gebhart/patrepeval huggingface dataset:
Study the effects of proton irradiation on GaAs/Ge solar cells (2010)

Proton energy dependence of radiation damage to GaAs/Ge solar cells irradiated by protons with various energies (50 keV, 200 keV, 1 MeV and 9.5 MeV) were analyzed by using PC1D simulation together with SRIM simulations to investigate their electrical properties. The degradation of the open-circuit voltage is highest for 50 keV irradiation and lowest for 9.5 MeV irradiation. According to SRIM simulations the above changes in electrical properties are mainly related to damage in different regions of the solar cells.
Lambda-Min Decoding Algorithm of Regular and Irregular LDPC Codes (2003)

In this paper, the decoding of low-density parity-check (LDPC) codes is considered. A new algorithm, named $\lambda-$Min algorithm, for updating extrinsic information is proposed. The $\lambda-$Min algorithm offers different trade-off performance versus complexity between the belief propagation (BP) algorithm (optimal but complex) and the universal most powerful (UMP) BP-based algorithm (simple but leading to significant performance degradation in some cases). Hardware implementation of the $\lambda-$Min algorithm in a serial mode is also discussed. Reduction up to 75 \% of the extrinsic memory information can be obtained with high rate LDPC code without any significant degradation of the performance.
Mitochondrial uncoupling as a target for drug development for the treatment of obesity (2001)

Mitochondrial proton cycling is responsible for a significant proportion of basal or standard metabolic rate, so further uncoupling of mitochondria may be a good way to increase energy expenditure and represents a good pharmacological target for the treatment of obesity. Uncoupling by 2,4-dinitrophenol has been used in this way in the past with notable success, and some of the effects of thyroid hormone treatment to induce weight loss may also be due to uncoupling. Diet can alter the pattern of phospholipid fatty acyl groups in the mitochondrial membrane, and this may be a route to uncoupling in vivo. Energy expenditure can be increased by stimulating the activity of uncoupling protein 1 (UCP1) in brown adipocytes either directly or through beta 3-adrenoceptor agonists. UCP2 in a number of tissues, UCP3 in skeletal muscle and the adenine nucleotide translocase have also been proposed as possible drug targets. Specific uncoupling of muscle or brown adipocyte mitochondria remains an attractive target for the development of antiobesity drugs.
The nociceptive flexion reflex in humans – review article (2002)

The nociceptive flexion reflex (NFR) is a physiological, polysynaptic reflex allowing for painful stimuli to activate an appropriate withdrawal response. NFR is easily measurable in clinical setting, and is a reliable and objective tool for measurement of an individual's pain experience. An exhaustive review of the literature, covering multiple search engines, indicates that the NFR method is valuable in studying the impact of diverse pharmacological and non-pharmacological interventions on the flexion reflex, in conditions of acute pain and in healthy volunteers. More recently, the NFR method has gained particular attention as a research tool in studies of central sensitization and persistent or chronic pain.
Activation of a CFTR-mediated chloride current in a rabbit corneal epithelial cell line. (2001)

In tRCE cells, there is gene expression and functional CFTR activity. Its presence may have important therapeutic implications in corneal epithelial diseases resulting from declines in transepithelial secretory and fluid transport activity.
PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes (2015)

Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS) can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS). This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.
Radiometal-Labeled Peptide−PNA Conjugates for Targeting bcl-2 Expression:  Preparation, Characterization, and in Vitro mRNA Binding (2002)

A new antisense peptide-peptide nucleic acid (peptide-PNA) conjugate, designed for targeting bcl-2 expression, has been radiolabeled, characterized, and evaluated for bcl-2 mRNA binding in a cell-free system. A PNA complementary to the first six codons of the bcl-2 gene was synthesized by standard solid-phase Fmoc chemistry and conjugated to a new derivative of 1,4,7,10-tetraazacyclododecane-N,N',N",N'"-tetraacetic acid (DOTA) that allows macrocyclic radiometal chelates to be incorporated into any sequence position of a peptide-PNA conjugate. The DOTA-PNA conjugate was then coupled to a membrane-permeating transduction peptide, PTD-4, designed for intracellular delivery of the radiolabeled PNA. The conjugate was characterized by HPLC and ESI-MS and labeled with (111)In and (90)Y to high specific activities (>1000 Ci/mmol) with high radiochemical purity. Northern blot analysis showed that (90)Y-PTD-4-K(DOTA)-anti-bcl-2-PNA bound specifically to as little as 50 fmol of bcl-2 mRNA, a result equivalent to that obtained with the analogous (32)P-labeled DNA antisense oligonucleotide. Thus, the mRNA targeting properties of (111)In- and (90)Y-PTD-4-K(DOTA)-anti-bcl-2-PNA demonstrate potential for diagnostic imaging and targeted radiotherapy applications in bcl-2-positive cancers.
Real-time interactive 3D manipulation of particles viewed in two orthogonal observation planes (2005)

The generalized phase contrast (GPC) method has been applied to transform a single TEM00 beam into a manifold of counterpropagating-beam traps capable of real-time interactive manipulation of multiple microparticles in three dimensions (3D). This paper reports on the use of low numerical aperture (NA), non-immersion, objective lenses in an implementation of the GPC-based 3D trapping system. Contrary to high-NA based optical tweezers, the GPC trapping system demonstrated here operates with long working distance (>10 mm), and offers a wider manipulation region and a larger field of view for imaging through each of the two opposing objective lenses. As a consequence of the large working distance, simultaneous monitoring of the trapped particles in a second orthogonal observation plane is demonstrated.
Emergent Properties of Reduced-Genome Escherichia coli (2006)

With the use of synthetic biology, we reduced the Escherichia coli K-12 genome by making planned, precise deletions. The multiple-deletion series (MDS) strains, with genome reductions up to 15%, were designed by identifying nonessential genes and sequences for elimination, including recombinogenic or mobile DNA and cryptic virulence genes, while preserving good growth profiles and protein production. Genome reduction also led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties.
Rapid Detection of Human Metapneumovirus Strains in Nasopharyngeal Aspirates and Shell Vial Cultures by Monoclonal Antibodies (2005)

ABSTRACT Monoclonal antibodies to human metapneumovirus (hMPV) were developed for direct fluorescent antibody (DFA) staining of nasopharyngeal aspirates from 40 infants with respiratory infections, as well as for hMPV identification in shell vial cultures. With reference to reverse transcription-PCR, DFA staining showed sensitivity, specificity, and positive and negative predictive values of 73.9%, 94.1%, 94.4%, and 72.7%, respectively. Monoclonal antibodies are useful for direct hMPV detection.
Sequestration of Zinc Oxide by Fimbrial Designer Chelators (2000)

Type 1 fimbriae are surface organelles of Escherichia coli. By engineering a structural component of the fimbriae, FimH, to display a random peptide library, we were able to isolate metal-chelating bacteria. A library consisting of 4 x 10(7) independent clones was screened for binding to ZnO. Sequences responsible for ZnO adherence were identified, and distinct binding motifs were characterized. The sequences selected exhibited various degrees of affinity and specificity towards ZnO. Competitive binding experiments revealed that the sequences recognized only the oxide form of Zn. Interestingly, one of the inserts exhibited significant homology to a specific sequence in a putative zinc-containing helicase, which suggests that searches such as this one may aid in identifying binding motifs in nature. The zinc-binding bacteria might have a use in detoxification of metal-polluted water.
Modulation of humoral islet autoimmunity by pancreas allotransplantation influences allograft outcome in patients with type 1 diabetes. (2000)

Pancreas transplantation in patients with type 1 diabetes presents allogeneic beta-cell autoantigens to the immune system long after the initial beta-cell destruction that leads to diabetes has occurred. The aims of this study were to determine whether re-exposure to beta-cell autoantigen through transplantation affect the humoral autoimmune response and whether its modulation correlates with graft outcome. Antibodies to the major autoantigens GAD (GADA) and protein tyrosine phosphatase IA-2 (IA-2A) were measured before and after transplantation in patients with type 1 diabetes who received pancreas and kidney allografts. In the 110 cases studied, pancreas graft survival was not significantly associated with the presence of GADA or IA-2A before transplantation. In the 75 patients with sequential follow-up samples up to 11.2 years after transplantation, autoantibodies were persistently undetectable in 44 cases (59%) and remained at stable detectable levels in 13 cases (17%). Substantial changes in antibody levels were found in 18 cases (24%), of which 13 cases (17%) had declining levels and 5 cases (7%) had marked increments after transplantation. Rising GADA and IA-2A levels in these five patients were predominantly of the IgG1 subclass, with progressive spreading of epitope reactivity. Pancreas graft function was lost 0.7-2.3 years after rising autoantibody levels in four of these five patients, and a significantly lower pancreas graft survival was found in patients with major rises in either GADA or IA-2A levels (P < 0.0001 vs. the remainder) and in patients having persistently high levels of IA-2A (P = 0.002 vs. stable antibody-negative patients). Kidney graft survival was not associated with islet autoantibody status. In conclusion, a minority of patients receiving pancreas allografts under generalized immunosuppression show a stimulation of islet autoantibody reactivity characteristic of that found in preclinical type 1 diabetes, which is almost invariably followed by graft function failure and resumption of insulin therapy.
Identification of novel circulating human embryonic blood stem cells (2000)

Using murine models, primitive hematopoietic cells capable of repopulation have been shown to reside in various anatomic locations, including the aortic gonad mesonephros, fetal liver, and bone marrow. These sites are thought to be seeded by stem cells migrating through fetal circulation and would serve as ideal targets for in utero cellular therapy. In humans, however, it is unknown whether similar stem cells exist. Here, we identify circulating hematopoeitic cells present during human in utero development that are capable of multilineage repopulation in immunodeficient NOD/SCID (nonobese diabetic/severe combined immunodeficient) mice. Using limiting dilution analysis, the frequency of these fetal stem cells was found to be 1 in 3.2 × 105, illustrating a 3- and 22-fold enrichment compared with full-term human cord blood and circulating adult mobilized–peripheral blood, respectively. Comparison of in vivo differentiation and proliferative capacity demonstrated that circulating fetal stem cells are intrinsically distinct from hematopoietic stem cells found later in human development and those derived from the fetal liver or fetal bone marrow compartment at equivalent gestation. Taken together, these studies demonstrate the existence of unique circulating stem cells in early human embryonic development that provide a novel and previously unexplored source of pluripotent stem cell targets for cellular and gene-based fetal therapies.
Two Photon Absorption, Nonlinear Refraction, And Optical Limiting In Semiconductors (1985)

Two-photon absorption coefficients /32 of ten direct gap semiconductors with band-gap energy Eg varying between 1 .4 and 3.7 eV were measured using 1.06 µm and 0.53 um picosecond pulses. $2 was found to scale as E43, as predicted by theory for the samples measured. Extension of the empirical relationship between $2 and Eg to InSb with Eg = 0.2 eV also provides agree-ment between previously measured values and the predicted 02. In addition, the absolute values of $2 are in excellent agreement (the average difference being <26%) with recent theory, which includes the effects of nonparabolic bands. The nonlinear refraction induced in these materials was monitored and found to agree well with the assumption that the self-refraction originates from the two-photon-generated free carriers. The observed self-defocusing yields an effective nonlinear index as much as two orders of magnitude larger than CS2 for comparable irradiances. This self-defocusing, in conjunction with two-photon absorption, was used to construct a simple, effective optical limiter that has high transmission at low input irradiance and low transmission at high input irradiance. The device is the optical analog of a Zener diode.
Effects of Three New Nitrosourea Analogs (CNCC, RFCNU and Chlorozotocin) on in vivo Destruction of L1210 Leukemia Cells and on the Immune Response (1986)

Three new nitrosourea analogs (CNCC, RFCNU, and chlorozotocin) had comparable activities in vivo against L1210 leukemia cells. In addition to the antileukemia effect, these drugs also decreased both the humoral immune response to sheep red blood cells and the delayed hypersensitivity reaction to oxazolone. The immunodepression induced by these agents lasted at least 25 days, and could not be reversed by the transplantation of normal syngenic bone marrow cells into treated animals.
SWAPSC: sliding window analysis procedure to detect selective constraints (2004)

SWAPSC is available at http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml distribution versions for both Linux and Windows operating systems are available, including manual and example files.
Interleukin-2 Receptor β Chain Gene: Generation of Three Receptor Forms by Cloned Human α and β Chain cDNA's (1989)

Interleukin-2 (IL-2) binds to two distinct receptor molecules, the IL-2 receptor alpha (IL-2R alpha, p55) chain and the newly identified IL-2 receptor beta (IL-2R beta, p70-75) chain. The cDNA encoding the human IL-2R beta chain has now been isolated. The overall primary structure of the IL-2R beta chain shows no apparent homology to other known receptors. Unlike the IL-2R alpha chain, the IL-2R beta chain has a large cytoplasmic region in which a functional domain (or domains) mediating an intracellular signal transduction pathway (or pathways) may be embodied. The cDNA-encoded beta chain binds and internalizes IL-2 when expressed on T lymphoid cells but not fibroblast cells. Furthermore, the cDNA gives rise to the generation of high-affinity IL-2 receptor when co-expressed with the IL-2R alpha chain cDNA.
Analysis of the resistance-nodulation-division and HOP families of cell envelope proteins in helicobacter pylori (2009)

This study was initiated to identify potential genes that play a functional role in the in vivo antibiotic resistance of Helicobacter pylori. Translational fusions of H. pylori genes to alkaline phosphatase were made to identify genes whose products were secreted or exported in Escherichia coli. The initial screen identified three potential H. pylori efflux genes of the bacterial resistance-nodulation-division family. One of the efflux systems was found to be expressed only in vivo and I was not able to identify efflux activity in in vitro-grown H. pylori. The overall results of these experiments were consistent with the suggestion that these efflux systems do not function in the in vitro intrinsic resistance of H. pylori to antibiotics. A second line of investigation analyzed members of the H. pylori Hop family of outer membrane/adhesin proteins. Exner et al. (Infection &amp; Immunity 63:1567-1572, 1995) previously described this family of 5 porin proteins based on extensive N-terminal amino acid similarity. This family was further expanded to include 32 proteins containing extensive C-terminal amino acid similarity by Tomb et al. (Nature 388:539-547, 1997). My analysis of the H. pylori genome has further expanded this family to 34 members. The DN A sequences encoding the conserved sequence motifs that are found within the Hop family had been proposed to function in homologous recombination to generate antigenic diversity or in response to environmental changes. However, my comparison of the sequences of the Hop family genes in two H. pylori strains suggested that the conserved sequences did not function in recombination. Based on molecular modeling of HopE, I proposed and tested, by linker insertion mutagenesis, the hypothesis that the conserved sequence motifs are part of a conserved structural motif. The overall results of these experiments supported the hypothesis that the conserved sequences encode a conserved structural motif for a family of β-barrel proteins.
Safety and Immunogenicity of an Inactivated Subvirion Influenza A (H5N1) Vaccine (2006)

A two-dose regimen of 90 mug of subvirion influenza A (H5N1) vaccine does not cause severe side effects and, in the majority of recipients, generates neutralizing antibody responses typically associated with protection against influenza. A conventional subvirion H5 influenza vaccine may be effective in preventing influenza A (H5N1) disease in humans. (ClinicalTrials.gov number, NCT00115986.).
Raman spectroscopic study of the rare-earth fullerides Eu6−xSrxC60 (2011)

We present Raman spectroscopic studies of the isostructural and isoelectronic Eu(6-x)Sr(x)C(60) (x = 0, 3, 5, 6) and Ba(6)C(60) compounds. The Raman spectra of the Eu-based fullerides show dramatic changes compared to the pure alkaline-earth systems, including significant broadening, splitting and frequency shifts of the fivefold degenerate H(g) intramolecular modes of C(60). Moreover, the A(g)(2) mode exhibits an even larger downshift and a remarkable broadening. These findings are consistent with distortions of the C(60) molecular cages and a considerable electron-phonon coupling strength-strongly enhanced in the Eu containing systems-originating from the strong orbital hybridization between the metal atom and the C(60) molecule.
Engineering Trehalose Synthesis in Lactococcus lactis for Improved Stress Tolerance (2011)

Trehalose accumulation is a common cell defense strategy against a variety of stressful conditions. In particular, our team detected high levels of trehalose in Propionibacterium freudenreichii in response to acid stress, a result that led to the idea that endowing Lactococcus lactis with the capacity to synthesize trehalose could improve the acid tolerance of this organism. To this end, we took advantage of the endogenous genes involved in the trehalose catabolic pathway of L. lactis, i.e., trePP and pgmB, encoding trehalose 6-phosphate phosphorylase and β-phosphoglucomutase, respectively, which enabled the synthesis of trehalose 6-phosphate. Given that L. lactis lacks trehalose 6-phosphate phosphatase, the respective gene, otsB, from the food-grade organism P. freudenreichii was used to provide the required activity. The trehalose yield was approximately 15% in resting cells and in mid-exponential-phase cells grown without pH control. The intracellular concentration of trehalose reached maximal values of approximately 170 mM, but at least 67% of the trehalose produced was found in the growth medium. The viability of mutant and control strains was examined after exposure to heat, cold or acid shock, and freeze-drying. The trehalose-producing strains showed improved tolerance (5- to 10-fold-higher survivability) to acid (pH 3) and cold shock (4°C); there was also a strong improvement in cell survival in response to heat shock (45°C), and no protection was rendered against dehydration. The insight provided by this work may help the design of food-grade strains optimized for the dairy industry as well as for oral drug delivery.
Point-of-Care Coagulation Testing (2000)

Several technologies are used in point-of-care monitoring of anticoagulation in outpatient anticoagulation clinics, cardiac surgery units, intensive-care units, and dialysis units. Prothrombin time and activated partial thromboplastin time are measured with standard coagulation systems; activated coagulation time is measured with a specially designed coagulometer, using whole blood specimens; and now some patients can measure their prothrombin time with self-obtained capillary blood samples, using instruments specifically designed for such applications. Quality control and quality assurance of point-of-care testing are particularly important because of the danger of adverse reaction to anticoagulation therapy.
Fuzzy logic in control systems: fuzzy logic controller. II (1990)

For pt.I see ibid., vol.20, no.2, p.404-18, 1990. The basic aspects of the FLC (fuzzy logic controller) decision-making logic are examined. Several issues, including the definitions of a fuzzy implication, compositional operators, the interpretations of the sentence connectives 'and' and 'also', and fuzzy inference mechanisms, are investigated. Defuzzification strategies, are discussed. Some of the representative applications of the FLC, from laboratory level to industrial process control, are briefly reported. Some unsolved problems are described, and further challenges in this field are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>