gebhart/patrepeval huggingface dataset:
Application of Transcranial Color-Coded Duplex Sonography in Stroke Diagnosis (2009)

Cerebrovascular diagnostics are increasingly important in stroke therapy, especially in cases when the time window for IV rtPA has exceeded, in follow-up and secondary prevention of ischemic stroke. Transcranial color-coded duplex sonography (TCCS), a noninvasive and flexible method for vascular and parenchymal imaging of the adult brain, and is considered complementary to CT- and MR-Angio as the investigator depicts intracranial hemodynamics including occlusions, stenosis and the sufficiency of collateral flow. After an introduction to the general technical requirements of the ultrasound system and the defined transcranial image planes important for stroke diagnostics we focus on intracranial arterial vessel occlusions and stenosis important for cerebral ischemia work-up. UCA have had a tremendous impact on TCCS application and are used in cases of unfavorable acoustic bone windows resulting in superior signal-to-noise and yield high and fast diagnostic confidence. In addition, new developments in ultrasound signal processing and transducer technology, such as harmonic B-mode and contrast burst imaging amongst others, take advantage of microbubble specific properties which allow for increased signal retrieval as well as separation of linear and non-linear acoustic responses. Bedside ultrasound perfusion sonography has gained special attention and first encouraging results have visualized and quantified perfusion defects in acute stroke patients. This review is aimed to guide the unexperienced sonographer to valid and important findings in intracranial cerebrovascular disease.
Relationship of the 37,000- and 40,000-M(r) tryptic fragments of islet antigens in insulin-dependent diabetes to the protein tyrosine phosphatase-like molecule IA-2 (ICA512). (1995)

Sera from patients with insulin-dependent diabetes immunoprecipitate 64,000-M(r) proteins, distinct from glutamate decarboxylase, that are cleaved to 37,000- and 40,000-M(r) fragments by trypsin. We investigated possible relationships between 37,000- or 40,000-M(r) fragments of antigen and the tyrosine phosphatase-like protein, IA-2 (ICA512). Antibodies from nondiabetic relatives bound differentially to 37,000- and 40,000-M(r) fragments indicating presence of distinct epitopes. Precursors of these fragments could be separated on immobilized lectins, suggesting different carbohydrate content. Levels of antibodies to 40,000-M(r) fragments were strongly associated with those to the intracellular domain of IA-2. Recombinant intracellular domain of IA-2 blocked binding of antibodies to 40,000-M(r) fragments expressed by insulinoma cells and partially blocked binding to 37,000-M(r) fragments. Furthermore, trypsinization of recombinant intracellular domain of IA-2 generated proteolytic fragments of identical M(r) to the 40,000-M(r) fragments of insulinoma antigen; 37,000-M(r) fragments were not generated. Thus, 40,000-M(r) fragments of islet autoantigen are derived from a protein similar or identical to the tyrosine phosphatase-like molecule, IA-2. The 37,000-M(r) fragments are derived from a different, although related, protein.
Interaction between the CCR5 chemokine receptors and microbial HSP70 (2006)

Evidence is presented that the microbial 70-kD heat shock protein (HSP70) binds to CCR5 chemokine receptors in CCR5-transfected cell lines and in primary human cells. Significant CCR5-mediated calcium mobilization was stimulated by HSP70 and inhibited with TAK 779, which is a specific CCR5 antagonist. HSP70-mediated activation of the p38 MAPK phosphorylation signaling pathway was also demonstrated in CCR5-transfected HEK 293 cells. Direct binding of three extracellular peptides of CCR5 to HSP70 was demonstrated by surface plasmon resonance. Functional evidence of an interaction between HSP70, CCR5 and CD40 was shown by enhanced production of CCL5 by HEK 293 cells transfected with both CD40 and CCR5. Primary monocyte-derived immature DC stimulated with HSP70 produced IL-12 p40, which showed dose-dependent inhibition of >90% on treatment with both TAK 779 and anti-CD40 mAb. Stimulation of IL-12 p40 or TNF-alpha by HSP70 was related to the differential cell surface expression of CCR5 in primary human immature and mature DC, and those with the homozygous triangle DeltaDelta32 CCR5 mutation. These findings may be of significance in the interaction between HSP70 and immune responses of CCR5+ T cells in HIV-1 infection, as well as in inflammatory bowel disease.
Studies on substrates and contacts for CIS films and devices (2002)

Nature of the glass/Mo substrates used in CIS solar cell structures influences the performance of the devices. Excessive Na diffusion from the commonly used soda-lime glass substrates through the Mo layer and its reaction with the processing atmosphere at the Mo/CIS interface may limit the efficiency of cells due to the formation of a high resistivity layer near this contact. A moderate level of Na diffusion, on the other hand, improves the efficiency of the cells, especially those fabricated on CIS films with low Cu/In stoichiometric ratios. The Na diffusion process depends on the type of glass substrate used and the nature of the Mo layer.
Systemic resistance in Arabidopsis induced by biocontrol bacteria is independent of salicylic acid accumulation and pathogenesis-related gene expression. (1996)

Systemic acquired resistance is a pathogen-inducible defense mechanism in plants. The resistant state is dependent on endogenous accumulation of salicylic acid (SA) and is characterized by the activation of genes encoding pathogenesis-related (PR) proteins. Recently, selected nonpathogenic, root-colonizing biocontrol bacteria have been shown to trigger a systemic resistance response as well. To study the molecular basis underlying this type of systemic resistance, we developed an Arabidopsis-based model system using Fusarium oxysporum f sp raphani and Pseudomonas syringae pv tomato as challenging pathogens. Colonization of the rhizosphere by the biological control strain WCS417r of P. fluorescens resulted in a plant-mediated resistance response that significantly reduced symptoms elicited by both challenging pathogens. Moreover, growth of P. syringae in infected leaves was strongly inhibited in P. fluorescens WCS417r-treated plants. Transgenic Arabidopsis NahG plants, unable to accumulate SA, and wild-type plants were equally responsive to P. fluorescens WCS417r-mediated induction of resistance. Furthermore, P. fluorescens WCS417r-mediated systemic resistance did not coincide with the accumulation of PR mRNAs before challenge inoculation. These results indicate that P. fluorescens WCS417r induces a pathway different from the one that controls classic systemic acquired resistance and that this pathway leads to a form of systemic resistance independent of SA accumulation and PR gene expression.
BIOCHEMISTRY OF MULTIDRUG RESISTANCE MEDIATED BY THE MULTIDRUG TRANSPORTER (1993)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Tumor cytotoxicity and endothelial Rac inhibition induced by TNP-470 in anaplastic thyroid cancer (2007)

Anaplastic thyroid carcinoma is an aggressive form of cancer with no treatment. Angiogenesis inhibitors, such as TNP-470, a synthetic derivative of fumagillin, have been shown to reduce tumor size and increase survival in heterotopic animal models of thyroid cancer. Our goals were to determine the effect of TNP-470 on anaplastic thyroid cancer using an orthotopic murine model, to identify the molecular pathways of TNP-470 actions on endothelial cells, and to determine the non-endothelial tumor effects of TNP-470. We injected human anaplastic thyroid carcinoma cells (DRO'90) into the thyroid glands of nude mice. Mice received TNP-470 (30 mg/kg) s.c. for 6 weeks. TNP-470 prolonged survival and reduced liver metastases. TNP-470 had direct cytotoxic effects on anaplastic thyroid carcinoma cells in vitro and in vivo. Paradoxically, TNP-470 increased vascular endothelial growth factor secretion from tumor cells in vitro and in vivo. However, there was no associated increase in tumor microvessel density. In endothelial cells, TNP-470 prevented vascular endothelial growth factor-induced endothelial permeability, intercellular gap formation, and ruffle formation by preventing Rac1 activation.
Trypsin induces epidermal proliferation and inflammation in murine skin (2004)

Human keratinocytes are known to express the protease-activated receptors, PAR-1 and PAR-2. Activation of PAR-1 results in increased proliferation, whereas PAR-2 activation results in decreased keratinocyte proliferation. Trypsin activates PAR-1 and in higher concentrations, PAR-2. The aim of this study was to evaluate the overall effect of trypsin on keratinocyte proliferation in a mouse in vivo and in vitro model. Daily topical application of 0.3-300 pmol trypsin/cm2 on hairless mouse skin induced dose-dependent epidermal hyperproliferation as determined by an increase in 5-bromo-2'-deoxyuridine incorporation of up to eight-fold in basal keratinocytes and an up to three-fold increase in keratinocyte layers. This was accompanied by an increased transepidermal water loss. These effects of trypsin were abolished by the addition of the trypsin inhibitor n-p-tosyl-l-lysine-chloromethyl ketone. Histological analysis revealed acanthosis, hypergranulosis, and spongiosis in the epidermis as well as vasodilatation and an inflammatory infiltrate in the upper dermis. In the murine keratinocyte cell line PAM-212 activation of PAR-1 with specific activating peptides resulted in a calcium influx and an increase of proliferation, whereas activation of PAR-2 caused a diminished proliferation. Incubation with trypsin, PAR-1-, and PAR-2-activating peptides induced cytokine-induced neutrophil chemoattractant (KC) mRNA expression as a marker for inflammation in PAM-212 in a dose-dependent manner. In conclusion, our results suggest that trypsin induces in vivo epidermal proliferation and inflammation. Proliferation seems not to be signaled by PAR activation, but PAR-2-induced KC chemokine expression may contribute in part to trypsin-induced inflammation.
Embedded Convolutional Face Finder (2006)

In this paper, a high-level optimization methodology is applied for the implementation of the well-known convolutional face finder (CFF) algorithm for real-time applications on cellular phone, such as teleconferencing, advanced user interfaces, pictures indexing and security access control. This face detector is based on a feature extraction and classification technique which consists in a pipeline of convolutions and subsampling operations. Design of embedded systems must find a good trade off between performance and code size due to the limited amount of resource available. We propose a methodology to cope with the main drawbacks of the CFF original implementation like floating point computation and memory allocation, to allow parallelism exploitation and perform algorithm optimizations. Results show that our embedded face detection system can accurately locate faces with less computational load and memory cost. It runs on a 275 MHz Starcore DSP at 9 QCIF images/s with state-of-the-art detection rates and very low false alarm rates
Type III‐dependent translocation of the Xanthomonas AvrBs3 protein into the plant cell (2002)

Many plant pathogenic bacteria utilize a conserved type III secretion system (TTSS) to deliver effector proteins into the host tissue. Indirect evidence has suggested that at least some effector proteins are translocated from the bacterial cytoplasm into the plant cell. Using an immunocytochemical approach, we demonstrate that the type III effector AvrBs3 from Xanthomonas campestris pv. vesicatoria localizes to nuclei of infected pepper leaves. Importantly, AvrBs3 translocation was observed in situ in native tissues of susceptible and resistant plants. AvrBs3 was detected in the nucleus as soon as 4 h post infection, which was dependent on a functional TTSS and the putative translocator HrpF. N-terminal AvrBs3 deletion derivatives are no longer secreted by the TTSS in vitro and could not be detected inside the host cells, suggesting that the N-terminus of AvrBs3 is important for secretion. Deletion of the nuclear localization signals in the AvrBs3 C-terminus, which are required for the AvrBs3-mediated induction of the hypersensitive reaction in resistant pepper plants, abolished AvrBs3 localization to the nucleus. This is the first report on direct evidence for translocation of a native type III effector protein from a plant pathogenic bacterium into the host cell.
Self-healing ring networks: gateway to public information networking (1990)

Self-healing networks are addressed from the viewpoint of enabling the evolution to a modern public information network through self-healing capabilities and the associated network architectures. The term digital city is used for the overall plan for the implementation and transition to a public information network. Public information networking refers to the future network infrastructure that will provide access, transport, and interconnectivity for voice, data, image, and broadband communications in a fault-tolerant, self-healing public network. The various aspects of digital city, including the marketplace assessment, network functional characteristics, physical network architecture, implications for the public network, and implementation strategies, are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SPECIFIC INACTIVATION OF PEPSIN BY A DIAZO KETONE (1966)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
HIV-1 infection induces functional alterations in human liver endothelial cells in primary culture (1994)

HIV infection triggers non-lethal functional alterations in cultured human liver sinusoidal endothelial cells, with a selective impairment in the storage and/or the excretion of endothelial-specific factors such as vWF. This functional modulation could play a role in the pathophysiology of HIV-induced disease.
Effect of Protein Kinase and Phosphatase Inhibitors on Expression of Hypoxia Inducible Factor 1 (1995)

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric bHLH-PAS protein essential for erythropoietin gene transcription in hypoxic cells. Here we show that both 2-aminopurine and sodium fluoride, inhibitors of serine/threonine kinases and phosphatases, respectively, interfered with the hypoxic induction of HIF-1 DNA-binding activity and expression of HIF-1 alpha and HIF-1 beta(ARNT) subunits. Genistein, an inhibitor of tyrosine kinases, completely blocked the synthesis of both HIF-1 subunits as well as HIF-1 DNA-binding activity. Sodium orthovanadate, an inhibitor of tyrosine phosphatases increased the basal level of HIF-1 proteins and HIF-1 activity. These data suggest that protein phosphorylation events play an important role in the hypoxia signal-transduction pathway that leads to synthesis of HIF-1 alpha and HIF-1 beta proteins and the induction of HIF-1 DNA-binding activity.
CAR: Clock with Adaptive Replacement (2004)

Abstract — CLOCK is a classical cache replacement policy dating back to 1968 that was proposed as a low-complexity approximation to LRU. On every cache hit, the policy LRU needs to move the accessed item to the most recently used position, at which point, to ensure consistency and correctness, it serializes cache hits behind a single global lock. CLOCK eliminates this lock contention, and, hence, can support high concurrency and high throughput environments such as virtual memory (for example, Multics, UNIX, BSD, AIX) and databases (for example, DB2). Unfortunately, CLOCK is still plagued by disadvantages of LRU such as disregard for “frequency”, susceptibility to scans, and low performance. As our main contribution, we propose a simple and elegant new algorithm, namely, CLOCK with Adaptive Replacement (CAR), that has several advantages over CLOCK: (i) it is scan-resistant; (ii) it is self-tuning and it adaptively and dynamically captures the “recency ” and “frequency ” features of a workload; (iii) it uses essentially the same primitives as CLOCK, and, hence, is low-complexity and amenable to a high-concurrency implementation; and (iv) it outperforms CLOCK across a wide-range of cache sizes and workloads. The algorithm CAR is inspired by the Adaptive Replacement Cache (ARC) algorithm, and inherits virtually all advantages of ARC including its high performance, but does not serialize cache hits behind a single global lock. As our second contribution, we introduce another novel algorithm, namely, CAR with Temporal filtering (CART), that has all the advantages of CAR, but, in addition, uses a certain temporal filter to distill pages with long-term utility from those with only short-term utility.
Biosynthetic lipid‐tagging of antibodies (1994)

Chemical conjugation of fatty acids to antibodies generates lipid-modified molecules which have found use in the targeting of liposome-mediated drug delivery and in liposome-based immunoassays. Alternatively, bacterial expression of antibodies as single-chain FV fragments fused to lipoprotein signal peptide and N-terminal sequence leads to in vivo enzymatic addition of a single glycerolipid group at the N-terminus of the molecule. This lipid-modification converts the antibody from a soluble protein into a functional membrane-bound molecule. These biosynthetically lipid-tagged antibodies may prove useful for immobilization of antibodies to membranes in various biotechnological applications.
An Intramolecular Prins Double Cyclization Catalyzed by Silyl Triflates1 (1997)

Several intramolecular Prins double cyclizations are reported. The 2-alkyl 5-hepten-1,2-diols and their analogues, 9−11, were prepared and oxidized to the aldehydes 6−8 under Swern conditions. Treatment of these α-hydroxy aldehydes with TBSOTf and a hindered base gave the products of an intramolecular Prins double cyclization, namely the 7-(silyloxy)-2-oxabicyclo[2.2.1]heptanes, 17−19, in 84−92% yield. These compounds were formed as single diastereomers with only the anti silyl ethers being obtained. The cyclizations occur when five-membered rings are being formed and when the initially formed cation is highly stabilized. Other substrates do not cyclize, e.g., when the α-hydroxy aldehydes 20−22, prepared from 26−28, are treated under similar conditions, none of the corresponding cyclization products, 23−25, were obtained.
Patterns of damage in genomic DNA sequences from a Neandertal (2007)

High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
Murine FGFR-1 is required for early postimplantation growth and axial organization. (1994)

We have explored the role of fibroblast growth factor receptor 1 (FGFR-1) in early embryonic development using three experimental systems: genetically deficient mice, in vitro blastocyst culture, and FGFR-1-deficient embryonic stem cells. Using these systems, we demonstrate that FGFR-1 is required for proper embryonic cell proliferation and for the correct axial organization of early postimplantation embryos but not for mesoderm formation. FGFR-1-deficient embryos display severe growth retardation both in vitro and in vivo and die prior to or during gastrulation. Although these mutants can form nonaxial tissues, such as the allantois, amnion, and yolk sac mesoderm, they display defective patterning of the primitive streak and other axial structures, and frequently exhibit truncations or disorganization of posterior embryonic regions. Such abnormalities are unlikely to be caused by intrinsic blocks in mesodermal differentiation, as FGFR-1-deficient ES cell lines form teratomas consisting of many mesodermal cell types.
Potentiation of Developmentally Regulated Plant Defense Response by AtWRKY18, a Pathogen-Induced Arabidopsis Transcription Factor (2002)

AtWRKY18 is a pathogen- and salicylic acid-induced Arabidopsis transcription factor containing the plant-specific WRKY zinc finger DNA-binding motif. In the present study, we have transformed Arabidopsis plants with AtWRKY18 under control of the cauliflower mosaic virus 35S promoter. Surprisingly, transgenic plants expressing high levels of AtWRKY18 were stunted in growth. When expressed at moderate levels, AtWRKY18 potentiated developmentally regulated defense responses in transgenic plants without causing substantial negative effects on plant growth. As they grew from seedling to mature stages, transgenic AtWRKY18 plant showed marked increase in the expression of pathogenesis-related genes and resistance to the bacterial pathogen Pseudomonas syringae, whereas wild-type plants exhibited little enhancement in these defense responses. Potentiation of developmentally regulated defense responses by AtWRKY18 was not associated with enhanced biosynthesis of salicylic acid but required the disease resistance regulatory protein NPR1/NIM1. Thus, AtWRKY18 can positively modulate defense-related gene expression and disease resistance. To study the regulated expression of AtWRKY18, we have identified a cluster of WRKY binding sites in the promoter of the gene and demonstrated that they acted as negative regulatory elements for the inducible expression of AtWRKY18. These negative cis-acting elements may prevent overexpression of AtWRKY18 during the activation of plant defense responses that could be detrimental to plant growth as inferred from the transgenic plants ectopically expressing the transgene.