gebhart/patrepeval huggingface dataset:
The relaxing protein system of striated muscle. Resolution of the troponin complex into inhibitory and calcium ion-sensitizing factors and their relationship to tropomyosin (1969)

1. A method involving isoelectric precipitation and chromatography on SE-Sephadex (sulphoethyl-Sephadex) is described for the preparation of the troponin complex free of tropomyosin from low-ionic-strength extracts of natural actomyosin and myofibrils. 2. Purified troponin complex required tropomyosin to inhibit the Mg(2+)-stimulated adenosine triphosphatase activity and superprecipitation of desensitized actomyosin in the presence of ethanedioxybis(ethylamine)tetra-acetate. An upper limit of 35000 for the ;molecular weight' of the troponin complex was derived from the amounts required to bring about 50% of the maximum inhibition of the Mg(2+)-stimulated adenosine triphosphatase activity of desensitized actomyosin of known concentration. 3. In the presence of dissociating reagents the troponin complex could be dissociated into inhibitory and Ca(2+)-sensitizing factors, which could be isolated separately on SE-Sephadex. The inhibitory factor inhibited the Mg(2+)-stimulated adenosine triphosphatase activity and superprecipitation of desensitized actomyosin independently of the concentration of free Ca(2+) in the medium. 4. The Ca(2+)-sensitizing factor changed its electrophoretic mobility on polyacrylamide gel in the presence of ethanedioxybis(ethylamine)tetra-acetate. It formed a complex with the inhibitory factor at low ionic strength and the original biological activity of the troponin complex could be restored on mixing the inhibitory factor with the Ca(2+)-sensitizing factor in the ratio of about 3:2. 5. Evidence is presented indicating that the ability of tropomyosin preparations to restore relaxing-protein-system activity to the troponin complex and their inhibitory effect on the Ca(2+)-stimulated adenosine triphosphatase activity of desensitized actomyosin are two properties of different stability to preparative procedures and tryptic digestion. This suggests that the relaxing protein system of muscle may contain another as yet uncharacterized component.
Interaction between grapefruit juice and midazolam in humans* (1995)

Pretreatment with grapefruit juice is associated with increased bioavailability and changes in the pharmacodynamics of midazolam that may be clinically important, particularly in patients with other causes for increased midazolam bioavailability such as advanced age, cirrhosis of the liver, and administration of other inhibitors of cytochrome P450.
Pharmacotherapy of chronic kidney disease and mineral bone disorder (2011)

The individual-based use of phosphate binders, vitamin D and calcimimetics, separately or in combination, constitute a reasonable approach to treat CKD-MBD. These treatments aim to achieve a rigorous control of phosphorus and parathormone levels, while avoiding calcium overload.
Efficacy of the glucagon-like peptide-1 agonist exenatide in the treatment of short bowel syndrome (2011)

Exenatide is a novel and safe treatment option for SBS. It produced substantial improvement in the bowel habits, nutritional status and quality of life of SBS patients. Successful treatment with exenatide may significantly reduce the need for parenteral nutrition and small bowel transplant.
Human skin cells support thymus-independent T cell development (2005)

Thymic tissue has previously been considered a requirement for the generation of a functional and diverse population of human T cells. We report that fibroblasts and keratinocytes from human skin arrayed on a synthetic 3-dimensional matrix support the development of functional human T cells from hematopoietic precursor cells in the absence of thymic tissue. Newly generated T cells contained T cell receptor excision circles, possessed a diverse T cell repertoire, and were functionally mature and tolerant to self MHC, indicating successful completion of positive and negative selection. Skin cell cultures expressed the AIRE, Foxn1, and Hoxa3 transcription factors and a panel of autoantigens. Skin and bone marrow biopsies can thus be used to generate de novo functional and diverse T cell populations for potential therapeutic use in immunosuppressed patients.
Mesoscopic Structural Heterogeneities in Room-Temperature Ionic Liquids (2011)

Ionic liquids represent an exciting novel class of materials with potentially enormous applicative impact; they are proposed as environmentally responsible replacements for the noxious volatile organic solvents, as smart separation and catalysis media, or to develop electrochemical devices, just to mention a few examples. Recently, compelling experimental as well as computational evidence highlighted the complexity of RTIL morphology at the mesoscopic spatial scale, as compared to traditional molecular liquids. In this Perspective, we report on our current understanding on the nature of structural heterogeneities in ionic liquids, describing new experimental data supporting a microphase segregation structural model for these systems and proposing topics for further study.
Percutaneous CT-guided biopsy of osseous lesion of the spine in patients with known or suspected malignancy. (2004)

CTGSB of osseous spinal lesions is an important tool in the workup of patients with known or suspected underlying neoplastic disease. However, a negative result must be confirmed with either close follow-up or, preferably, open biopsy, especially in cases of sclerotic lesions for which diagnostic accuracy is decreased and the false-negative rate is high.
Inhibition of cell growth mediated by plasmids encoding p53 anti-sense. (1987)

p53 is an oncogene product which has been shown to be directly involved in malignant transformation. Furthermore, it has been proposed that this protein plays an essential role in the control of cell proliferation. In the present study, we investigated the involvement of p53 in growth regulation of cells by employing anti-sense RNA methodology to inhibit p53 expression. Transfection with p53-specific constructs spanning the entire mRNA molecule or the 5' region of the gene led to reduced p53 protein synthesis. Clones derived from such transfected cells exhibited a slower rate of DNA synthesis, as assayed by incorporation of [3H]thymidine. In most cases, transfection of plasmids encoding anti-sense RNA eventually brought about the complete cessation of cell proliferation. No such effects were observed in L12 cells, which do not synthesize p53 and therefore do not depend on p53 expression for their growth, thus excluding the possibility of a non-specific toxic effect exerted by the anti-sense p53 RNA. These findings support the notion that p53 is essential for continuous cell proliferation.
Characterization of cellobiose fermentations to ethanol by yeasts (1983)

Twenty-two different yeasts were screened for their ability to ferment both glucose and cellobiose. The fermentation characteristics of Candida lusitaniae (NRRL Y-5394) and C. wickerhamii (NRRL Y-2563) were selected for further study because their initial rate of ethanol production from cellobiose was faster than the other test cultures. C. lusitaniae produced 44 g/L ethanol from 90 g/L cellobiose after 5-7 days. When higher carbohydrate concentrations were employed, fermentation ceased when the ethanol concentration reached 45-60 g/L. C. lusitaniae exhibited barely detectable levels of beta-glucosidase, even though the culture actively fermented cellobiose. C. wickerhamii produced ethanol from cellobiose at a rate equivalent to C. lusitaniae; however, once the ethanol concentration reached 20 g/L, fermentation ceased. Using p-nitrophenyl-beta-D-glucopyranoside (pNPG) as substrate, beta-glucosidase (3-5 U/mL) was detected when C. wickerhamii was grown anaerobically on glucose or cellobiose. About 35% of the beta-glucosidase activity was excreted into the medium. The cell-associated activity was highest against pNPG and salicin. Approximately 100-fold less activity was detected with cellobiose as substrate. When empolying these organisms in a simultaneous saccharification-fermentation of avicel, using Trichoderma reesei cellulase as the saccharifying agent, 10-30% more ethanol was produced by the two yeasts capable of fermenting cellobiose than by the control, Saccharomyces cerevisiae.
Hexamethyldisilazane-Mediated Controlled Polymerization of α-Amino AcidN-Carboxyanhydrides (2007)

Ring-opening polymerizations of α-amino acid N-carboxyanhydrides (NCAs) initiated with amines typically form polypeptides with uncontrolled molecular weights and broad molecular weight distributions. However, we found that hexamethyldisilazane (HMDS)-mediated controlled NCA polymerizations gave polypeptides with predictable molecular weights and narrow molecular weight distributions. Using MS, NMR, and FT-IR, we demonstrated that the initiation step involved the cleavage of the N−Si bond of HMDS and the formation of a trimethylsilyl carbamate (TMS-CBM) terminal group. Polypeptide chains were propagated through the migration of TMS of the TMS-CBM end group to the incoming monomer and formed a new TMS-CBM terminal group. This organosilicon reagent mediated NCA polymerization offers a metal-free strategy for the convenient synthesis of homo- or block polypeptides with predictable molecular weights and narrow molecular weight distributions.
STAT3 noncell-autonomously controls planar cell polarity during zebrafish convergence and extension (2004)

Zebrafish signal transducer and activator of transcription 3 (STAT3) controls the cell movements during gastrulation. Here, we show that noncell-autonomous activity of STAT3 signaling in gastrula organizer cells controls the polarity of neighboring cells through Dishevelled-RhoA signaling in the Wnt-planar cell polarity (Wnt-PCP) pathway. In STAT3-depleted embryos, although all the known molecules in the Wnt-PCP pathway were expressed normally, the RhoA activity in lateral mesendodermal cells was down-regulated, resulting in severe cell polarization defects in convergence and extension movements identical to Strabismus-depleted embryos. Cell-autonomous activation of Wnt-PCP signaling by DeltaN-dishevelled rescued the defect in cell elongation, but not the orientation of lateral mesendodermal cells in STAT3-depleted embryos. The defect in the orientation could be rescued by transplantation of shield cells having noncell-autonomous activity of STAT3 signaling. These results suggest that the cells undergoing convergence and extension movement may sense the gradient of signaling molecules, which are expressed in gastrula organizer by STAT3 and noncell-autonomously activate PCP signaling in neighboring cells during zebrafish gastrulation.
Activation of KATP channels by H2S in rat insulin‐secreting cells and the underlying mechanisms (2005)

H2S is an important gasotransmitter, generated in mammalian cells from L-cysteine metabolism. As it stimulates K(ATP) channels in vascular smooth muscle cells, H2S may also function as an endogenous opener of K(ATP) channels in INS-1E cells, an insulin-secreting cell line. In the present study, K(ATP) channel currents in INS-1E cells were recorded using the whole-cell and single-channel recording configurations of the patch-clamp technique. K(ATP) channels in INS-1E cells have a single-channel conductance of 78 pS. These channels were activated by diazoxide and inhibited by gliclazide. ATP (3 mm) in the pipette solution inhibited K(ATP) channels in INS-1E cells. Significant amount of H2S was produced from INS-1E cells in which the expression of cystathinonie gamma-lyase (CSE) was confirmed. After INS-1E cells were transfected with CSE-targeted short interfering RNA (CSE-siRNA) or treated with DL-propargylglycine (PPG; 1-5 mm) to inhibit CSE, endogenous production of H2S was abolished. Increase in extracellular glucose concentration significantly decreased endogenous production of H2S in INS-1E cells, and increased insulin secretion. After transfection of INS-1E cells with adenovirus containing the CSE gene (Ad-CSE) to overexpress CSE, high glucose-stimulated insulin secretion was virtually abolished. Basal K(ATP) channel currents were significantly reduced after incubating INS-1E cells with a high glucose concentration (16 mm) or lowering endogenous H2S level by CSE-siRNA transfection. Under these conditions, exogenously applied H2S significantly increased whole-cell K(ATP) channel currents at concentrations equal to or lower than 100 microm. H2S (100 microm) markedly increased open probability by more than 2-fold of single K(ATP) channels (inside-out recording) in native INS-1E cells (n = 4, P < 0.05). Single-channel conductance and ATP sensitivity of K(ATP) channels were not changed by H2S. In conclusion, endogenous H2S production from INS-1E cells varies with in vivo conditions, which significantly affects insulin secretion from INS-1E cells. H2S stimulates K(ATP) channels in INS-1E cells, independent of activation of cytosolic second messengers, which may underlie H2S-inhibited insulin secretion from these cells. Interaction among H2S, glucose and the K(ATP) channel may constitute an important and novel mechanism for the fine control of insulin secretion from pancreatic beta-cells.
CD38 is functionally dependent on the TCR/CD3 complex in human T cells (1998)

One of the functions of surface CD38 is the induction of phosphorylation of discrete cytoplasmic substrates and mobilization of cytoplasmic calcium (Ca2+). The present work addresses the issue of whether the signaling mediated via CD38 operates through an independent pathway or, alternatively, is linked to the TCR/CD3 signaling machinery. We studied the signals elicited through CD38 by the specific agonistic IB4 monoclonal antibody (mAb) by monitoring the levels of cytoplasmic Ca2+ and the induced phenotypic and functional variations in T cell growth. IB4 mAb presented the unique ability to increase cytoplasmic Ca2+ levels, which correlated with the phosphorylation of the PLC-gamma1. These effects were blocked by phorbol 12-myristate 13-acetate (PMA) and were dependent on the presence of a functional TCR/CD3 surface complex, no effects being recorded on mutant Jurkat cells lacking part of the CD3 structures. CD38 signaling appeared to share with TCR/CD3 the ability to induce apoptotic cell death in Jurkat T cells, an event paralleled by specific up-regulation of the Fas molecule and inhibited by cyclosporin A. CD28, a costimulatory molecule, is synergized by increasing CD38-induced apoptotic cell death. The results indicate the existence of a strong functional interdependence between CD38 and TCR/CD3.
Efficient embedded memory testing with APG (2003)

This paper describes the unique hardware features designed in a traditional hardware Algorithmic Pattern Generator (APG) to make full functional Direct Access Testing (DAT) of embedded memories with different data widths easier in a high volume production environment. The APG support software enables the encapsulation of pattern design for various sizes of embedded memories or arrays to significantly reduce the pattern complexity and generation effort.
Bombolitins, a new class of mast cell degranulating peptides from the venom of the bumblebee Megabombus pennsylvanicus. (1985)

Five structurally related heptadecapeptides rich in hydrophobic amino acids have been discovered in the venom of the bumblebee Megabombus pennsylvanicus. We have named them bombolitin I (Ile-Lys-Ile-Thr-Thr-Met-Leu-Ala-Lys-Leu-Gly-Lys-Val-Leu-Ala-His-Val-NH2 ), bombolitin II (Ser-Lys-Ile-Thr-Asp-Ile-Leu-Ala-Lys-Leu-Gly-Lys-Val-Leu-Ala-His-Val-NH2 ), bombolitin III (Ile-Lys-Ile-Met-Asp-Ile-Leu-Ala-Lys-Leu-Gly-Lys-Val-Leu-Ala-His-Val-NH2 ), bombolitin IV (Ile-Asn-Ile-Lys-Asp-Ile-Leu-Ala-Lys-Leu-Val-Lys-Val-Leu-Gly-His-Val-NH2 ), and bombolitin V (Ile-Asn-Val-Leu-Gly-Ile-Leu-Gly-Leu-Leu-Gly-Lys-Ala-Leu-Ser-His-Leu-NH2 ). Bombolitins are structurally and functionally very similar. They lyse erythrocytes and liposomes, release histamine from rat peritoneal mast cells, and stimulate phospholipase A2 from different sources. The threshold dose is 0.5-2.5 micrograms/ml depending on the peptide and the bioassay. Bombolitin V is as potent as the well-known melittin in lysing guinea pig erythrocytes (ED50 = 0.7 microgram/ml = 4 X 10(-7) M) and is 5 times more potent than mastoparan in causing mast cell degranulation, making it one of the most potent degranulating peptides discovered so far (ED50 = 2 micrograms/ml = 1.2 X 10(-6) M). The bombolitins represent a unique structural class of peptides but they have the same biological properties as melittin (from honeybees), mastoparan (wasps, hornets, and yellow jackets), and crabrolin (European hornets). This unusual circumstance (peptides with different amino acid sequences having the same biological properties) may be a manifestion of their amphiphilic nature, a property these peptides have in common.
Gating properties of acetylcholine receptors at developing rat endplates (1985)

The gating properties of acetylcholine receptors (AChRs) change during the development of rat soleus endplates. During the first 3 weeks after birth, the apparent mean channel open time (tau) decreases severalfold and the single-channel conductance (gamma) increases 50%. To better understand this phenomenon, we used a combination of noise analysis, analysis of miniature endplate currents (MEPCs), and single-channel recordings to quantify the relative levels of fast and slow AChR activity at developing soleus endplates. When the same endplates were studied with both noise analysis and MEPC analysis, results obtained with the two techniques were strongly correlated, but MEPC analysis yielded higher estimates of the relative amount of slow channel activity. Experiments designed to examine the distribution of fast and slow channels gave no evidence for a gradient of either channel type within individual endplates; rather, fast and slow channels appeared to be mixed together. However, the relative amount of fast and slow channel activity did vary markedly among different endplates within individual muscles. In agreement with earlier studies, we found a progressive decrease in the relative amount of slow channel activity during the first 3 weeks after birth. However, our data indicate that this process begins sooner than reported previously and takes longer to complete. Some of the same endplates that were studied physiologically were also examined in the electron microscope to test the hypothesis that changes in AChR gating might be related to ultrastructural changes such as the formation of folds. The physiological and ultrastructural results were essentially uncorrelated.
Ricin Poisoning (2005)

Health care workers and public health officials should consider ricin poisoning in patients with gastrointestinal or respiratory tract illness in the setting a credible threat. Poison control centers and public health authorities should be notified of any known illness associated with ricin exposure.
Challenges and opportunities for non-antibody scaffold drugs (2015)

The first candidates from the promising class of small non-antibody protein scaffolds are now moving into clinical development and practice. Challenges remain, and scaffolds will need to be further tailored toward applications where they provide real advantages over established therapeutics to succeed in a rapidly evolving drug development landscape.
Molecular Modeling, Synthesis, and Biological Evaluation of Macrocyclic Calpain Inhibitors (2009)

The design and elaboration of a series of macrocyclic templates that exhibit a propensity to adopt a beta-strand-like peptide-backbone conformation led to potent and selective inhibitors of calpain 2. Macrocycle 1 retarded calcium-induced opacification in an ovine-lens culture assay and is a lead compound for the development of a drug for cataract treatment. Cbz=carbobenzyloxy.
28. rAAV2/9 Mediated Gene Delivery of Acid α-Glucosidase Corrects the Cardiac Phenotype in a Mouse Model of Pompe Disease (2006)

The long term goal of this project is to develop a clinically relevant gene therapy approach for the treatment of Pompe Disease. Pompe Disease is a form of muscular dystrophy and metabolic myopathy caused by mutations in the acid alpha glucosidase (GAA) gene. An insufficient amount of GAA leads to the accumulation of glycogen in lysosomes and consequent cellular dysfunction. Cardio-respiratory failure typically occurs in the early onset patients within the first year of life. We have characterized the cardiac phenotype in our mouse model (gaa-/-) at various ages. Through ECG analysis we observe a shortened PR interval by 3 months of age (gaa-/-33.41±1.35ms, cont 44.95±1.58ms) mimicking the conduction phenotype in the human Pompe population. Abnormal amounts of glycogen are observed in lysosomes as demonstrated by the periodic acid shift (PAS) stain. MRI analysis shows a decrease in stroke volume (SV)(gaa-/-36.13±1.19ul, cont 51.84±3.59ul) and a decrease in cardiac output (CO)(gaa-/-7.95±0.26ml/min, cont 11.40±0.79ml/ min) at 3 months and an increase in mass (gaa-/-181.99±10.7mg, cont 140.79±5.12mg) by 12 months. This model of cardiac dysfunction is being used to develop a cardiac gene delivery technique which can be applied to many genetically inherited cardiomyopathies. Previously, we have shown that intra-venous (IV) delivery of recombinant adeno-associated virus type 1 (rAAV2/1) pseudotype capsid carrying the CMV-hgaa construct to 1 day old gaa-/- neonates restores GAA activity in mice. Also, LacZ transgene delivery using the IV administration route and rAAV2/9 pseudotype capsid resulted in 200 fold higher levels of expression in cardiac tissue than rAAV2/1. Additional experiments showed transduction following delivery to adults. We have now combined rAAV2/9 with the clinically relevant IV administration route in order to deliver the human GAA (hgaa) gene to gaa-/- mice. Neonates treated with rAAV2/9-CMV-hgaa at a range of doses (4×105vg 4×108vg 4×1010vg) have demonstrated sustained PR interval correction (39.38±2.42 ms). PAS stains as well as NMR analysis have shown less glycogen accumulation in cardiac tissue of treated gaa-/- mice as compared to untreated mice. MRI analysis shows an increase in SV and CO. Adult gaa-/- mice have also been treated using this strategy and are being assessed in order to determine if we have the ability to reverse the effects of Pompe Disease in mice already presenting the cardiac phenotype. While the focus of this project is on correction of the cardiac phenotype of Pompe Disease, our systemic delivery route, use of the CMV promoter and the fact that GAA is a secreted enzyme all promote correction throughout the body. GAA activity is observed in other tissues of treated mice including skeletal muscles and liver. These studies have demonstrated the ability of rAAV2/9 to be administered systemically using the IV delivery route, transcend the vasculature, transduce tissues throughout the body and ultimately prevent presentation of the cardiac phenotypes of Pompe Disease.
Evolution of subsurface hydrogen from boron-doped Si(100) (1997)

The reactions of atomic hydrogen with boron-doped Si(100) were studied using temperature programmed desorption (TPD). In addition to adsorbing at surface sites, hydrogen penetrates into boron-doped Si(100) samples and gets trapped by forming subsurface boron–hydrogen complexes. H2-TPD spectra, taken after exposure to atomic hydrogen, showed, in addition to the well known dihydride (680 K) and monohydride (795 K) desorption features, two peaks at 600 and 630 K due to decomposition of subsurface boron–hydrogen complexes. Increasing total hydrogen uptake with increasing dosing temperature (1.7 ML at 300 K, 4.2 ML at 500 K), suggests an activation barrier for subsurface hydrogen uptake. A quantitative correlation between boron concentration and subsurface hydrogen uptake is shown.