gebhart/patrepeval huggingface dataset:
Cloning of the Chromosome Breakpoint of Neoplastic B Cells with the t(14;18) Chromosome Translocation (1984)

From an acute B-cell leukemia cell line, a DNA probe was obtained that was specific for chromosome 18 and flanked the heavy chain joining region of the immunoglobulin heavy chain locus on chromosome 14. This probe detected rearrangement of the homologous DNA segment in the leukemic cells and in follicular lymphoma cells with the t(14:18) chromosome translocation but not in other neoplastic or normal B or T cells. The probe appears to identify bcl-2, a gene locus on chromosome 18 (band q21) that is unrelated to known oncogenes and may be important in the pathogenesis of B-cell neoplasms with this translocation.
Flexible Silver Nanowire Meshes for High-Efficiency Microtextured Organic-Silicon Hybrid Photovoltaics (2012)

Hybrid organic-silicon heterojunction solar cells promise a significant reduction on fabrication costs by avoiding energy-intensive processes. However, their scalability remains challenging without a low-cost transparent electrode. In this work, we present solution-processed silver-nanowire meshes that uniformly cover the microtextured surface of hybrid heterojunction solar cells to enable efficient carrier collection for large device area. We systematically compare the characteristics and device performance with long and short nanowires with an average length/diameter of 30 μm/115 nm and 15 μm/45 nm, respectively, to those with silver metal grids. A remarkable power conversion efficiency of 10.1% is achieved with a device area of 1 × 1 cm(2) under 100 mW/cm(2) of AM1.5G illumination for the hybrid solar cells employing long wires, which represents an enhancement factor of up to 36.5% compared to the metal grid counterpart. The high-quality nanowire network displays an excellent spatial uniformity of photocurrent generation via distributed nanowire meshes and low dependence on efficient charge transport under a high light-injection condition with increased device area. The capability of silver nanowires as flexible transparent electrodes presents a great opportunity to accelerate the mass deployment of high-efficiency hybrid silicon photovoltaics via simple and rapid soluble processes.
Characterization and biologic properties of 5,12-dihydroxy derivatives of eicosapentaenoic acid, including leukotriene B5 and the double lipoxygenase product. (1984)

Leukotriene B5 (LTB5) and three stereoisomers were prepared biosynthetically from eicosapentaenoic acid and compared with the analogous derivatives of arachidonic acid for their chemotactic and aggregating effects on human neutrophilic polymorphonuclear leukocytes. Leukotriene B4 (LTB4), LTB5, and the 6-trans-diastereoisomers of each were generated by activating polymorphonuclear leukocytes with the calcium ionophore A23187 in the presence of 14C-labeled and unlabeled arachidonic acid or 14C-labeled and unlabeled eicosapentaenoic acid, respectively. The double lipoxygenase products, (5S,12S)-6-trans-8-cis-LTB4 and (5S,12S)-6-trans-8-cis-LTB5, were generated from 5S-hydroxyeicosatetraenoic acid and racemic 5-hydroxyeicosapentaenoic acid intermediates by incubation with platelet sonicates. The products of each reaction were isolated by reverse-phase-high performance liquid chromatography and identified by their retention times relative to the appropriate totally synthetic standards, ultraviolet absorption spectra, immunoreactivity in a radioimmunoassay for LTB4, and, for all but the double lipoxygenase products, by incorporation of radiolabel from the specific polyunsaturated fatty acid source. When the concentration of LTB5 eliciting maximum chemotactic response of human polymorphonuclear leukocytes, 50 ng/ml (1.5 X 10(-7) M), and that eliciting a maximum aggregation response, 20 ng/ml (5.9 X 10(-8) M), were compared with the interpolated values of LTB4 eliciting comparable effects, the potency of LTB5 relative to LTB4 was approximately 1:8 as a chemotactic agent and about 1:20 as an aggregating agent. The double lipoxygenase products and the resolved 6-trans-diastereoisomers of the pentaene and tetraene series were about 2 logs less active as chemotactic factors than LTB4 and only (5S,12S)-6-trans-8-cis-LTB4 had even minimal aggregating activity.
Treatment With Streptococcal Preparation (OK-432) Suppresses Anti-Islet Autoimmunity and Prevents Diabetes in BB Rats (1988)

We have recently shown that a streptococcal preparation (OK-432) inhibits insulitis and prevents diabetes in nonobese diabetic (NOD) mice, an animal model of insulin-dependent diabetes mellitus (IDDM). We extended this study to another model of IDDM, namely BB rats. Male and female BB rats were injected weekly with 0.2 mg OK-432 i.p. starting from 5 to 6 wk and continuing through 20 or 30 wk of age. The cumulative incidence of IDDM over 20 wk in the OK-432-treated BB rats (4 of 54, 7.4%) was significantly (P less than .01) lower than that found in the nontreated BB rats (13 of 47, 27.7%). We examined some of these rats as follows. All of the OK-432-treated BB rats tested showed normal glucose levels before and after oral glucose administrations, as did the nontreated and nondiabetic BB rats. Histological examination of pancreatic sections revealed that the OK-432-treated rats retained a greater number of intact islets without infiltration of the mononuclear cells than did the nontreated BB rats. A preliminary in vitro study further demonstrated that the cytotoxic activities of spleen cells against a rat insulinoma cell line, RIN, were suppressed in the OK-432-treated rat. However, the treatment of BB rats with OK-432 showed no suppressive effects in the spleen cell number, the responsiveness of spleen cells to concanavalin A, the populations of OX19+, W3/25+, and OX8+ peripheral blood lymphocytes, or in the titers of cell surface antibody against RIN. These results suggest that a nonimmunosuppressive immunomodulator such as OK-432 may be useful as an agent for immunotherapy of IDDM.
Engineering Approaches to Energy Balance and Obesity: Opportunities for Novel Collaborations and Research (2007)

Energy balance disorders account for a large public health burden. The obesity epidemic in particular is one of the most rapidly evolving public health problems of our day. At present, two-thirds of American adults and one-sixth of American children and adolescents are considered either overweight or obese. Public health concern about obesity is high because of the increased risk and increased mortality of cardiovascular disease, Type 2 diabetes, many forms of cancer, gallbladder disease, and osteoarthritis. These risks increase with the severity of the obesity. Excess adipose tissue, representing fat storage, ultimately derives from an imbalance between energy intake and energy expenditure. Conversely, undesirable and inadvertent loss of body weight and muscle mass, as seen in aging and cachectic states of chronic diseases such as heart failure and cancer, have serious clinical and functional consequences without satisfactory clinical or behavioral solutions. Innovative engineering technologies could help to address unresolved problems in energy balance, intake, and expenditure. Novel sensors, devices, imaging technologies, nanotechnologies, biomaterials, technologies to detect biochemical markers of energy balance, mathematical modeling, systems biology, and other approaches could be developed, evaluated, and leveraged through multidisciplinary collaborations. Engineers, physical scientists, and mathematicians can work with scientists from other relevant disciplines who possess expertise in obesity and nutrition. Furthermore, the possibility of re-engineering the "built environment" to encourage higher levels of physical activity has been suggested as another promising and important approach to which engineers can contribute (see http://www.obesityresearch.nih.gov). Ultimately, systematic application of the "Engineering Approach" can help in developing the needed technologies and tools to facilitate research and eventually support therapeutic advances and behavioral change. This article summarizes important public health concerns related to disordered energy balance and describes research priorities identified at a recent National Science Foundation-National Institutes of Health workshop. Research funding opportunities are described as posted on the NIH Guide to Grants and Contracts (see http://www.nih.gov/grants/guide).
Femtosecond cellular transfection using a nondiffracting light beam (2007)

The ability to permeate selectively the cell membrane and introduce therapeutic agents is a key goal in cell biology. Optical transfection is a powerful methodology but requires exact focusing due to the required two-photon power density. The authors use a Bessel beam that obviates the need to locate precisely the cell membrane, permitting two-photon excitation along a line leading to cell transfection. Assuming a minimum efficiency of 20%, the Bessel beam offers transfection at axial distances 20 times greater than that of its Gaussian equivalent. Furthermore, the authors demonstrate cell transfection beyond obstacles due to the self-healing nature of the Bessel beam.
Adenovirus Targeting to Prostate-Specific Membrane Antigen through Virus-Displayed, Semirandom Peptide Library Screening (2010)

The convergence of phage-displayed peptide libraries and recombinant viral vectors launched a promising new direction in targeted viral gene therapeutics, but the translation of targeting peptides to functional cancer therapeutic agents has been challenging. Here, we report progress in developing a successful strategy to optimize targeted viral infection through adenovirus-displayed, semirandom peptide libraries. A phage-derived peptide targeting the prostate-specific membrane antigen (PSMA) was genetically incorporated into the adenoviral capsid Fiber protein and flanked by random peptide cassettes. The resulting adenovirus library was biopanned against PSMA-expressing cells and tumors to identify a PSMA-retargeted adenovirus. While the initial peptide alone could not target viral infection, the selected virus preferentially infects PSMA-expressing cells through the targeting peptide and infects LNCaP tumors after intravenous injection. Our results indicate that virus-displayed, semirandom peptide libraries can be used to optimize targeting infection. This approach represents a novel principle for developing targeted agents in a variety of disease models.
A Single-Point Mutation in the Extreme Heat- and Pressure-Resistant Sso7d Protein from Sulfolobus solfataricus Leads to a Major Rearrangement of the Hydrophobic Core, (1999)

Sso7d is a basic 7-kDa DNA-binding protein from Sulfolobus solfataricus, also endowed with ribonuclease activity. The protein consists of a double-stranded antiparallel beta-sheet, onto which an orthogonal triple-stranded antiparallel beta-sheet is packed, and of a small helical stretch at the C-terminus. Furthermore, the two beta-sheets enclose an aromatic cluster displaying a fishbone geometry. We previously cloned the Sso7d-encoding gene, expressed it in Escherichia coli, and produced several single-point mutants, either of residues located in the hydrophobic core or of Trp23, which is exposed to the solvent and plays a major role in DNA binding. The mutation F31A was dramatically destabilizing, with a loss in thermo- and piezostabilities by at least 27 K and 10 kbar, respectively. Here, we report the solution structure of the F31A mutant, which was determined by NMR spectroscopy using 744 distance constraints obtained from analysis of multidimensional spectra in conjunction with simulated annealing protocols. The most remarkable finding is the change in orientation of the Trp23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. This prevents the formation of a cavity in the hydrophobic core of the mutant, which would arise in the absence of structural rearrangements. We found additional changes produced by the mutation, notably a strong distortion in the beta-sheets with loss in several hydrogen bonds, increased flexibility of some stretches of the backbone, and some local strains. On one hand, these features may justify the dramatic destabilization provoked by the mutation; on the other hand, they highlight the crucial role of the hydrophobic core in protein stability. To the best of our knowledge, no similar rearrangement has been so far described as a result of a single-point mutation.
Hyperhomocysteinemia and Retinal Vascular Occlusive Disease (2002)

High plasma homocysteine is a risk factor for retinal vascular occlusive disease so it may be useful to measure homocysteine in the management of these patients. A randomized, controlled trial is required to study the effect of lowering with homocysteine folic acid and other B vitamins on the risk of recurrent vascular occlusion in the same eye or its development in the fellow eye.
Rule Induction by EDA with Instance-Subpopulations (2009)

In this paper, a new rule induction method by using EDA with instance-subpopulations is proposed. The proposed method introduces a notion of instance-subpopulation, where a set of individuals matching a training instance. Then, EDA procedure is separately carried out for each instance-subpopulation. Individuals generated by each EDA procedure are merged to constitute the population at the next generation. We examined the proposed method on Breast-cancer in Wisconsin and Chess End-Game. The comparisons with other algorithms show the effectiveness of the proposed method.
Hematopoietic stem cell expansion and generation: the ways to make a breakthrough (2015)

Hematopoietic stem cell transplantation (HSCT) is the first field where human stem cell therapy was successful. Flooding interest on human stem cell therapy to cure previously incurable diseases is largely indebted to HSCT success. Allogeneic HSCT has been an important modality to cure various diseases including hematologic malignancies, various non-malignant hematologic diseases, primary immunodeficiency diseases, and inborn errors of metabolism, while autologous HSCT is generally performed to rescue bone marrow aplasia following high-dose chemotherapy for solid tumors or multiple myeloma. Recently, HSCs are also spotlighted in the field of regenerative medicine for the amelioration of symptoms caused by neurodegenerative diseases, heart diseases, and others. Although the demand for HSCs has been growing, their supply often fails to meet the demand of the patients needing transplant due to a lack of histocompatible donors or a limited cell number. This review focuses on the generation and large-scale expansion of HSCs, which might overcome current limitations in the application of HSCs for clinical use. Furthermore, current proof of concept to replenish hematological homeostasis from non-hematological origin will be covered.
A mixed prototype waveform/CELP coder for sub 3 kbit/s (1993)

CELP (code-excited linear prediction) analysis-by-synthesis speech coders do not make a distinction between voiced and unvoiced speech frames. For sub-3 kbit/s coding it is necessary to separate unvoiced and voiced frames and code-voiced speech using an inherently periodic scheme. The authors address these problems by using a prototype waveform coder for voiced frames while retaining a CELP algorithm for unvoiced frames. For voiced speech a single residual prototype is selected to represent a section of 25 ms. Prototypes are interpolated across the frame to provide a smooth evolution of amplitude and harmonic content. Two coding schemes for the prototypes are discussed: a pitch harmonic scheme operating in the DFT (discrete Fourier transform) domain and an impulsive codebook time-domain technique. Unvoiced frames are coded using a standard CELP architecture excluding the adaptive codebook search. The overall bit rate using either of the voiced frame coding algorithms is shown to be sub-3 kbit/s for good communications quality speech.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recognition Sequence Design for Peptidyl Modulators of β-Amyloid Aggregation and Toxicity (1999)

beta-Amyloid (Abeta), the primary protein component of Alzheimer's plaques, is neurotoxic when aggregated into fibrils. We have devised a modular strategy for generating compounds that inhibit Abeta toxicity, based on linking a recognition element for Abeta to a disrupting element designed to interfere with Abeta aggregation. One such compound, with the 15-25 sequence of Abeta as the recognition element and a lysine hexamer as the disrupting element, altered Abeta aggregation kinetics and protected cells from Abeta toxicity [Ghanta et al. (1996) J. Biol. Chem. 271, 29525]. To optimize the recognition element, peptides of 4-8 residues composed of overlapping sequences within the 15-25 domain were synthesized, along with hybrid compounds containing those recognition sequences coupled to a lysine hexamer. None of the recognition peptides altered Abeta aggregation kinetics and only two, KLVFF and KLVF, had any protective effect against Abeta toxicity. The hybrid peptide KLVFF-KKKKKK dramatically altered Abeta aggregation kinetics and aggregate morphology and provided significantly improved protection against Abeta toxicity compared to the recognition peptide alone. In contrast, FAEDVG-KKKKKK possessed only modest inhibitory activity and had no marked effect on Abeta aggregation. The scrambled sequence VLFKF was nearly as effective a recognition domain as KLVFF, suggesting the hydrophobic characteristics of the recognition sequence are critical. None of the cytoprotective peptides prevented Abeta aggregation; rather, they increased aggregate size and altered aggregate morphology. These results suggest that coupling recognition with disrupting elements is an effective generalizable strategy for the creation of Abeta inhibitors. Significantly, prevention of Abeta aggregation may not be required for prevention of toxicity.
Recent Advances in the Polymerase Chain Reaction (1991)

The polymerase chain reaction (PCR) has dramatically altered how molecular studies are conducted as well as what questions can be asked. In addition to simplifying molecular tasks typically carried out with the use of recombinant DNA technology, PCR has allowed a spectrum of advances ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences. PCR can provide insights into the intricacies of single cells as well as the evolution of species. Some recent developments in instrumentation, methodology, and applications of the PCR are presented in this review.
The plasminogen activation system in melanoma cell lines and in melanocytic lesions (1996)

A large body of evidence suggests a role for the proteolytic plasminogen activation system in invasion and metastatic spread of tumor cells including melanoma cells. Plasminogen activation by human melanoma cell lines and B16 mouse melanoma cell lines has been extensively studied. Apart from expression of urokinase-type plasminogen activator, melanoma cells differ from cells derived from other tumors in the abundant expression of tissue-type plasminogen activator. The possible role of both types of plasminogen activator in metastatic spread of melanoma cells is discussed. In recent years the localization of mRNAs and proteins of the plasminogen activation system and of related proteins in cutaneous melanocytic tumor progression has been well documented. A possible mechanism for migration of melanoma cells in vivo is suggested.
FPGA performance versus cell granularity (2002)

An experimental approach was used to investigate the relationship between the performance of an FPGA (field-programmable gate array) and its basic cell granularity. Over a large set of design examples it was found that a four or five input cell achieves minimum average critical path delay for a wide range of programmable switch time constant, tau /sub s/. As expected, the 'optimal' cell granularity was found to increase gradually as tau /sub s/ increases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to serine (Pro)enzymes: A comparative thermodynamic study (1991)

The binding of the recombinant proteinase inhibitor eglin c from the leech Hirudo medicinalis to serine (pro)enzymes belonging to the chymotrypsin and subtilisin families has been investigated from the thermodynamic viewpoint, between pH 4.5 and 9.5 and from 10 degrees C to 40 degrees C. The affinity of eglin c for the serine (pro)enzymes considered shows the following trend: Leu-proteinase [the leucine specific serine proteinase from spinach (Spinacia oleracea L.) leaves] greater than human leucocyte elastase congruent to human cathepsin G congruent to subtilisin Carlsberg congruent to bovine alpha-chymotrypsin greater than bovine alpha-chymotrypsinogen A congruent to porcine pancreatic elastase congruent to bovine beta-trypsin. The serine (pro)enzyme-inhibitor complex formation is an entropy-driven process. On increasing the pH from 4.5 to 9.5, the affinity of eglin c for the serine (pro)enzymes considered increases thus reflecting the acid pK shift of the invariant hystidyl catalytic residue from approximately to 6.9 in the free serine proteinases and bovine alpha-chymotrypsinogen A to congruent to 5.1 in the serine (pro)enzyme-inhibitor complexes. Considering the known molecular models, the observed binding behaviour of eglin c was related to the inferred stereochemistry of the serine (pro)enzyme-inhibitor contact regions.
Use of 8-methoxypsoralen and long-wavelength ultraviolet radiation for decontamination of platelet concentrates (1989)

Transmission of viral diseases through blood products remains an unsolved problem in transfusion medicine. We have developed a psoralen photochemical system for decontamination of platelet concentrates in which platelets are treated with long wavelength ultraviolet radiation (UVA, 320–400 nm) in the presence of 8-methoxypsoralen (8-MOP). Bacteria, RNA viruses, and DNA viruses ranging in genome size from 1.2 x 10(6) daltons, encompassing the size range of human pathogens, were inoculated into platelet concentrates and subjected to treatment. This system inactivated 25 to 30 logs/h of bacteria Escherichia coli or Staphylococcus aureus, 6 logs/h of bacteriophage fd, 0.9 log/h of bacteriophage R17 and 1.1 logs/h of feline leukemia virus (FeLV) in platelet concentrates maintained in standard storage bags. Platelet integrity and in vitro function before, immediately following photochemical treatment, and during prolonged storage after treatment, were evaluated by measuring: (1) extracellular pH; (2) platelet yields; (3) extracellular lactate dehydrogenase (LDH) levels; (4) platelet morphology; (5) platelet aggregation responsiveness; (6) thromboxane beta-2 (TXB-2) production; (7) dense body secretion; and (8) alpha granule secretion. These assays demonstrated that this photochemical inactivation system inactivated bacteria and viruses in platelet concentrates with minimal adverse effects on the in vitro function of platelets in comparison to untreated control concentrates maintained under current, standard blood bank conditions.
Optical-Diffraction-Based Modulation Of Photoresist Profile For Microlithography Applications (1989)

A novel method for obtaining a tapered profile in photoresist is proposed. On the mask near the main features we add some slits smaller than the resolution limit of the projection optics at a distance also smaller than the resolution limit. In such a way, a controlled sloped profile can be obtained. We have applied this method to open tapered contacts and vias (contacts between two levels of metal) without using the thermal reflow technique of borophos-phosilicate glass, optimizing the configuration of the subresolved slits by means of a simplified mathematical model. There is experimental evidence that contacts can still be opened up to the diffraction limit of the projection optics.