gebhart/patrepeval huggingface dataset:
Preconditioning of isolated rabbit cardiomyocytes: induction by metabolic stress and blockade by the adenosine antagonist SPT and calphostin C, a protein kinase C inhibitor (1994)

Glucose-free preincubation protects ischaemic isolated myocytes from subsequent ischaemia. The degree of protection is great enough to account for protection seen in intact hearts, following preconditioning protocols. Protection is blocked by SPT and a highly specific protein kinase C inhibitor, calphostin C. Protection from ischaemic injury that seems to mimic ischaemic preconditioning can be induced in isolated cardiomyocytes, and appears dependent on adenosine receptors and activation of protein kinase C.
Evolution of genotypic and phenotypic resistance to Enfuvirtide in HIV‐infected patients experiencing prolonged virologic failure (2004)

Four heavily antiretroviral-experienced HIV-infected patients had significant plasma HIV-RNA reductions (>1 log) after beginning an Enfuvirtide (ENF)-based rescue regimen. However, all had viral rebound shortly thereafter, sustaining high levels of plasma viremia over 80 weeks. These patients developed rapidly genotypic and phenotypic resistance to ENF. Mutations within the HR1 env region were selected (N43D in three and G36V/D in one), resulting in high-level phenotypic resistance to ENF. Interestingly, two patients had a sustained CD4+ T-cell increase and two maintained stable CD4+ T-cell counts despite virologic failure under ENF. The possible mechanisms involved in this response were examined. Changes in virus tropism from R5 to R5/X4 were observed in two patients, in parallel with increases in ENF phenotypic resistance. Low levels of T-cell activation, T-cell turnover, and cytotoxic T lymphocyte (CTL) activity were found in all four patients. An overall increase in the proportion of viruses released from cells of the macrophage lineage was observed. In summary, single mutations at the HR1 env region result in significant loss of susceptibility to ENF. Despite virologic failure, these patients may maintain elevated CD4+ counts through a reduction in their overall immune activation.
Perception of Brassinosteroids by the Extracellular Domain of the Receptor Kinase BRI1 (2000)

An assay was developed to study plant receptor kinase activation and signaling mechanisms. The extracellular leucine-rich repeat (LRR) and transmembrane domains of the Arabidopsis receptor kinase BRI1, which is implicated in brassinosteroid signaling, were fused to the serine/threonine kinase domain of XA21, the rice disease resistance receptor. The chimeric receptor initiates plant defense responses in rice cells upon treatment with brassinosteroids. These results, which indicate that the extracellular domain of BRI1 perceives brassinosteroids, suggest a general signaling mechanism for the LRR receptor kinases of plants. This system should allow the discovery of ligands for the LRR kinases, the largest group of plant receptor kinases.
Penis Transplantation (2017)

We have shown that it is feasible to perform penile transplantation with excellent results. Furthermore, this experience demonstrates that penile transplantation can be successfully performed with conventional immunosuppression. We propose that our successful penile transplantation pilot experience represents a proof of concept for an evolution in reconstructive transplantation.
Pulsus Paradoxus: An Objective Measure of Severity in Croup (1998)

We used a noninvasive monitor of arterial pressure to determine the utility of pulsus paradoxus (PP) as an objective severity measure in croup. We performed a prospective, blinded comparison of PP in children with croup versus healthy control subjects, analyzed the relationship between PP and Westley croup score (WCS), and observed the effect of racemic epinephrine (RE) on PP and WCS in a subgroup of patients with severe croup. The PP and WCS were measured at presentation and in severe patients after treatment with RE. Mean PP was 6.1 +/- 1.8 (SD) mm Hg (n = 29) in control subjects compared with a mean of 17.8 +/- 11.2 (SD) mm Hg (n = 28) in patients with croup (p < 0.00001). There was significant concordance between baseline WCS and PP (Spearman's rho: 0.68; p = 0.0001). The mean decrease in PP after RE was 7.5 +/- 11.8 (SD) mm Hg (p = 0.05; n = 12). The magnitude of decrease in PP after RE has significant concordance with the concurrent decrease in WCS (Spearman's rho: 0.73; p < 0.007). PP is elevated in children with croup, and the magnitude of elevation correlates with severity as measured by the WCS. PP may have utility as a research tool to objectively measure the severity of upper airway obstruction in croup.
Plasmid transformation by electroporation of Leuconostoc paramesenteroides and its use in molecular cloning (1989)

In this report, we demonstrate the utility of electroporation as an efficient method for genetic transformation of Leuconostoc paramesenteroides. We optimized several factors which determine the transformation frequency, resulting in transformation efficiencies of up to 4 x 10(3) transformants per micrograms of pNZ12 DNA, which contains the promiscuous Lactococcus lactis pSH71 replicon. Slightly lower efficiencies were obtained with a deletion derivative of the broad-host-range plasmid pAM beta 1. These plasmids could be stably maintained in L. paramesenteroides NZ6009 for more than 100 generations, even in the absence of selective pressure. In order to show the use of the developed host-vector system, we cloned the Lactococcus lactis gene encoding phospho-beta-galactosidase in L. paramesenteroides. Expression of this heterologous gene in L. paramesenteroides under control of Lactococcus lactis expression signals was evident from the presence, in transformants, of phospho-beta-galactosidase activity and a specific phospho-beta-galactosidase protein band on Western blots (immunoblots). In addition, we transformed a lactose-deficient derivative of L. paramesenteroides with a plasmid carrying a Lactococcus lactis-Escherichia coli lacZ gene fusion. The resulting transformants synthesized high levels of beta-galactosidase, indicating the efficiency of heterologous gene expression signals in L. paramesenteroides.
Patient-Controlled Analgesia (2005)

One of the most common methods for providing postoperative analgesia is via patient-controlled analgesia (PCA). Although the typical approach is to administer opioids via a programmable infusion pump, other drugs and other modes of administration are available. This article reviews the history and practice of many aspects of PCA and provides extensive guidelines for the practice of PCA-administered opioids. In addition, potential adverse effects and recommendations for their monitoring and treatment are reviewed.
Effects of pH and Ca2+ on Heterodimer and Heterotetramer Formation by Chromogranin A and Chromogranin B (1996)

The two major proteins of the secretory vesicles of neuroendocrine cells, chromogranin A (CGA) and chromogranin B (CGB), have been shown to undergo pH- and Ca2+-dependent conformational changes and aggregation and have been suggested to play essential roles during secretory vesicle biogenesis in the trans-Golgi network. CGA has been shown to exist primarily in a tetrameric state at pH 5.5 and primarily in a dimeric state at pH 7.5, and CGB has been shown to exist in a monomeric state at both pH 5.5 and pH 7.5. Using purified CGA and CGB, it recently has been shown that CGA interacts with CGB at pH 5.5 (Yoo, S. H.(1996) J. Biol. Chem. 271, 1558-1565). In expanding this investigation, we have studied the temperature dependence of the pH-dependent interaction of CGA and CGB by analytical ultracentrifugation and found that two molecules of CGA bound to two molecules of CGB at pH 5.5 with DeltaG0 values of -43.6 kcal/mol in the absence of Ca2+ at 37 degrees C and -40.3 kcal/mol in the presence of 0.1 mM Ca2+. However, one molecule of CGA bound to one molecule of CGB at pH 7.5 with DeltaG0 values of -13.6 kcal/mol in the absence of Ca2+ at 37 degrees C. The magnitude of DeltaG0 values increased with increasing temperatures at both pH values. However, the values for enthalpy and entropy changes decreased with increasing temperatures in both pH levels, suggesting formation of more ordered structures. In the absence of Ca2+ at pH 5. 5, the heterotetramerization reaction at 37 degrees C was entropically driven, whereas in the presence of Ca2+ (0.1 mM) the heterotetramerization was virtually an enthalpic reaction. On the other hand, the heterodimer formation in the absence of Ca2+ at pH 7. 5 showed large negative enthalpy and entropy changes at 37 degrees C, indicating an enthalpic interaction compensated by entropic changes. In view of the interaction of tetrameric CGA with tetrameric inositol 1,4,5-trisphosphate (IP3) receptor and the existence of heterotetrameric IP3 receptor in the cell, the heterotetramer formation by CGA and CGB not only raises the possibility of interaction between the heterotetrameric chromogranin and heterotetrameric IP3 receptor but also appears to reflect their important roles in the cell.
Microassembly technologies for MEMS (1998)

Microassembly promises to extend MEMS beyond the confines of silicon micromachining. This paper surveys research in both serial and parallel microassembly. The former extends conventional `pick and place' assembly into the micro- domain, where surface forces play a dominant role. Parallel assembly involves the simultaneous precise organization of an ensemble of micro components. This can be achieved by microstructure transfer between aligned wafers or arrays of binding sites that trap an initially random collection of parts. Binding sites can be micromachined cavities or electrostatic traps: short-range attractive forces and random agitation of the parts serve to fill the sites. Microassembly strategies should furnish reliable mechanical bonds and electrical interconnection between the micropart and the target substrate or subassembly.
Learning Deep Representations of Fine-Grained Visual Descriptions (2016)

State-of-the-art methods for zero-shot visual recognition formulate learning as a joint embedding problem of images and side information. In these formulations the current best complement to visual features are attributes: manuallyencoded vectors describing shared characteristics among categories. Despite good performance, attributes have limitations: (1) finer-grained recognition requires commensurately more attributes, and (2) attributes do not provide a natural language interface. We propose to overcome these limitations by training neural language models from scratch, i.e. without pre-training and only consuming words and characters. Our proposed models train end-to-end to align with the fine-grained and category-specific content of images. Natural language provides a flexible and compact way of encoding only the salient visual aspects for distinguishing categories. By training on raw text, our model can do inference on raw text as well, providing humans a familiar mode both for annotation and retrieval. Our model achieves strong performance on zero-shot text-based image retrieval and significantly outperforms the attribute-based state-of-the-art for zero-shot classification on the Caltech-UCSD Birds 200-2011 dataset.
Expression and regulation of erythrocyte auto‐antibodies in mice following immunization with rat erythrocytes (1989)

Mice immunized with intact rat red blood cells (RBC) developed serum auto-antibodies (some of which were mouse specific) to the RBC membrane components spectrin and antigens of 100 and 81 kDa as shown by Western blotting and enzyme-linked immunosorbent assay as well as RBC surface-bound autoantibodies detected by the Coombs' test. In order to discover whether these autoantibodies were induced and controlled in similar or different ways, mice were challenged with a variety of rat and mouse RBC preparations. In addition, the ability of recipients given spleen cells from the above donors to generate autoantibody responses to intact rat RBC was measured. It was found that all the autoantibodies were induced in mice challenged with rat RBC ghosts but none following immunization with butanol-extracted rat RBC ghosts or intact mouse RBC. By contrast, mice injected with mouse RBC ghosts made autoantibodies to spectrin and to the 100-kDa band. Spleen cells from mice primed with intact rat RBC, rat RBC ghosts or butanol-extracted rat RBC ghosts curtailed Coombs' autoantibody production of recipient mice challenged with intact rat RBC. Serum from recipients of spleen cells primed with intact rat RBC or the butanol extract generally failed to react with rat or mouse spectrin or with the 81-kDa band, although antibody was detected to the rat 100-kDa band. Recipients of rat RBC ghost-primed spleen cells produced antibody to rat and mouse spectrin and to rat 100-kDa band but not to mouse 100-kDa or rat or mouse 81-kDa bands. Occasionally, suppression of antibody to the rat-specific 38-kDa band was observed in recipients of intact rat RBC-primed spleen cells. It is therefore suggested that regulation of cross-reactive and mouse-specific autoantibodies as well as rat-specific antibodies occurs in an independent, determinant-specific manner.
Genetic therapies for cystic fibrosis lung disease (2011)

The aim of gene therapy for cystic fibrosis (CF) lung disease is to efficiently and safely express the CF transmembrane conductance regulator (CFTR) in the appropriate pulmonary cell types. Although CF patients experience multi-organ disease, the chronic bacterial lung infections and associated inflammation are the primary cause of shortened life expectancy. Gene transfer-based therapeutic approaches are feasible, in part, because the airway epithelium is directly accessible by aerosol delivery or instillation. Improvements in standard delivery vectors and the development of novel vectors, as well as emerging technologies and new animal models, are propelling exciting new research forward. Here, we review recent developments that are advancing this field of investigation.
A Novel Human Cancer Vaccine Elicits Cellular Responses to the Tumor-Associated Antigen, Human Chorionic Gonadotropin β (2004)

Although other hCG vaccines have been shown to be capable of eliciting antibody responses to hCGbeta, this is the first time that cellular immune responses to hCGbeta have been induced by a vaccine in a human system. This DC-targeted hCGbeta vaccine holds promise for the management of a number of cancers and merits additional clinical development.
Characterization of the expression of the hepatitis C virus F protein (2003)

Hepatitis C virus (HCV) is an important human pathogen that affects 170 million people worldwide. The HCV genome is approximately 9.6 kb in length and encodes a polyprotein that is proteolytically cleaved to generate at least 10 mature viral protein products. Recently, a new protein, named F, has been described to be expressed through a ribosomal frameshift within the capsid-encoding sequence, a mechanism unique among members of the family Flavidiridae: Here, expression of the F protein was investigated in an in vitro transcription/translation assay. Its expression in mammalian cells was confirmed using specific recombinant vaccinia viruses; under these conditions, protein expression is dependent on the HCV IRES. The F protein was tagged with firefly luciferase or the Myc epitope to facilitate its identification. Ribosomal frameshifting was dependent on the presence of mutations in the capsid-encoding sequence. No frameshifting was detected in the absence of any mutation. Furthermore, analysis of the F protein in time-course experiments revealed that the protein is very unstable and that its production can be stabilized by the proteasome inhibitor MG132. Finally, indirect immunofluorescence studies have localized the F protein in the cytoplasm, with notable perinuclear detection.
NMR Solution Structure of α-Conotoxin ImI and Comparison to Other Conotoxins Specific for Neuronal Nicotinic Acetylcholine Receptors, (1999)

Alpha-Conotoxins, peptides produced by predatory species of Conus marine snails, are potent antagonists of nicotinic acetylcholine receptors (nAChRs), ligand-gated ion channels involved in synaptic transmission. We determined the NMR solution structure of the smallest known alpha-conotoxin, ImI, a 12 amino acid peptide that binds specifically to neuronal alpha7-containing nAChRs in mammals. Calculation of the structure was based on a total of 80 upper distance constraints and 31 dihedral angle constraints resulting in 20 representative conformers with an average pairwise rmsd of 0.44 A from the mean structure for the backbone atoms N, Calpha, and C' of residues 2-11. The structure of ImI is characterized by two compact loops, defined by two disulfide bridges, which form distinct subdomains separated by a deep cleft. Two short 310-helical regions in the first loop are followed by a C-terminal beta-turn in the second. The two disulfide bridges and Ala 9 form a rigid hydrophobic core, orienting the other amino acid side chains toward the surface. Comparison of the three-dimensional structure of ImI to those of the larger, 16 amino acid alpha-conotoxins PnIA, PnIB, MII, and EpI-also specific for neuronal nAChRs-reveals remarkable similarity in local backbone conformations and relative solvent-accessible surface areas. The core scaffold is conserved in all five conotoxins, whereas the residues in solvent-exposed positions are highly variable. The second helical region, and the specific amino acids that the helix exposes to solvent, may be particularly important for binding and selectivity. This comparative analysis provides a three-dimensional structural basis for interpretation of mutagenesis data and structure-activity relationships for ImI as well other neuronal alpha-conotoxins.
Huntington’s Disease Does Not Appear to Increase the Risk of Diabetes Mellitus (2009)

Huntington's disease (HD) is an autosomal, dominantly inherited, neurodegenerative disorder characterised by neurological, cognitive and psychiatric symptoms. HD has been associated with diabetes mellitus, which is, to some extent, supported by studies in transgenic HD mice. In transgenic mice, the severity of the diabetic phenotype appears to correlate with the length of a polyglutamine expansion in the protein huntingtin. In the present study, we investigated the association between diabetes mellitus and HD by performing an oral glucose-tolerance test (OGTT) to evaluate the glucose-tolerance status and OGTT-related insulin release in 14 HD patients. Furthermore, we expressed N-terminal huntingtin fragments with different polyglutamine lengths in an insulinoma-cell line (INS-1E) to investigate how mutant huntingtin influences glucose-stimulated insulin release in vitro. We found no difference between a group of early- and middle-stage HD patients and a large group of control individuals in any of the assessed variables. However, the glucose-stimulated induction of insulin release was significantly reduced in the insulinoma-cell line expressing highly expanded huntingtin compared to cells expressing huntingtin with modestly elongated polyglutamine stretches. These data indicate that insulin release from beta-cells expressing mutant huntingtin appears to be polyglutamine length-dependent, and that polyglutamine lengths within the range normally found in adult onset HD do not influence insulin release. This challenges the assumption of an increased risk of diabetes among HD patients, although our results do not exclude a changed glucose tolerance in end-stage HD patients or in patients with juvenile onset HD. It also raises the question of which extent transgenic mice models reflect the pathology of human HD in this regard.
Are Pruritus and Scratching the Cough of the Skin? (2007)

Pruritus is not the equivalent of the cough of the skin, but itch and scratch can certainly be defined as such. In physiological conditions, they share the same function: to exclude a foreign body. Itch/scratching and cough could be selective responses for the same diseases, mainly atopic diseases, and their pathophysiology is similar (role of C fibers and mast cells; role of histamine, substance P and tachykinins). This is an intriguing analogy rather than a pathophysiological identity. It may be inappropriate for many disease settings. Itch and cough can be triggered or enhanced by stress. This similarity is very interesting because it could give rise to many new research ideas.
Fully homomorphic encryption using ideal lattices (2009)

We propose a fully homomorphic encryption scheme -- i.e., a scheme that allows one to evaluate circuits over encrypted data without being able to decrypt. Our solution comes in three steps. First, we provide a general result -- that, to construct an encryption scheme that permits evaluation of arbitrary circuits, it suffices to construct an encryption scheme that can evaluate (slightly augmented versions of) its own decryption circuit; we call a scheme that can evaluate its (augmented) decryption circuit bootstrappable.
100-GHz Transistors from Wafer-Scale Epitaxial Graphene (2010)

The high carrier mobility of graphene has been exploited in field-effect transistors that operate at high frequencies. Transistors were fabricated on epitaxial graphene synthesized on the silicon face of a silicon carbide wafer, achieving a cutoff frequency of 100 gigahertz for a gate length of 240 nanometers. The high-frequency performance of these epitaxial graphene transistors exceeds that of state-of-the-art silicon transistors of the same gate length.
Quantifying Chemical Structure and Machine‐Learned Atomic Energies in Amorphous and Liquid Silicon (2019)

Abstract Amorphous materials are being described by increasingly powerful computer simulations, but new approaches are still needed to fully understand their intricate atomic structures. Here, we show how machine‐learning‐based techniques can give new, quantitative chemical insight into the atomic‐scale structure of amorphous silicon ( a ‐Si). We combine a quantitative description of the nearest‐ and next‐nearest‐neighbor structure with a quantitative description of local stability. The analysis is applied to an ensemble of a ‐Si networks in which we tailor the degree of ordering by varying the quench rates down to 10 10 K s −1 . Our approach associates coordination defects in a ‐Si with distinct stability regions and it has also been applied to liquid Si, where it traces a clear‐cut transition in local energies during vitrification. The method is straightforward and inexpensive to apply, and therefore expected to have more general significance for developing a quantitative understanding of liquid and amorphous states of matter.
FOXP3+ regulatory T cells: Current controversies and future perspectives (2006)

Regulatory T cells (Treg) provide protection from autoimmune disease, graft-versus-host disease, transplant rejection and overwhelming tissue destruction during infections. Conversely, high Treg numbers enable cancer cells to evade the host immune response. Thus, Treg are seen as an important tool to manipulate the immune response. However, as the immunological community is trying to move this knowledge from mice to humans, contradictory results regarding the number and function of Treg in various diseases are appearing. This problem arises because we cannot clearly define Treg populations on the basis of expression of CD25 and other cell surface markers in humans. This review addresses the utility of the FOXP3 forkhead transcription factor for the identification of Treg populations and summarizes recent data on the expression of FOXP3 in lymphomas. It is crucial to really understand Treg biology before attempting therapies, including (i) the injection of expanded Treg to cure autoimmune disease or prevent graft-versus-host disease or (ii) the depletion or inhibition of Treg in cancer therapy. For instance, new data arising from the study of haematological malignancies highlight the additional complexity of systems where malignant cell populations may also be direct Treg targets.