gebhart/patrepeval huggingface dataset:
Macro-based hardware compilation of Java/sup TM/ bytecodes into a dynamic reconfigurable computing system (2003)

This paper presents a new approach to synthesize to reconfigurable hardware (HW) user-specified regions of a program, under the assumption of "virtual HW" support. The automation of this approach is supported by a compiler front-end and by an HW compiler under development. The front-end starts from the Java bytecodes and, therefore, supports any language that can be compiled to the JVM (Java Virtual Machine) model. It extracts from the bytecodes all the dependencies inside and between basic blocks. This information is stored in representation graphs more suitable to efficiently exploit the existent parallelism in the program than those typically used in high-level synthesis. From the intermediate representations the HW compiler exploits the temporal partitions at the behavior level, resolves memory access conflicts, and generates the VHDL descriptions at register-transfer level that will be mapped into the reconfigurable HW devices.
SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis. (1996)

Gibberellins (GAs) are a major class of plant hormones that control many developmental processes, including seed development and germination, flower and fruit development, and flowering time. Genetic studies with Arabidopsis thaliana have identified two genes involved in GA perception or signal transduction. A semidominant mutation at the GIBBERELLIN INSENSITIVE (GAI) locus results in plants resembling GA-deficient mutants but exhibiting reduced sensitivity to GA. Recessive mutations at the SPINDLY (SPY) locus cause a phenotype that is consistent with constitutive activation of GA signal transduction. Here we show that a strong allele of spy is completely epistatic to gai, indicating that SPY acts downstream of GAI. We have cloned the SPY gene and shown that it encodes a new type of signal transduction protein, which contains a tetratricopeptide repeat region, likely serving as a protein interaction domain, and a novel C-terminal region. Mutations in both domains increase GA signal transduction. The presence of a similar gene in Caenorhabditis elegans suggests that SPY represents a class of signal transduction proteins that is present throughout the eukaryotes.
Unidirectional Alignment of CdSe Nanorods (2003)

Cadmium selenide nanorods, unique nanostructures which possess bright and up to 100% polarized photoluminescence, now can be arranged unidirectionally in a single line. The method is based on the chemical attachment of nanorods to the surface of a single cleaved semiconductor nanolayer and exploits a combination of wet-chemical and epitaxial growth techniques to produce templated semiconductor nanostructures. The nanotemplate here is a ZnS layer with a thickness less than the diameter of the nanorods. Binding the nanorods to the template, the limited space provokes an enhanced alignment of the rods along the ZnS layer which can be proved by the high polarization degree of the nanorods emission.
PEGylation of Antibody Fragments for Half-Life Extension (2012)

Antibody fragments (Fab’s) represent important structure for creating new therapeutics. Compared to full antibodies Fab’ fragments possess certain advantages, including higher mobility and tissue penetration, ability to bind antigen monovalently and lack of fragment crystallizable (Fc) region-mediated functions such as antibody-dependent cell mediated cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC). The main drawback for the use of Fab’s in clinical applications is associated with their short half-life in vivo, which is a consequence of no longer having the Fc region. To exert meaningful clinical effects, the half-life of Fab’s need to be extended, which has been achieved by postproduction chemical attachment of polyethylene glycol (PEG) chain to protein using PEGylation technology. The most suitable approach employs PEG-maleimide attachment to cysteines, either to the free hinge cysteine or to C-terminal cysteines involved in interchain disulfide linkage of the heavy and light chain. Hence, protocols for mono-PEGylation of Fab via free cysteine in the hinge region and di-PEGylation of Fab via interchain disulfide bridge are provided in this chapter.
Immunotherapy for Recalcitrant Warts in Children Using Intralesional Mumps or Candida Antigens (2003)

Intralesional injection of mumps and Candida skin test antigens has been shown to be effective in the treatment of warts. Warts are generally difficult to treat in children. To determine the efficacy of intralesional skin test antigen injection for the treatment of resistant warts in children, we treated 47 pediatric patients with one or more warts with intralesional injection of mumps or Candida skin test antigen into one wart. Twenty-two patients (47%) with resistant warts experienced complete resolution of treated warts. An average of 3.78 treatments were necessary. An additional 34% of children had a greater than 25% improvement in their warts. Sixty-eight percent of subjects with more than one wart also noted at least partial resolution (greater than 25% resolution) of untreated warts at distant sites, with 34% experiencing complete resolution. We concluded that intralesional injection of skin test antigens is an effective therapy for children who have recalcitrant, nongenital, cutaneous warts.
A direct binding assay for rheumatoid factor serum antiglobulins using fluorescein-labelled Fc fragment of human immunoglobulin-G. (1978)

A simple routine method is described for the quantitation of antiglobulin (rheumatoid factor) in human serum irrespective of its immunoglobulin class. Papain Fc fragment of human IgG is labelled with fluorescein isothiocyanate and incubated with the serum. Bound Fc is separated from free Fc by precipitation with polyethylene glycol and measured by the fluorescence of the precipitate. Results are expressed as a percentage of the binding obtained with a normal pool serum. About 60% of seronegative rheumatoid sera and 96% of seropositive rheumatoid sera gave results more than 2SD above the mean value for normal sera. Only 17% of osteoarthritis sera gave positive results by the same criterion. A relationship is also deduced to show that if the test is carried out at a number of Fc concentrations a double reciprocal plot of bound Fc against free Fc enables both the total antiglobulin and the ratio of binding constants of antiglobulin for Fc and for IgG to be calculated. This ratio is approximately unity. Under the standard conditions the results correspond to a measurement of approximately 30% of the total antiglobulins present.
Controllable Orientation of the Peptide-Based Surfactant at Air-Water Interface (1997)

Abstract A polypeptide-based amphiphile, poly(γ-methyl l-glutamate)-polyethyleneglycol block copolymer (PMG-PEG), formed a stable monolayer membrane at the air-water interface. The orientation of the α-helical amphiphile in the membrane was shown to be strongly dependent on the surface pressure.
Human papillomavirus detection by hybrid capture and its possible clinical use. (1994)

AIMS--To determine the sensitivity of the hybrid capture method for human papillomavirus (HPV) detection and potential clinical uses as a screening method for the identification of cervical intraepithelial neoplasia. METHODS--The presence of oncogenic types of HPV was tested for in samples taken from the cervix at colposcopy, and compared with detection by polymerase chain reaction (PCR) in 60 patients. Both sets of results were corrected with the pathology determined by biopsy and smear cytology. RESULTS--Hybrid capture detection showed 86% agreement with PCR. Eighty three percent of CIN 3 lesions, 62% of CIN 2, 59% of CIN 1 and 21% of normal controls were positive for oncogenic HPV types. CONCLUSION--The hybrid capture detection method is reliable, sensitive, and easy to use. The addition of HPV testing to cytological screening would detect a greater proportion of cervical dysplasia with a higher false positive rate.
Acute Phase Mediators Modulate Thrombin-activable Fibrinolysis Inhibitor (TAFI) Gene Expression in HepG2 Cells (2003)

Thrombin-activable fibrinolysis inhibitor (TAFI) has recently been identified as a positive acute phase protein in mice, an observation that may have important implications for the interaction of the coagulation, fibrinolytic, and inflammatory systems. Activated TAFI (TAFIa) inhibits fibrinolysis by removing the carboxyl-terminal lysines from partially degraded fibrin that are important for maximally efficient plasminogen activation. In addition, TAFIa has been shown to be capable of removing the carboxyl-terminal arginine residues from the anaphylatoxins and bradykinin, thus implying a role for the TAFI pathway in the vascular responses to inflammation. In the current study, we investigated the ability of acute phase mediators to modulate human TAFI gene expression in cultured human hepatoma (HepG2) cells. Surprisingly, we found that treatment of HepG2 cells with a combination of interleukin (IL)-1 and IL-6 suppressed endogenous TAFI mRNA abundance in HepG2 cells (~60% decrease), while treatment with IL-1 or IL-6 alone had no effect. Treatment with IL-1 and/or IL-6 had no effect on TAFI promoter activity as measured using a luciferase reporter plasmid containing the human TAFI 5'-flanking region, whereas treatment with IL-1 and IL-6 in combination, but not alone, decreased the stability of the endogenous TAFI mRNA. Treatment with the synthetic glucocorticoid dexamethasone resulted in a 2-fold increase of both TAFI mRNA levels and promoter activity. We identified a functional glucocorticoid response element (GRE) in the human TAFI promoter between nucleotides 92 and 78. The GRE was capable of binding the glucocorticoid receptor, as assessed by gel mobility shift assays, and mutation of this element markedly decreased the ability of the TAFI promoter to be activated by dexamethasone.
Three-dimensional optical tomography of hemodynamics in the human head (2001)

We report on the first three-dimensional, volumetric, tomographic localization of vascular reactivity in the brain. To this end we developed a model-based iterative image reconstruction scheme that employs adjoint differentiation methods to minimize the difference between measured and predicted data. The necessary human-head geometry and optode locations were determined with a photogrammetric method. To illustrate the performance of the technique, the three-dimensional distribution of changes in the concentration of oxyhemoglobin, deoxyhemoglobin, and total hemoglobin during a Valsalva maneuver were visualized. The observed results are consistent with previously reported effects concerning optical responses to hemodynamic perturbations.
The relation between solution association and surface activity of the hydrophobin HFBI from Trichoderma reesei (2007)

Hydrophobins are small fungal surface active proteins that self-assemble at interfaces into films with nanoscale structures. The hydrophobin HFBI from Trichoderma reesei has been shown to associate in solution into tetramers but the role of this association on the function of HFBI has remained unclear. We produced two HFBI variants that showed a significant shift in solution association equilibrium towards the tetramer state. However, this enhanced solution association did not alter the surface properties of the variant HFBIs. The results show that there is not a strong relationship between HFBI solution association state and surface properties such as surface activity.
Identification and characterization of novel low-temperature-inducible promoters of Escherichia coli (1992)

Escherichia coli promoters that are more active at low temperature (15 to 20 degrees C) than at 37 degrees C were identified by using the transposon Tn5-lac to generate promoter fusions expressing beta-galactosidase (beta-Gal). Tn5-lac insertions that resulted in low-temperature-regulated beta-Gal expression were isolated by selecting kanamycin-resistant mutants capable of growth on lactose minimal medium at 15 degrees C but which grew poorly at 37 degrees C on this medium. Seven independent mutants were selected for further studies. In one such strain, designated WQ11, a temperature shift from 37 degrees C to either 20 or 15 degrees C resulted in a 15- to 24-fold induction of beta-Gal expression. Extended growth at 20 or 15 degrees C resulted in 36- to 42-fold-higher beta-Gal expression over that of cells grown at 37 degrees C. Treatment of WQ11 with streptomycin, reported to induce a response similar to heat shock, failed to induce beta-Gal expression. In contrast, treatment with either chloramphenicol or tetracycline, which mimics a cold shock response, resulted in a fourfold induction of beta-Gal expression in strain WQ11. Hfr genetic mapping studies complemented by physical mapping indicated that in at least three mutants (WQ3, WQ6, and WQ11), Tn5-lac insertions mapped at unique sites where no known cold shock genes have been reported. The Tn5-lac insertions of these mutants mapped to 81, 12, and 34 min on the E. coli chromosome, respectively. The cold-inducible promoters from two of the mutants (WQ3 and WQ11) were cloned and sequenced, and their temperature regulation was examined. Comparison of the nucleotide sequences of these two promoters with the regulatory elements of other known cold shock genes identified the sequence CCAAT as a putative conserved motif.
Anticancer agents sensitize tumor cells to tumor necrosis factor-related apoptosis-inducing ligand-mediated caspase-8 activation and apoptosis. (2001)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a new cytokine that was proposed to specifically induce apoptosis of cancer cells. In tumor cells that are resistant to the cytokine, subtoxic concentrations of chemotherapeutic drugs can restore the response to TRAIL. The present study further explores the mechanisms that determine tumor cell sensitivity to TRAIL by comparing four human colon carcinoma cell lines We show that colon cancer cell sensitivity to TRAIL-induced apoptosis and cytotoxicity correlates with the expression of the death receptors TRAIL-R1 and TRAIL-R2 at the cell surface, as determined by now cytometry, whereas the two decoy receptors TRAIL-R3 and TRAIL-R4 can be detected only in permeabilized cells. Clinically relevant concentrations of cisplatin and doxorubicin sensitize the most resistant colon cancer cell lines to TRAIL-induced cell death without modifying the expression nor the localization of TRAIL receptors in these cells. TRAIL induces the activation of procaspase-8 and triggers caspase-dependent apoptosis off colon cancer cells. Cytotoxic drugs lower the signaling threshold required for TRAIL-induced procaspase-8 activation. In turn, caspase-8 cleaves Bid, a BH3 domain-containing proapoptotic molecule of the Bcl-2 family and activates effector caspases. Together, these data indicate that chemotherapeutic drugs sensitize colon tumor cells to TRAIL-mediated caspase-8 activation and apoptosis.
In Vivo Delivery of Morpholino Oligos by Cell-Penetrating Peptides (2013)

Morpholino oligos (Morpholinos) are widely used tools for knocking down gene expression and are currently in a clinical trial for treatment of Duchene muscular dystrophy. A Morpholino analog has been in a clinical trial as a potential anti-bioterrorism agent for inhibiting replication of deadly Marburg viral infection. The cellular uptake of Morpholinos can been greatly increased by conjugation with cell-penetrating peptides (CPP). The use of the CPP-Morpholino conjugates (PPMOs) in vivo has been broadly demonstrated in viral, bacterial, genetic and other diseases. The following aspects of PPMOs will be discussed in this paper including chemistry, stability, antisense specificity, mechanism of cellular uptake, in vivo efficacy, tissue distribution, pharmacokinetics, toxicity and the human clinical trials. PPMOs are powerful research tools for studying gene function in animals and their properties are being improved as potential human therapeutic agents.
A nonimmunogenic sarcoma transduced with the cDNA for interferon gamma elicits CD8+ T cells against the wild-type tumor: correlation with antigen presentation capability. (1992)

To be recognized by CD8+ T lymphocytes, target cells must process and present peptide antigens in the context of major histocompatibility complex (MHC) class I molecules. The nonimmunogenic, low class I-expressing, methylcholanthrene (MCA)-induced murine sarcoma cell line, MCA 101, is a poor presenter of endogenously generated viral antigens to specific CD8+ T lymphocytes and cannot be used to generate tumor infiltrating lymphocytes (TIL). Since interferon gamma (IFN-gamma) has been shown to upregulate three sets of molecules important for antigen processing and presentation, we retrovirally transduced wild-type MCA 101 (101.WT) tumor with the mIFN-gamma cDNA to create the 101.NAT cell line. Unlike 101.WT, some clones of retrovirally transduced 101.NAT tumor expressed high levels of class I, and could be used to generate CD8+ TIL. More importantly, these TIL were therapeutic in vivo against established pulmonary metastases from the wild-type tumor. Although not uniformly cytotoxic amongst several separate cultures, these TIL did specifically release cytokines (IFN-gamma and tumor necrosis factor-alpha) in response to 101.WT targets. 101.WT's antigen presentation deficit was also reversed by gene modification with mIFN-gamma cDNA. 101.NAT had a greatly improved capacity to present viral antigens to CD8+ cytotoxic T lymphocytes. These findings show that a nonimmunogenic tumor, incapable of generating a CD8+ T cell immune response, could be gene-modified to generate a therapeutically useful immune response against the wild-type tumor. This strategy may be useful in developing treatments for tumor histologies not thought to be susceptible to T cell-based immunotherapy.
A 1,7 code EEPR4 read channel IC with an analog noise whitened detector (2002)

Performance of a partial response (PR) channel is usually reduced by noise correlation. Noise whitening is used to halve the complexity of an analog 1,7 code EEPR4 look-ahead detector to achieve performance comparable to that of a full Viterbi detector. The 0.8 /spl mu/m BiCMOS chip is a fully integrated read/write channel IC that operates in excess of 300 MSample/s (200 Mb/s). The 16.4 mm/sup 2/ 0.8 /spl mu/m BiCMOS chip dissipates 1.3 W at 200 Mb/s.
Silica Modified PP Fiber for Improving Crack-Resistance of Cementitious Composites (2011)

To improve the interfacial bonding properties of polypropylene fiber-cement matrix, a new type of nano-silica modified polypropylene fibers was prepared by direct blend-spinning. As a comparison, Another polypropylene fiber was modified by surface chemical deposition of the silica particles by sol-gel method. The distribution of nano-particles on the fiber surface was observed with scanning electron microscope (SEM). This paper focuses on the effects on crack-resistance properties of fiber reinforced mortar(FRM) and present the mechanism of improving fiber-matrix interfacial properties, especially. The results demonstrate that the modified fiber with well-distributed of nano-silica has excellent mechanical properties, and crack resistance. The interfacial property of fiber-matrix is improved because of silica’s hydration activity. As the use of two kinds of modified fiber, the cementitious materials crack area is significantly decreased. In conclusion, the modified fiber by chemical deposition method which has slightly better overall performance.
The mRNAs encoding acidic FGF, basic FGF and FGF receptor are coordinately downregulated during myogenic differentiation (1991)

Acidic and basic fibroblast growth factors (FGFs) are members of a family of proteins that exert pleiotropic effects in a range of cell types including skeletal myocytes. Previous studies demonstrate that exogenously supplied FGFs stimulate proliferation of myoblasts and inhibit their differentiation in culture, but little information is available concerning endogenous expression of FGFs by skeletal myocytes. In this study acidic and basic FGF mRNAs were found to be expressed in murine and rat skeletal muscle, and expression was demonstrated to vary with the tissue and species examined. Myogenic cell lines were then analyzed to determine if FGFs are expressed in myoblasts, and if so, whether expression is regulated during myogenic differentiation. Murine Sol 8 and rat L6 myoblasts were found to express acidic and basic FGF mRNAs, and the expression of both growth factors was downregulated at the transcriptional level during myogenic differentiation. A decrease in expression of the mouse homologue of the human FGF receptor paralleled the decrease in acidic and basic FGF mRNAs in Sol 8 cells, indicating that the decrease in FGF receptor abundance previously observed during myogenic differentiation is regulated at the mRNA level. The results of this study suggest that a coordinate decrease in endogenously produced acidic and basic FGFs and their cognate receptor may participate in the regulation of myogenic differentiation. Furthermore, the observation that expression of a myogenic determination gene, myogenin, increases as FGF transcripts decline, together with previous data demonstrating suppression of myogenin expression by FGF, suggest a mechanism whereby endogenously produced FGFs may exert their effect on differentiation.
Getting more from the two-hybrid system: N-terminal fusions to LexA are efficient and sensitive baits for two-hybrid studies (1997)

Two-hybrid methods detect interactions between two proteins fused at the C-termini of, respectively, a DNA-binding domain and the activation domain of a transcriptional activator. Thus the N-terminus of none of these proteins is available for interaction. We have tested whether a bait protein with a reverted polarity (i.e. N-bait-LexA-C) is suitable for two-hybrid interaction. We show that such constructs give a specific interaction signal, and document two cases where the sensitivity is dramatically increased. Such constructs might lead to the identification of partners missed during classical two-hybrid screens.
Man-made quantum wells: A new perspective on the finite square-well problem (1984)

The observation of man-made quantum size effects is now possible due to advances in semiconductor technology. Interest in quantum-well heterostructures and superlattices has added a new dimension to both the application and perspective of the traditional discussion of a particle in a box. This paper addresses these new perspectives and presents in an elementary manner the techniques employed to model single and multiple square wells in semiconductors. A brief overview of semiconductor microlayer devices is followed by a discussion of the physics of quantum-well heterostructures. Since the behavior of these structures is described by the finite square well, a simple iterative technique to solve for the bound states of single or multiple (coupled) square wells is presented. The iterative technique is quite general and powerful, yet the physical ideas and the mathematics are straightforward and simple. Finally, computer simulation is employed to illustrate the interaction between multiple coupled wells; the results are compared with those obtained via the usual Kronig–Penney model.