is required. Rpb3 facilitates recruitment of the polymerase complex to specific transcription factors and is necessary for the transactivation of many genes. Its association with IGFBP-3 provides a functional role for IGFBP-3 in the direct modulation of gene transcription.
Structural Modal Identification Through High Speed Camera Video: Motion Magnification (2014)

Video cameras offer the unique capability of collecting high density spatial data from a distant scene of interest. They could be employed as remote monitoring or inspection sensors because of their commonplace use, simplicity, and relatively low cost. The difficulty is in interpreting the video data into a usable format that is familiar to engineers such as displacement. A methodology called motion magnification, developed for visualizing exaggerated versions of small displacements, is extended to modal identification in structures. Experiments in a laboratory setting on a cantilever beam were performed to verify the method against accelerometer and laser vibrometer measurements. Motion magnification is used for modal analysis of cantilever beams to visualize mode shapes and calculate mode shape curvature as a basis for damage detection. Suggestions for applications of this methodology and challenges in real-world implementations are given.
Adrenergic Induction of HSV-1 Ocular Shedding in Rabbits (1986)

Four groups of latently infected rabbits were induced to shed HSV-1 into the tear film by a one-time ocular iontophoresis of 6-hydroxydopamine (6-HD) followed 3 days later by five consecutive days of twice daily topical epinephrine (Epi). Groups 1 and 4 had both eyes inoculated and Groups 2 and 3 had only one eye inoculated. Groups 1 and 2 had eyes swabbed to detect HSV-1, and Groups 3 and 4 had eyes washed. Group 1 was iontophoresed with 1.0% 6-HD at 0.5 mAmp for 5 min, and Groups 2, 3 and 4 were iontophoresed with 0.1% 6-HD at 0.75 mAmp for 5 min. Group 1 received topical 2.0% Epi, and Groups 2, 3, and 4 received topical 1.0% Epi. Inoculated eyes in all groups shed HSV-1 during the induction period. The peak of HSV-1 shedding occurred on the last day of Epi application for Groups 1 and 2, and on the day after the last Epi application for Groups 3 and 4. The ratio of total positive tear film samples to total samples for inoculated eyes that received 6-HD and Epi were 53/119 (45%), 38/87 (44%), 24/66 (36%), and 14/33 (42%) for Groups 1, 2, 3, and 4, respectively. Therefore, even reduced concentrations of 6-HD and Epi, as well as beginning Epi 3 days after 6-HD, induced HSV-1 ocular shedding.
Hypoxia inducible factors in cancer stem cells (2010)

Oxygen is an essential regulator of cellular metabolism, survival, and proliferation. Cellular responses to oxygen levels are monitored, in part, by the transcriptional activity of the hypoxia inducible factors (HIFs). Under hypoxia, HIFs regulate a variety of pro-angiogenic and pro-glycolysis pathways. In solid cancers, regions of hypoxia are commonly present throughout the tissue because of the chaotic vascular architecture and regions of necrosis. In these regions, the hypoxic state fluctuates in a spatial and temporal manner. Transient hypoxic cycling causes an increase in the activity of the HIF proteins above what is typical for non-pathologic tissue. The extent of hypoxia strongly correlates to poor patient survival, therapeutic resistance and an aggressive tumour phenotype, but the full contribution of hypoxia and the HIFs to tumour biology is an area of active investigation. Recent reports link resistance to conventional therapies and the metastatic potential to a stem-like tumour population, termed cancer stem cells (CSCs). We and others have shown that within brain tumours CSCs reside in two niches, a perivascular location and the surrounding necrotic tissue. Restricted oxygen conditions increase the CSC fraction and promote acquisition of a stem-like state. Cancer stem cells are critically dependant on the HIFs for survival, self-renewal, and tumour growth. These observations and those from normal stem cell biology provide a new mechanistic explanation for the contribution of hypoxia to malignancy. Further, the presence of hypoxia in tumours may present challenges for therapy because of the promotion of CSC phenotypes even upon successful killing of CSCs. The current experimental evidence suggests that CSCs are plastic cell states governed by microenvironmental conditions, such as hypoxia, that may be critical for the development of new therapies targeted to disrupt the microenvironment.
Use of a Multiplex Molecular Beacon Platform for Rapid Detection of Methicillin and Vancomycin Resistance in Staphylococcus aureus (2005)

Drug resistance, particularly vancomycin and methicillin resistance, in Staphylococcus aureus continues to emerge as a significant public health threat in both the hospital and community settings. In addition to the limited treatment options, S. aureus strains acquire and express numerous virulence factors that continue to increase its ability to cause a wide spectrum of human disease. As a result, empirical treatment decisions are confounded and there is a heightened need for a diagnostic test (or assay) to rapidly identify antibiotic resistance and specific virulence determinants and indicate the appropriate treatment. To that end we developed a platform using multiplex molecular beacon probes with real-time PCR for the rapid detection of drug resistance-determining genes and virulence factors in S. aureus. In this study, we demonstrate the specificity and sensitivity of our platform for detection of the genes conferring methicillin (mecA) and vancomycin (vanA) resistance as well as a gene encoding the virulence factor Panton-Valentine leucocidin (lukF) in S. aureus isolates.
Accumulation of fructosyl-lysine and advanced glycation end products in the kidney, retina and peripheral nerve of streptozotocin-induced diabetic rats (2003)

The accumulation of AGEs (advanced glycation end products) in diabetes mellitus has been implicated in the biochemical dysfunction associated with the chronic development of microvascular complications of diabetes--nephropathy, retinopathy and peripheral neuropathy. We investigated the concentrations of fructosyl-lysine and AGE residues in protein extracts of renal glomeruli, retina, peripheral nerve and plasma protein of streptozotocin-induced diabetic rats and normal healthy controls. Glycation adducts were determined by LC with tandem MS detection. In diabetic rats, the fructosyl-lysine concentration was increased markedly in glomeruli, retina, sciatic nerve and plasma protein. The concentrations of N (epsilon)-carboxymethyl-lysine and N (epsilon)-carboxyethyl-lysine were increased in glomeruli, sciatic nerve and plasma protein, and N(epsilon)-carboxymethyl-lysine also in the retina. Hydroimidazolone AGEs derived from glyoxal, methylglyoxal and 3-deoxylglucosone were major AGEs quantitatively. They were increased in the retina, nerve, glomeruli and plasma protein. AGE accumulation in renal glomeruli, retina, peripheral nerve and plasma proteins is consistent with a role for AGEs in the development of nephropathy, retinopathy and peripheral neuropathy in diabetes. High-dose therapy with thiamine and Benfotiamine suppressed the accumulation of AGEs, and is a novel approach to preventing the development of diabetic complications.
Schwann cells express erythropoietin receptor and represent a major target for Epo in peripheral nerve injury (2005)

Erythropoietin (Epo) expresses potent neuroprotective activity in the peripheral nervous system; however, the underlying mechanism remains incompletely understood. In this study, we demonstrate that Epo is upregulated in sciatic nerve after chronic constriction injury (CCI) and crush injury in rats, largely due to local Schwann cell production. In uninjured and injured nerves, Schwann cells also express Epo receptor (EpoR), and its expression is increased during Wallerian degeneration. CCI increased the number of Schwann cells at the injury site and the number was further increased by exogenously administered recombinant human Epo (rhEpo). To explore the activity of Epo in Schwann cells, primary cultures were established. These cells expressed cell-surface Epo receptors, with masses of 71 and 62 kDa, as determined by surface protein biotinylation and affinity precipitation. The 71-kDa species was rapidly but transiently tyrosine-phosphorylated in response to rhEpo. ERK/MAP kinase was also activated in rhEpo-treated Schwann cells; this response was blocked by pharmacologic antagonism of JAK-2. RhEpo promoted Schwann cell proliferation, as determined by BrdU incorporation. Cell proliferation was ERK/MAP kinase-dependent. These results support a model in which Schwann cells are a major target for Epo in injured peripheral nerves, perhaps within the context of an autocrine signaling pathway. EpoR-induced cell signaling and Schwann cell proliferation may protect injured peripheral nerves and promote regeneration.
Mechanism of Stabilization of Helical Conformations of Polypeptides by Water Containing Trifluoroethanol (1996)

For conjugates Ac-Hel1-Alan-OH, n = 1−6, of the previously characterized reporting, conformational template Ac-Hel1, increases in helicity induced by trifluoroethanol (TFE) in water have been related to a simple function of the peptide length n, yielding the helix propagation constant sAla, which increases from 1.0 to 1.5 for χTFE = 0−20 mol %. The per-residue helicity increase is similar to the increase in te state stability induced by TFE in monoamide conjugates Ac-Hel1-NHR. Addition of TFE to water significantly increases the rate of interconversion of s-cis/s-trans amide conformers for Ac-Pro-NHMe, consistent with a significant and selective destabilization of the planar resonance-stabilized amide. In dilute aqueous solution TFE increases helicity by selectively destabilizing amide functions that are solvent exposed, with the consequence that compact conformations such as helices that maximize intramolecular amide−amide hydrogen bonding and minimize amide solvent exposure are selectively favored.
Improving the DLS Workflow (2012)

Abstract In this paper, we describe improved hardware to connect a semiconductor tester or applications board to a laser scanning microscope (LSM) for performing dynamic laser stimulation (DLS). The hardware, called DXGlue, simplifies the DLS workflow and enables new applications. We describe its precise monitoring of the fail rate and fail mode, its use for time resolved DLS and the enabling of long test loops with short laser dwell times.