gebhart/patrepeval huggingface dataset:
Compact directly diode-pumped femtosecond Nd:glass chirped-pulse-amplification laser system (1997)

An all-solid-state longitudinally diode-pumped Nd:glass chirped-pulse-amplification laser system producing pulses of 50-MW peak power has been developed. The diode-pumped Nd:glass regenerative amplifier produces pulses with energies as great as 56microJ at a 1-kHz repetition rate and pulse durations as short as 450 fs after compression in a compact single holographic-transmission-grating stretcher-compressor arrangement. Further, spectral gain shaping was shown to extend the bandwidth that was supported in the low-gain amplifier. To the best of our knowledge, this system provides the highest peak and average power obtained from a directly diode-pumped femtosecond laser.
Control of Glutamate Clearance and Synaptic Efficacy by Glial Coverage of Neurons (2001)

Analysis of excitatory synaptic transmission in the rat hypothalamic supraoptic nucleus revealed that glutamate clearance and, as a consequence, glutamate concentration and diffusion in the extracellular space, is associated with the degree of astrocytic coverage of its neurons. Reduction in glutamate clearance, whether induced pharmacologically or associated with a relative decrease of glial coverage in the vicinity of synapses, affected transmitter release through modulation of presynaptic metabotropic glutamate receptors. Astrocytic wrapping of neurons, therefore, contributes to the regulation of synaptic efficacy in the central nervous system.
Separation of sublethal and lethal effects of polymorphonuclear leukocytes on Escherichia coli. (1990)

Escherichia coli ingested by PMN promptly stop growing and form no colonies in nutrient agar, but metabolize near normally for up to several hours. The bactericidal/permeability increas- ing protein (BPI) of PMN also inhibits E. coli growth without initial metabolic impairment. We recently showed that BPI- treated E. coli, although unable to grow in normal nutrient agar, can form colonies in this medium plus 0.1% BSA, as long as their metabolism is maintained, indicating that biochemical impairment is a better indicator of death than growth arrest (1990. J. Clin. Invest. 85:853-860). We have now reexamined the fate of ingested E. coli. Rabbit PMN ingest > 85% of several rough E. coli strains in 15 min, but > 80% of these bacteria, while unable to form colonies in conventional agar, grow normally on agar plus 0.1% BSA. Thus, the PMN under these conditions promptly stop growth of ingested E. coli without killing. Adding nonlethal concentrations of normal human serum (NHS) before, but not after ingestion, acceler- ates killing and, in parallel, loss of bacterial metabolism (tl/2 < 0.5 h vs. > 3 h, respectively, with and without NHS). The rapid killing of both rough and smooth E. coli pretreated with NHS is lost after C7 depletion (C7-D) and restored when C7 is replenished. Similar results are obtained with human PMN. In contrast, ingested Staphylococcus epidermidis, opsonized with either NHS or C7-D serum rapidly stop metabolizing and do not form colonies in nutrient agar with or without BSA. Respiratory burst activity is the same during ingestion of E. coli (with or without NHS) and S. epidermidis. Killing of E. coli J5 (however, not of 0111-B4) by BPI is also accelerated by pre- treatment with NHS but not C7-D human serum. These findings indicate that late complement components are needed for efficient killing of both rough and smooth E. coli by PMN, and that BPI is the principal intracellular agent acting on ingested rough E. coli. (J. Clin. Invest.
A software authentication system for the prevention of computer viruses (1992)

In the absence of systematic techniques to detect the existence of computer viruses, preventing suspicious software from entering the system at the initial point of entry appears to be the best method to protect computing resources against attacks of computer viruses. Currently, software is distributed primarily by diskettes instead of online transmission. Diskettes are more susceptible to modification and masquerading while on-line transmission usually follows proper user/message authentication. A software authentication system is proposed which does not require a mutually trusted center of both software vendors and users, or users' interaction with any key center. Vendors assume responsibility by signing released software and users verify the authenticity of received software before using it. Through such an authentication process, users eliminate the risk of running “unlicensed” or modified programs, thus eliminating the possibility of virus infections.
Spatiotemporal variation of metabolism in a plant circadian rhythm: The biological clock as an assembly of coupled individual oscillators (2001)

The complex dynamic properties of biological timing in organisms remain a central enigma in biology despite the increasingly precise genetic characterization of oscillating units and their components. Although attempts to obtain the time constants from oscillations of gene activity and biochemical units have led to substantial progress, we are still far from a full molecular understanding of endogenous rhythmicity and the physiological manifestations of biological clocks. Applications of nonlinear dynamics have revolutionized thinking in physics and in biomedical and life sciences research, and spatiotemporal considerations are now advancing our understanding of development and rhythmicity. Here we show that the well known circadian rhythm of a metabolic cycle in a higher plant, namely the crassulacean acid metabolism mode of photosynthesis, is expressed as dynamic patterns of independently initiated variations in photosynthetic efficiency (phi(PSII)) over a single leaf. Noninvasive highly sensitive chlorophyll fluorescence imaging reveals randomly initiated patches of varying phi(PSII) that are propagated within minutes to hours in wave fronts, forming dynamically expanding and contracting clusters and clearly dephased regions of phi(PSII). Thus, this biological clock is a spatiotemporal product of many weakly coupled individual oscillators, defined by the metabolic constraints of crassulacean acid metabolism. The oscillators operate independently in space and time as a consequence of the dynamics of metabolic pools and limitations of CO(2) diffusion between tightly packed cells.
Neovascularization in human germ cell tumors correlates with a marked increase in the expression of the vascular endothelial growth factor but not the placenta-derived growth factor. (1996)

Neoangiogenesis is a prerequisite for tumor growth and metastasis. In germ cell cancer patients with the disease limited to the testicle (stage A), tumor-associated neovascularization is predictive of metastatic disease (stage B). To investigate the molecular mechanisms underlying neovascularization in human germ cell tumors (GCTs), we analysed the expression of two angiogenic growth factors, vascular endothelial growth factor (VEGF) and placenta growth factor (P1GF), and of their receptors (FLT-1) and Flk-1/KDR) in a panel of testicular tumors. In this study we show a marked increase in VEGF expression in 36/44 (81.8%) primary testicular-derived GCTs, as compared to normal testis, that significantly correlates with a high density of intratumor microvessels (r = 0.72461, P < 0.001; n = 24). As determined by RT - PCR and/or Western blot, the predominant VEGF isoforms expressed in GCTs are the VEGF121 and VEGF165, which are more efficiently secreted by the cells, and thus more active in eliciting angiogenesis. Conversely, in the case of PIGF, only a weak correlation with the vascular density of tumors is observed (r = 0.26599, P < 0.05; n = 24). Northern blot analysis also revealed significant up-regulation of VEGF/ PIGF receptors in highly vascularized germ cell tumors, compared to normal testes. These findings suggest that VEGF may act in a paracrine manner to induce neovascularization, oedema extravasation and cyst formation in human germ cell tumors. The correlation between VEGF expression and the vascular density of tumors, suggest that the evaluation of VEGF expression may be of help in predicting patients at risk for metastatic diseases. Finally, we demonstrate that VEGF up-regulation may occur at the RNA level since no gene amplification is observed; conversely, in in vitro models such as the embryonal stem cell line NTERA-2 and the choricarcinoma JEG-3 cell line, VEGF (but not PIGF) mRNA expression is regulated by hypoxic stress.
A short proof for the multi-deletion error correction property of Helberg codes (2016)

A short proof for the s-deletion error-correction property of Helberg codes is given.
Buffered Steiner trees for difficult instances (2001)

Buffer insertion has become an increasingly critical optimization in high performance design. The problem of finding a delay-optimal buffered Steiner tree has been an active area of research, and excellent solutions exist for most instances. However, current approaches fail to adequately solve a particular class of real-world “difficult” instances which are characterized by a large number of sinks, variations in sink criticalities, and varying polarity requirements. We propose a new Steiner tree construction called C-Tree for these instance types. When combined with van Ginneken style buffer insertion, C-Tree achieves higher quality solutions with fewer resources compared to traditional approaches.
Somatic recombination of heavy chain variable region transgenes with the endogenous immunoglobulin heavy chain locus in mice. (1992)

Transgenic lines of mice were derived by using plasmid constructs containing DNA encoding an antibody heavy chain variable-diversity-joining region (VH-D-JH) and various amounts of 5' and 3' flanking DNA but lacking any repetitive isotype switch (S) or constant (C) region DNA. Unexpectedly, many of the antibody VH regions expressed by B-cell hybridomas generated from immunized transgenic mice were found to be of transgenic origin. Further analyses showed that somatic events had generated hybrid genomic loci in the mice containing the transgenic VH-D-JH gene and plasmid sequences 5' of endogenous heavy chain C region genes. Thus, VH-D-JH transgenes lacking S and C region DNA can recombine with endogenous Igh DNA, leading to the expression of transgene-encoded antibody.
Anticancer Properties of a Novel Class of Tetrafluorinated Thalidomide Analogues (2015)

Thalidomide has demonstrated clinical activity in various malignancies affecting immunomodulatory and angiogenic pathways. The development of novel thalidomide analogs with improved efficacy and decreased toxicity is an ongoing research effort. We recently designed and synthesized a new class of compounds, consisting of both tetrafluorinated thalidomide analogues (Gu973 and Gu998) and tetrafluorobenzamides (Gu1029 and Gu992). In this study, we demonstrate the antiangiogenic properties of these newly synthesized compounds. We examined the specific antiangiogenic characteristics in vitro using rat aortic rings with carboxyamidotriazole as a positive control. In addition, further in vitro efficacy was evaluated using human umbilical vein endothelial cells (HUVEC) and PC3 cells treated with 5 and 10 μmol/L doses of each compound. All compounds were seen to reduce microvessel outgrowth in rat aortic rings as well as to inhibit HUVECs to a greater extent, at lower concentrations than previously tested thalidomide analogs. The antiangiogenic properties of the compounds were also examined in vivo in fli1:EGFP zebrafish embryos, where all compounds were seen to inhibit the extent of outgrowth of newly developing blood vessels. In addition, Gu1029 and Gu973 reduced the anti-inflammatory response in mpo:GFP zebrafish embryos, whereas Gu998 and Gu992 showed no difference. The compounds' antitumor effects were also explored in vivo using the human prostate cancer PC3 xenograft model. All four compounds were also screened in vivo in chicken embryos to investigate their teratogenic potential. This study establishes these novel thalidomide analogues as a promising immunomodulatory class with anticancer effects that warrant further development to characterize their mechanisms of action.
Use of a generic polymerase chain reaction assay detecting human T-lymphotropic virus (HTLV) types I, II and divergent simian strains in the evaluation of individuals with indeterminate HTLV serology (1997)

In countries with a low prevalence of human T-lymphotropic virus (HTLV) infection, indeterminate HTLV serologies are a major problem in blood bank screening because of the uncertainties about infection in these cases. The recent discovery of two new types of simian T-lymphotropic viruses (STLV), which give an HTLV-indeterminate serology, raises the question whether indeterminate serologies in humans may be linked to new types of HTLV. Starting from a Tax sequence alignment of all available primate T-cell lymphotropic virus strains (PTLV), including the two new types STLV-PH969 and STLV-PP1664, we developed generic and type-specific nested polymerase chain reactions (PCRs). The generic PCR proved to be highly sensitive and cross-reactive for all four types of PTLV, while the discriminatory PCRs had a high sensitivity and a specificity of 100%. There was no cross-reactivity with human immunodeficiency virus (HIV), ensuring correct interpretation of results from coinfected patients. Among the 77 serologically indeterminate samples tested, 6 were found to be HTLV-1 PCR positive and 1 was HTLV-II PCR positive. Sequencing of one of the HTLV-I PCR positives excluded PCR contamination, and revealed a divergent type of HTLV-I. The majority of the seroindeterminate samples (91%) were however HTLV-PCR negative, and no new types of HTLV were found. This new assay can identify otherwise undetected HTLV-I or HTLV-II infections and is a useful tool of screening for new types of HTLV among seroindeterminate samples.
The Complement Factor C5a Contributes to Pathology in a Rat Model of Amyotrophic Lateral Sclerosis (2008)

Complement activation products are elevated in the cerebrospinal fluid and spinal cord of patients with amyotrophic lateral sclerosis (ALS). In this study, we demonstrate complement system involvement in a rodent model of ALS (human SOD1(G93A) transgenic rats). With end-stage disease, SOD1(G93A) rats displayed marked deposition of C3/C3b, and a significant up-regulation of the C5aR in the lumbar spinal cord. This was associated with increased numbers of C5aR-positive astrocytes. However, expression of C5L2, the alternative receptor for C5a, was highest on motor neurons early in the disease process. To determine the contribution of C5a to the pathology displayed by this model of ALS, rats were administered an orally active, selective C5aR antagonist (PMX205; 1 mg/kg/day, oral). Animals treated with PMX205 displayed a significant extension of survival time and a reduction in end-stage motor scores, as compared with vehicle-treated rats. PMX205-treated animals also displayed reduced levels of astroglial proliferation in the lumbar spinal cord. This study provides the first demonstration of an involvement of C5a in an ALS model and suggests that inhibitors of complement activation could be beneficial in the treatment of this neurodegenerative disease.
Added value of transoesophageal echocardiography during transseptal puncture performed by inexperienced operators (2011)

Routine 2D TEE in addition to traditional fluoroscopic TP appears to be very useful to guide the TP assembly in a correct puncture position and thus, to avoid TP-related complications. However, further randomized prospective comparative studies are necessary to support these suggestions.
Normal patterns of human upper small bowel motor activity recorded by prolonged radiotelemetry. (1980)

In order to characterise human interdigestive cyclical motor activity, and its interruption by food, jejunal pressure changes in healthy volunteers were recorded continuously for 24 hours, using an ingested pressure-sensitive radiotelemetry capsule tethered at the duodenojejunal flexure. In 20 studies, the subjects fasted throughout; in another 20 studies they received a single standard meal. Using this technique, fasting motor complexes were easily detected. There was considerable variation in interdigestive cycle duration and in the interruption caused by food. The data were not normally distributed. The study indicates that any descriptions of 'atypical' jejunal motility patterns must take into account the wide variations seen in health, before they can be regarded as representing dysfunction or disease.
Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing (2010)

Our results confirm that fetal DNA is shorter than maternal DNA. The enrichment of fetal DNA by size selection, however, may not provide a dramatic increase in sensitivity for assays that rely on length measurement in situ because of a trade-off between the fetal DNA fraction and the number of molecules being counted.
T cell memory is short-lived in the absence of antigen. (1991)

Immunological memory has generally been ascribed to the development of long-lived memory cells that can persist for years in the absence of renewed antigenic encounter. In the experiments reported here, we have adoptively transferred memory T cells in the presence and absence of priming antigen and assessed their functional survival. The results indicate that, in contrast to the traditional view, the maintenance of T cell memory requires the presence of antigen, suggesting that memory, like tolerance, is an antigen-dependent process rather than an antigen-independent state.
Synergism in Multicomponent Self-Propagating Molecular Assemblies (2010)

Multicomponent self-propagating molecular assemblies (SPMAs) have been generated from an organic chromophore, a redox-active polypyridyl complex, and PdCl2. The structure of the multicomponent SPMA is not a linear combination of two assemblies generated with a single molecular constituent. Surface-confined assemblies formed from only the organic chromophore and PdCl2 are known to follow linear growth, whereas the combination of polypyridyl complexes and PdCl2 results in exponential growth. The present study demonstrates that an iterative deposition of both molecular building blocks with PdCl2 results in an exponentially growing assembly. The nature of the assembly mechanism is dictated by the polypyridyl complex and overrides the linear growth process of the organic component. Relatively smooth, multicomponent SPMAs have been obtained with a thickness of ∼20 nm on silicon, glass, and indium−tin oxide (ITO) coated glass. Detailed information of the structure and of the surface-assembly chemistry were obtained using transmission optical (UV/Vis) spectroscopy, ellipsometry, atomic force microscopy (AFM), synchrotron X-ray reflectivity (XRR), and electrochemistry.
Imaging‐guided convection‐enhanced delivery and gene therapy of glioblastoma (2003)

In a prospective phase I/II clinical study, we treated eight patients suffering from recurrent glioblastoma multiform with stereotactically guided intratumoral convection-enhanced delivery of an HSV-1-tk gene-bearing liposomal vector and systemic ganciclovir. Noninvasive identification of target tissue together with assessment of vector-distribution volume and the effects of gene therapy were achieved using magnetic resonance imaging and positron emission tomography. The treatment was tolerated well without major side effects. In two of eight patients, we observed a greater than 50% reduction of tumor volume and in six of eight patients focal treatment effects. Intracerebral infusion of contrast medium before vector application displayed substantial inhomogeneity of tissue staining indicating the need of test infusions to monitor the mechanical distribution of vectors. Visualization of therapeutic effects on tumor metabolism and documentation of gene expression using positron emission tomography indicated that molecular imaging technology appears to be essential for the further development of biological treatment strategies.
Visual and ocular morbidity in severe open‐globe injuries presenting to a regional eye centre in New Zealand (2018)

The incidence and severity of OGI in NZ are comparable to global statistics. Surgical repair can effectively recover vision, predicted well by the OTS. We identified at-risk groups to target with education and prevention strategies.
Cellular gene expression altered by human cytomegalovirus: Global monitoring with oligonucleotide arrays (1998)

Mechanistic insights to viral replication and pathogenesis generally have come from the analysis of viral gene products, either by studying their biochemical activities and interactions individually or by creating mutant viruses and analyzing their phenotype. Now it is possible to identify and catalog the host cell genes whose mRNA levels change in response to a pathogen. We have used DNA array technology to monitor the level of approximately 6,600 human mRNAs in uninfected as compared with human cytomegalovirus-infected cells. The level of 258 mRNAs changed by a factor of 4 or more before the onset of viral DNA replication. Several of these mRNAs encode gene products that might play key roles in virus-induced pathogenesis, identifying them as intriguing targets for further study.
Quantitative Analysis of Biomarkers Defines an Optimal Biological Dose for Recombinant Human Endostatin in Primary Human Tumors (2004)

The data suggest that endostatin had optimal biological activity at doses approximately 250 mg/m(2) in our cohort of patients. Endostatin's failure to induce high levels of TC death may explain its lack of significant clinical activity in this Phase I trial.
Blood flow-dependent prostaglandin F2αregulates intestinal glucose uptake from the blood (1999)

Intestinal glucose uptake (GUi) from blood increased when blood flow (BF) was increased. The increase in BF could elevate shear stress. Therefore, we hypothesize that shear stress-induced release of autacoids mediates the increase in GU(i). A surgically separated segment of small intestine was perfused in situ with the use of an arterial circuit in anesthetized cats. Arterial and portal blood samples were taken simultaneously for assessment of GU(i). Adenosine was used to elevate intestinal BF. The GU(i) increased by 45.0 +/- 18.3 from 25.3 +/- 3.8 micromol. min(-1). 100 g tissue(-1) when the BF increased about four times. It was not a direct effect of adenosine because GU(i) was not altered if the flow was held constant. This increase was blocked by a cyclooxygenase inhibitor, indomethacin, but not by nitric oxide synthase blocker N(G)-nitro-L-arginine methyl ester. Furthermore, prostaglandin F(2alpha) (PGF(2alpha)) but not PGE(2) or PGI(2) reversed the blockade of the increase in GU(i) after indomethacin during elevated blood flow, whereas they had no influence on basal uptake. The results suggest that shear stress-induced release of PGF(2alpha) mediated the increase in GU(i) when blood flow was elevated.
Design of wide-angle solar-selective absorbers using aperiodic metal-dielectric stacks (2009)

Spectral control of the emissivity of surfaces is essential in applications such as solar thermal and thermophotovoltaic energy conversion in order to achieve the highest conversion efficiencies possible. We investigated the spectral performance of planar aperiodic metal-dielectric multilayer coatings for these applications. The response of the coatings was optimized for a target operational temperature using needle-optimization based on a transfer matrix approach. Excellent spectral selectivity was achieved over a wide angular range. These aperiodic metal-dielectric stacks have the potential to significantly increase the efficiency of thermophotovoltaic and solar thermal conversion systems. Optimal coatings for concentrated solar thermal conversion were modeled to have a thermal emissivity <7% at 720K while absorbing >94% of the incident light. In addition, optimized coatings for solar thermophotovoltaic applications were modeled to have thermal emissivity <16% at 1750K while absorbing >85% of the concentrated solar radiation.