gebhart/patrepeval huggingface dataset:
Identification, transfer, and characterization of cloned herpes simplex virus invasiveness regions (1989)

Following peripheral inoculation of experimental animals, herpes simplex virus type 2 (HSV-2) strains are more virulent than HSV-1 strains, and clinical studies suggest that they possess enhanced virulence in humans. One dramatic type-specific difference in virulence is observed following inoculation of the chorioallantoic membrane (CAM) of the chicken embryo: HSV-2, but not HSV-1, makes large pocks on the CAM, invades the mesoderm, generalizes in the embryo, and kills the chicken. These properties have been believed to be specific for HSV-2, and their molecular basis is unknown. We now report that an HSV-1 strain, ANG, behaves even more efficiently than HSV-2. In addition, we have transferred restriction fragments of ANG DNA to another HSV-1 strain, 17 syn+, conferring the CAM virulence phenotype on the normally CAM-avirulent 17 syn+. Like ANG, these recombinant viruses are 10(6)-fold more virulent (PFU/50%) lethal dose [LD50] ratio, less than or equal to 10(2)) than the parental 17 syn+ strain (PFU/LD50 ratio, greater than or equal to 10(8)). A molecularly cloned library of ANG DNA was used to identify two distinct regions containing the virulence functions. Transfer of sequences contained in either cloned ANG EcoRI fragment A (0.49 to 0.64 map units) or F (0.32 to 0.42 map units) DNA to 17 syn+ confers CAM virulence, whereas other cloned regions of the ANG genome do not. Using cloned DNA, we derived and plaque purified several virulent recombinant viruses with inserts from either the ANG EcoRI fragment A (INV-I) or F (INV-II) areas. In each instance, the transfer of the cloned INV-I or INV-II sequences enhanced virulence for the chicken embryo 10(6)-fold (PFU/LD50 ratio, less than or equal to 10(2]. In addition, the transfer of the cloned ANG EcoRI-F INV-II sequences resulted in a 10(3)-fold enhancement of neuroinvasiveness and virulence for mice. Following footpad inoculation, these recombinants kill mice with a PFU/LD50 ratio of approximately 10(3) (similar to HSV-2 strains) compared with 10(6) for 17 syn+. Thus, we have identified, cloned, and transferred two DNA regions from HSV-1 ANG which contain virulence genes (INV-I and INV-II) important in mesodermal invasiveness on the CAM and, in the case of INV-II, neuroinvasiveness in the mouse. In each instance, the recombinant HSV-1 viruses have attained enhanced virulence beyond that described for HSV-1 strains and similar to that seen with HSV-2.(ABSTRACT TRUNCATED AT 400 WORDS)
F2-Lasers: High-Resolution Micromachining System for Shaping Photonic Components (2001)

Abstract: We describe a new high-resolution 157-nm optical processing system for micromachining optical materials with record short -wavelength F 2 laser radiation. © 2001 Optical Society of America CIS codes: (060.2340) Fiber optics components 1. Introduction The F 2 -laser defines the short-wavelength forefront of today’s commercial laser systems. The 157 -nm light supports high resolution patterning of ~100 nm features [1] while a large 7.9-eV photon energy drives strong absorption mechanisms for processing our most difficult materials. The F 2 -laser photons can access near-bandedge states in fused silica, germanosilicate [2-4], and other [5] glasses to smoothly microsculpt surfaces and to imprint refractive index structures with ∆n > 3 x 10 -3 [3,4] for a broad range of new applications in photonics processing and trimming. Microfabrication also extends to weakly absorbing polymers like polyethylene, PMMA, and PTFE [6-10] for potential biomedical, electronic, and MEMs applications . The recent addition of the F
Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 Å resolution (2000)

Cellulases are traditionally classified as either endoglucanases or cellobiohydrolases on the basis of their respective catalytic activities on crystalline cellulose, which is generally hydrolysed more efficiently only by the cellobiohydrolases. On the basis of the Trichoderma reesei cellobiohydrolase II structure, it was proposed that the active-site tunnel of cellobiohydrolases permitted the processive hydrolysis of cellulose, whereas the corresponding endoglucanases would display open active-site clefts [Rouvinen, Bergfors, Teeri, Knowles and Jones (1990) Science 249, 380-386]. Glycoside hydrolase family 6 contains both cellobiohydrolases and endoglucanases. The structure of the catalytic core of the family 6 endoglucanase Cel6B from Humicola insolens has been solved by molecular replacement with the known T. reesei cellobiohydrolase II as the search model. Strangely, at the sequence level, this enzyme exhibits the highest sequence similarity to family 6 cellobiohydrolases and displays just one of the loop deletions traditionally associated with endoglucanases in this family. However, this enzyme shows no activity on crystalline substrates but a high activity on soluble substrates, which is typical of an endoglucanase. The three-dimensional structure reveals that the deletion of just a single loop of the active site, coupled with the resultant conformational change in a second 'cellobiohydrolase-specific' loop, peels open the active-site tunnel to reveal a substrate-binding groove.
Statistical Techniques for Natural Language Parsing (1997)

I review current statistical work on syntactic parsing and then consider part-of-speech tagging, which was the first syntactic problem to successfully be attacked by statistical techniques and also serves as a good warm-up for the main topic-statistical parsing. Here, I consider both the simplified case in which the input string is viewed as a string of parts of speech and the more interesting case in which the parser is guided by statistical information about the particular words in the sentence. Finally, I anticipate future research directions.
Gene transfer by naked DNA into adult mouse brain. (1996)

Nonviral gene transfer into the central nervous system could provide a basis for therapeutic uses and fundamental research. We show that naked DNA injected intracerebrally into the mouse brain can provide expression of a reporter protein. Expression is dose dependent, being maximal for 150 mu g DNA injected. We observed less than 5 days expression of the luciferase transgene, which is not improved with plasmid preparations virtually free of lipopolysaccharide. Thus, the adult brain behaves as striated muscle for naked DNA uptake and transcription, albeit at a much lower efficiency. In neither adult brain nor muscle did complexation of DNA with cationic lipid improve transgene expression. Double immunolabeling using cell-specific markers shows that both neurons and glia are transfected by naked DNA gene transfer methodology.
Direction estimation using compressive sampling array processing (2009)

We propose a new architecture, the compressive sampling (CS) array, for array based applications, by exploiting compressive sampling in the spatial domain. With random projections (or selections) of the array elements, we can transform a large size array into a small size array. We also propose two approaches of direction-of-arrival (DoA) estimation using our CS array, I. (joint) CS recovery, and II. CS beamformers. As a result we can greatly reduce the hardware complexity and software complexity while still maintaining the high resolution achieved as if a large size array were used.
Requirement for sphingosine 1–phosphate receptor-1 in tumor angiogenesis demonstrated by in vivo RNA interference (2004)

Angiogenesis, or new blood vessel formation, is critical for the growth and spread of tumors. Multiple phases of this process, namely, migration, proliferation, morphogenesis, and vascular stabilization, are needed for optimal tumor growth beyond a diffusion-limited size. The sphingosine 1–phosphate (S1P) receptor-1 (S1P(1)) is required for stabilization of nascent blood vessels during embryonic development. Here we show that S1P(1) expression is strongly induced in tumor vessels. We developed a multiplex RNA interference technique to downregulate S1P(1) in mice. The small interfering RNA (siRNA) for S1P(1) specifically silenced the cognate transcript in endothelial cells and inhibited endothelial cell migration in vitro and the growth of neovessels into subcutaneous implants of Matrigel in vivo. Local injection of S1P(1) siRNA, but not a negative control siRNA, into established tumors inhibited the expression of S1P(1) polypeptide on neovessels while concomitantly suppressing vascular stabilization and angiogenesis, which resulted in dramatic suppression of tumor growth in vivo. These data suggest that S1P(1) is a critical component of the tumor angiogenic response and argue for the utility of siRNA technology in antiangiogenic therapeutics.
Methanol/Gasoline Blends as Automotive Fuel (1975)

&lt;div class="htmlview paragraph"&gt;An experimental program was conducted by the Energy Research &amp;amp; Development Administration's Bartlesville (Okla.) Energy Research Center to determine the effect on exhaust emissions and fuel economy when methanol is added to conventional motor fuel, that is, gasoline. Ten 1974 and 1975 model vehicles were used in the study. Ambient temperature was varied from 20° to 100°F to determine temperature effects while using methanol/gasoline blends. Emissions were generally modified as a consequence of the fact that the addition of methanol to gasoline alters both the fuel vapor pressure and the stoichiometry of the air-fuel mixture. Fuel economy was generally decreased by methanol addition.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Moderate mileage accumulation using 10% methanol fuel showed no deterioration either in emissions control or of fuel-related engine components. Driveability differences between methanol 10% blends and gasoline were detectable but were judged not to be objectionable.&lt;/div&gt;
Spontaneous, Lower-Extremity Venous Thrombosis in Children (1973)

Spontaneous lower-extremity venous thrombosis, although common in adults, is not mentioned in current pediatric textbooks. Case records from 1952 to 1972 at the Children's Hospital of Denver were reviewed, and 28 cases of venous thrombosis unrelated to local venous catheterization or venous surgery were identified. Local infection, trauma, and immobilization were the most important predisposing factors. The most frequent diagnostic findings were local tenderness and increased size of the involved extremity. Complications developed in seven of 28 cases, including three suspected cases of pulmonary emboli and three cases of staphylococcal septicemia. There was one fatality. Specific conclusions about therapy from this study could not be made. However, with venous thrombosis in children, it is recommended to identify local predisposing infections, obtain blood cultures, and treat with antibiotics when indicated.
The VesiVax system: a method for rapid vaccine development (2007)

The VesiVax system is based upon the concept that highly potent vaccines can be designed by engineering proteins that are capable of stably inserting themselves into liposomes. Such a nanoscale liposomal particle can then serve as an immunogen for vaccine development. The VesiVax vaccine technology platform is designed to make it relatively easy to engineer and produce new vaccines quickly. Vaccines based on the VesiVax system have been designed against the influenza virus and herpes simplex type 2 virus, the causative agents of the "flu" and genital herpes, respectively. Both vaccines have been tested in animal models and have demonstrated significant protective efficacy from challenge with lethal doses of virus. Assays of the immunological parameters suggest that both T and B cell responses can be elicited by VesiVax vaccines. The safety profile of the VesiVax vaccines is expected to be much better than that of vaccines prepared by conventional techniques. Taken together, the inherent flexibility of the VesiVax platform is expected to facilitate the rapid development of new vaccines which are effective at stimulating protective immune responses.
Treatment of Acute Cluster Headache with Sumatriptan (1991)

Sumatriptan is an effective and well-tolerated treatment for acute attacks of cluster headache.
FasL:Fas ratio--a prognostic factor in breast carcinomas. (2000)

Programmed cell death (apoptosis) is primarily mediated by Fas ligand (FasL; CD95L) and the Fas receptor (Fas; CD95). In this study, FasL was detected by immunohistochemical analysis in 85% of breast carcinomas and 14% of fibroadenomas randomly chosen, indicating that high expression of FasL might play a role in tumor pathology. FasL and Fas levels as well as FasL:Fas ratios were further ascertained in 215 human breast tumors, including 199 invasive ductal carcinomas, by real-time quantitative reverse transcription-PCR and compared with expression levels and ratios found in 25 normal human tissues, in 37 fibroadenomas, and in 5 normal breast tissues. Among breast carcinomas, high FasL mRNA expression seems to be positively correlated with histological grading (n = 212; P<0.0001). A ratio of FasL:Fas mRNA transcripts >1 is found to be significantly associated with decreased patient's disease-free survival (n = 211; P<0.03) and increased mortality (n = 211; P = 0.19). A FasL:Fas ratio >1 is related to tumor progression scored by histological grading (n = 212; P<0.02). The selection process leading to highly aggressive breast tumor variants might be enhanced by FasL-mediated tumor fratricide, eventually a possible target for novel therapeutic strategies.
Cell surface syndecan-1 on distinct cell types differs in fine structure and ligand binding of its heparan sulfate chains. (1994)

Heparan sulfate (HS) can bind a large variety of biological effectors, including extracellular matrix components, growth factors, chemokines, degradative enzymes, and protease inhibitors. Where studied, HS is known to be structurally heterogeneous and to vary in sulfation pattern between cells and tissues. Because heparan sulfate can represent several distinct proteoglycans, we asked whether the structural variation in the heparan sulfate chains of a single species of cell surface proteoglycan is a reproducible, differentiated characteristic and whether the variation can result in distinct biological functions. We studied the molecular structure and binding affinity for type I collagen and fibroblast growth factor-2 of syndecan-1 purified from the surfaces of NMuMG normal murine mammary gland epithelia, NIH/3T3 fibroblasts, and BALB/3T3 endothelioid cells. Syndecan-1 from these cell types varied in molecular mass largely due to variation in the length of the HS chains. Although the highly sulfated and N-acetylated domains in these HS chains were organized similarly, the number of highly sulfated domains differed. The disaccharide compositions were also similar except for reproducible and consistent differences in the amount of hexuronic acid-N-sulfated-6-O-sulfated glucosamine and 2-O-sulfated hexuronic acid-N-sulfated glucosamine. These differences were confirmed by oligosaccharide mapping, which showed cell type-specific variations in the composition of the highly sulfated domains. These structural variations correlated with cell type-specific differences in the affinity of syndecan-1 and its isolated HS chains for type I collagen. However, no differences in affinity for fibroblast growth factor-2 were detected. The results indicate that the size, fine structure, and ligand affinity of the HS chains on a single proteoglycan species differ in a consistent and reproducible manner between cell types. Thus, the variation in structure and binding ability of HS on syndecan-1 is a differentiated characteristic of the cell type that can enable cells to respond distinctly to the HS-binding effectors in the cellular microenvironment.
The glucocorticoid receptor mediates a survival signal in human mammary epithelial cells. (2000)

Complex autocrine and paracrine signaling pathways control the multiple cycles of epithelial cell proliferation and involution characteristic of the human mammary gland. Activation of these pathways can lead to cell division, cell cycle arrest, apoptosis, or survival; their aberrant regulation often contributes to malignant transformation. In this report, we show that glucocorticoid signals a potent survival pathway in the immortalized human mammary epithelial cell line MCF10A. Withdrawal of glucocorticoid from defined media triggers apoptosis, despite the presence of epidermal growth factor and insulin. Apoptosis is accelerated by ectopic expression of c-Myc and blocked by overexpression of Bcl2. Although MCF10A cells can undergo apoptosis after CD95/Fas receptor activation, cell death caused by glucocorticoid withdrawal is independent of CD95/ Fas receptor signaling. The mechanism through which glucocorticoid inhibits apoptosis is also independent of phosphatidylinositol 3-kinase activity and its downstream target Akt, thus establishing the existence of a novel epithelial cell survival pathway mediated by glucocorticoids.
Rapid assay for detection ofEschenchia colixanthine-guanine phosphoribosyltransferase activity in transduced cells (1985)

Cultured mammalian cells transduced with the Escherichia coli gene, Ecogpt, synthesize the bacterial enzyme xanthine-guanine phosphoribosyl transferase (XGPT) (1). This paper describes a method for measuring XGPT activity in crude cell extracts by following the conversion of 14C-xanthine (X) to 14C-xanthine monophosphate (XMP) and 14C-xanthosine (XR) by thin layer chromatography. The method is rapid, easy to use, sensitive and linear over a wide range of XGPT activity and has been useful for detecting XGPT in cells that were transiently transfected or stably transformed with Ecogpt. During our studies, we have found that a human cell line (XP20S) converts xanthine to XMP. This activity is probably catalyzed by a variant hypoxanthine-guanine phosphoribosyltransferase (HGPT) since the low activity is readily inhibited by hypoxanthine. A low level of conversion of X to XMP may explain why some cell lines are not killed in a medium containing mycophenolic acid and X.
IL-10 expression profiling in human monocytes (2002)

Abstract Interleukin-10 (IL-10) is a potent anti-inflammatory cytokine with numerous immunomodulatory effects, including the inhibition of proinflammatory cytokine production. The mechanisms by which IL-10 exerts these effects still remain largely unknown. As there is evidence that suggests IL-10-mediated cytokine suppression requires the induction of an intermediate gene, we have used gene-chip technology to identify IL-10-inducible genes in human monocytes. We have been able to identify a total of 19 genes that are up-regulated in response to IL-10. Three of these genes had been identified previously: IL-1ra, suppressors of cytokine signaling-3, and CD163; however, the other 16 represent newly identified IL-10-responsive genes. Further analysis of the regulation of eight of these genes showed a remarkable specificity to regulation by lipopolysaccharides (LPS) and IL-10, but not by other anti-inflammatory mediators such as IL-4 and transforming growth factor-β, suggesting that two diverse stimuli such as IL-10 and LPS may engage common signaling mechanisms.
Effect of tissue-harvesting site on yield of stem cells derived from adipose tissue: implications for cell-based therapies (2008)

The stromal vascular fraction (SVF) of adipose tissue contains an abundant population of multipotent adipose-tissue-derived stem cells (ASCs) that possess the capacity to differentiate into cells of the mesodermal lineage in vitro. For cell-based therapies, an advantageous approach would be to harvest these SVF cells and give them back to the patient within a single surgical procedure, thereby avoiding lengthy and costly in vitro culturing steps. However, this requires SVF-isolates to contain sufficient ASCs capable of differentiating into the desired cell lineage. We have investigated whether the yield and function of ASCs are affected by the anatomical sites most frequently used for harvesting adipose tissue: the abdomen and hip/thigh region. The frequency of ASCs in the SVF of adipose tissue from the abdomen and hip/thigh region was determined in limiting dilution and colony-forming unit (CFU) assays. The capacity of these ASCs to differentiate into the chondrogenic and osteogenic pathways was investigated by quantitative real-time polymerase chain reaction and (immuno)histochemistry. A significant difference (P = 0.0009) was seen in ASC frequency but not in the absolute number of nucleated cells between adipose tissue harvested from the abdomen (5.1 +/- 1.1%, mean +/- SEM) and hip/thigh region (1.2 +/- 0.7%). However, within the CFUs derived from both tissues, the frequency of CFUs having osteogenic differentiation potential was the same. When cultured, homogeneous cell populations were obtained with similar growth kinetics and phenotype. No differences were detected in differentiation capacity between ASCs from both tissue-harvesting sites. We conclude that the yield of ASCs, but not the total amount of nucleated cells per volume or the ASC proliferation and differentiation capacities, are dependent on the tissue-harvesting site. The abdomen seems to be preferable to the hip/thigh region for harvesting adipose tissue, in particular when considering SVF cells for stem-cell-based therapies in one-step surgical procedures for skeletal tissue engineering.
Analyzing Selected Mapping for Peak-to-Average Power Reduction in OFDM (2005)

Orthogonal frequency division multiplexing (OFDM) has become a popular modulation method in high-speed wireless communications. By partitioning a wideband fading channel into flat narrowband channels, OFDM is able to mitigate the detrimental effects of multipath fading using a simple one-tap equalizer. However, in the time domain OFDM signals suffer from large envelope variations, which are often characterized by the peak-to-average ratio (PAR). High PAR signals, like OFDM, require that transmission amplifiers operate at very low power efficiencies to avoid clipping.\n\nIn this thesis we review the most popular OFDM PAR-reduction techniques and demonstrate that selected mapping (SLM) is a particularly promising reduction technique. In a SLM system, an OFDM symbol is mapped to a set of quasi-independent equivalent symbols and then the lowest-PAR symbol is selected for transmission. The tradeoff for PAR reduction in SLM is computational complexity as each mapping requires an additional inverse fast fourier transform (IFFT) operation in the\ntransmitter.\n\nIn additional to an overview of current SLM work, we present a thorough analysis of SLM as well as several novel SLM proposals. First, we derive the closed-form expression for the expected PAR in an SLM system. The expected PAR can be thought of as a metric of PAR reduction capability. Second, we provide a power analysis of SLM to determine if the computational power costs outweigh the power saved through PAR reduction. Through this analysis, we show that SLM is capable of several Watts of net power savings when used in a wireless transmission system. Third, we propose that a PAR threshold should be set in SLM. Such thresholding leads to significant complexity decreases. Fourth, we derive the maximum likelihood (ML) and maximum \textit{a posteriori} (MAP) detection metrics for blind SLM (BSLM) and threshold BSLM respectively. Lastly, we demonstrate that by using monomial phase sequences in SLM blind phase sequence detection is possible with a single FFT operation in the receiver.