gebhart/patrepeval huggingface dataset:
Biological properties of extracellular vesicles and their physiological functions (2015)

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV‐mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd‐sourcing, drawing on the unique EV expertise of academia‐based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.
Anti-c-myc antibody 9E10: epitope key positions and variability characterized using peptide spot synthesis on cellulose (2001)

The 9E10 antibody epitope (EQKLISEEDL) derives from a protein sequence in the human proto-oncogen p62(c-myc) and is widely used as a protein fusion tag. This myc-tag is a powerful tool in protein localization, immunochemistry, ELISA or protein purification. Here, we characterize the myc-tag epitope by substitutional analysis and length variation using peptide spot synthesis on cellulose. The key amino acids of this interaction are the core residues LISE. The shortest peptide with a strong binding signal is KLISEEDL. Dissociation constants of selected peptide variants to the antibody 9E10 were determined. scFv constructs with the shortest possible myc-tags were successfully detected by Western blot and ELISA, giving a signal comparable to that of the original myc-tag.
Nanoscale gold pillars strengthened through dislocation starvation (2006)

It has been known for more than half a century that crystals can be made stronger by introducing defects into them, i.e., by strain-hardening. As the number of defects increases, their movement and multiplication is impeded, thus strengthening the material. In the present work we show hardening by dislocation starvation, a fundamentally different strengthening mechanism based on the elimination of defects from the crystal. We demonstrate that submicrometer sized gold crystals can be 50 times stronger than their bulk counterparts due to the elimination of defects from the crystal in the course of deformation.
Fibrillarin-associated Box C/D Small Nucleolar RNAs inTrypanosoma brucei (2000)

We report the identification of 17 box C/D fibrillarinassociated small nucleolar RNAs (snoRNAs) from the ancient eukaryote, Trypanosoma brucei. To systematically isolate and characterize these snoRNAs, the T. brucei cDNA for the box C/D snoRNA common protein, fibrillarin, was cloned and polyclonal antibodies to the recombinant fibrillarin protein were generated in rabbits. Immunoprecipitations from T. brucei extracts with the anti-fibrillarin antibodies indicated that this trypanosomatid has at least 30 fibrillarin-associated snoRNAs. We have sequenced seventeen of them and designated them TBR for T. brucei RNA 1-17. All of them bear conserved box C, D, C, and D elements, a hallmark of fibrillarin-associated snoRNAs in eukaryotes. Fourteen of them are novel T. brucei snoRNAs. Fifteen bear potential guide regions to mature rRNAs suggesting that they are involved in 2-O-ribose methylation. Indeed, eight ribose methylations have been mapped in the rRNA at sites predicted by the snoRNA sequences. Comparative genomics indicates that six of the seventeen are the first trypanosome homologs of known yeast and vertebrate methylation guide snoRNAs. Our results indicate that T. brucei has many fibrillarin-associated box C/D snoRNAs with roles in 2-O-ribose methylation of rRNA and that the mechanism for targeting the nucleotide to be methylated at the fifth nucleotide upstream of box D or D originated in early eukaryotes.
A Distinctive PdCl2-Mediated Transformation of Fe-Based Metallogels into Metal–Organic Frameworks (2014)

Simple, efficient conversion of viable Fe3+-based metallogels into Fe-metal–organic frameworks (MOFs) has been achieved by PdCl2-mediated gel degradation. The metallogels and the resulting MOFs have been characterized, and a probable mechanism for the event has been elucidated.
Selective in vivo antitumor effects of monoclonal anti-I-A antibody on B cell lymphoma. (1987)

In a study of the biologic consequences of using monoclonal antibodies (mAb) with specificity for I-A for the elimination of an I-A-bearing B cell lymphoma, it was found that, despite the presence of I-A on a number of normal cell types and the propensity of anti-I-A to induce modulation of I-A and I-E on normal cells in vivo, a substantial effect on lymphoma growth could be measured in mAb-treated hosts. Unlike I-A on normal cells, tumor I-A failed to modulate in vivo, and 50% of animals could be cured of lymphoma by multiple doses of anti-I-A mAb. With a sensitive spleen tumor colonization assay, it was shown that neither T lymphocytes nor natural killer cells were involved in tumor elimination by anti-I-A mAb. In addition, C3 depletion only minimally affected the ability of anti-I-A to inhibit tumor growth, suggesting that complement-dependent lysis of tumor cells was not a major mechanism. Spleen cells from long term survivors of tumor challenge and mAb treatment functioned normally as antigen-presenting cells and in the recognition of alloantigens, and serum Ig levels were somewhat higher than in untreated mice; thus, such therapy can be carried out without compromising the immune reactivity of long term survivors.
Recent Case Histories of New Well Applications for Horizontal Drilling (1990)

Abstract In the tradition of other papers that have reviewed horizontal technology and experience (1,2,3), this paper will present a relatively current summary of the status of horizontal drilling. The result of an extensive review of the published literature, careful study of numerous post-well reports, and personal conversations with drilling engineers and directional drilling supervisors who have conducted horizontal drilling operations, the following brief discussions of case histories describe a variety of drilling methods which were used in oilfields in various parts of the world. It will be evident that in the past few years great strides have been made to advance horizontal drilling in three main disciplines. These are: Well planningDrilling mechanics, andRig site operations
Role of L3T4-bearing T-cell populations in experimental murine chlamydial salpingitis (1991)

A role for both the cellular and humoral components of the immune response has been established for chlamydial infection. The significance of helper (L3T4) T cells was evaluated by using a Chlamydia trachomatis murine salpingitis model for upper genital tract chlamydial infection. Mouse oviducts were inoculated with C. trachomatis by using the mouse pneumonitis agent (MoPn) or control medium. Mice depleted of L3T4-bearing lymphocytes had significantly higher (P less than 0.05) numbers of organisms recovered at day 7 postinoculation. The rate of hydrosalpinx formation was significantly higher in the mice depleted of L3T4-bearing lymphocytes (27 of 31 [87%] ) than in the infected undepleted group (8 of 16 [50%] ) (P less than 0.01). The geometric mean antichlamydial immunoglobulin G titers at day 54 postinoculation were significantly higher in the L3T4-depleted mice (mean titer, 2,030) than in the undepleted group (mean titer, 776; P less than 0.05). The rate of fertility was lower in the L3T4-depleted group (2 of 31 [6%]) than in the infected, undepleted mice (2 of 16 [13%]), but this difference did not reach statistical significance. In conclusion, the greater persistence of organisms in the oviduct and higher rates of hydrosalpinx formation in mice depleted of L3T4-bearing cells suggests that these cells play a role in the clearing of organisms following infection and thus in reducing the degree of oviduct obstruction and damage.
Strategies in developing promising histone deacetylase inhibitors (2009)

Histone deacetylases (HDACs) are a family of enzymes that have been of interest in drug discovery for more than 30 years. Inhibitors of HDACs are potential therapeutics for various diseases, such as neurodegenerative diseases, inflammation, viral infection, and especially cancer. Most HDAC inhibitors (HDACi) are designed for cancer therapy. In 2006, suberoylanilide hydroxamic acid was approved by the US Food and Drug Administration for once-daily oral treatment of advanced cutaneous T-cell lymphoma. In the meantime, there have been aggressive efforts to bring HDACi to the market for every major tumor type, either as a single therapy or in combination, and a number of compounds are currently undergoing clinical trials. Multiple strategies have been applied to the rational design of drugs targeting HDACs by taking advantage of the new developments in proteomics, chemogenomics, cheminformatics, and computational chemistry/biology. Herein, we review the current methods successfully used in developing novel HDACi.
Ultrastructural Localization of Calcium in Psoriatic and Normal Human Epidermis (1991)

With ion capture cytochemistry, we previously demonstrated the distribution of calcium ions in murine epidermis, a pattern consistent with a role for this ion in the regulation of epidermal differentiation. Because of the known proliferation and differentiation defects in psoriasis, we compared the calcium distribution of involved vs uninvolved psoriatic lesions and normal human epidermis. Whereas normal human and uninvolved psoriatic epidermis revealed increased calcium-containing precipitates in the uppermost stratum granulosum, in contrast the basal layer of psoriatic lesions contained less extracellular calcium, a condition that favored enhanced proliferation. Moreover, all psoriatic suprabasal cell layers displayed heavier than normal concentrations of calcium, indicating loss of the normal calcium gradient that programs terminal differentiation. This abnormal profile may account for the differentiation defects (eg, parakeratosis) that occur in psoriasis. Finally, psoriatic lesions displayed retained ionic Ca in intercellular domains of the upper stratum granulosum with absence of normal intercellular bilayers, findings that may underlie the abnormal desquamation and permeability barrier in psoriasis.
Microwave Filters (2010)

The general theory of microwave filter design based on lumped-element circuit is described in this chapter. The lowpass prototype filters with Butterworth, Chebyshev and quasielliptic characteristics are synthesized, and the prototype filters are then transformed to bandpass filters by lowpass to bandpass frequency mapping. By using immitance inverters ( J - or K -inverters), the bandpass filters can be realized by the same type of resonators. One design example is given to verify the theory on how to design microwave filters.
Disrupting the Pairing Between let-7 and Hmga2 Enhances Oncogenic Transformation (2007)

MicroRNAs (miRNAs) are approximately 22-nucleotide RNAs that can pair to sites within messenger RNAs to specify posttranscriptional repression of these messages. Aberrant miRNA expression can contribute to tumorigenesis, but which of the many miRNA-target relationships are relevant to this process has been unclear. Here, we report that chromosomal translocations previously associated with human tumors disrupt repression of High Mobility Group A2 (Hmga2) by let-7 miRNA. This disrupted repression promotes anchorage-independent growth, a characteristic of oncogenic transformation. Thus, losing miRNA-directed repression of an oncogene provides a mechanism for tumorigenesis, and disrupting a single miRNA-target interaction can produce an observable phenotype in mammalian cells.
Sol–Gel Preparation of Thick PZN–PZT Film Using a Diol‐Based Solution Containing Polyvinylpyrrolidone for Piezoelectric Applications (2005)

Dense and crack‐free lead zinc niobate–lead zirconate titanate (PZN–PZT) films were deposited on silicon and glass substrates by spin coating using a sol containing propanediol and polyvinylpyrrolidone. Single‐layer PZN–PZT films as thick as 0.80 μm were deposited by a single spin coating with successive heat treatments at 250° and 700°C. After heat treatment, the films were dense, crack free, and optically transparent. In addition, the crystallographic orientation of the thick film was controllable by adjusting the heat‐treatment conditions. The ferroelectric properties of the (111)‐oriented film were superior to those of the (100)‐oriented film. On the other hand, the piezoelectric and dielectric properties of the (100)‐oriented film were better than those of the (111)‐oriented film. The piezoelectric coefficients ( d 33 ) of the PZN–PZT films of 4.0‐μm‐thickness were 192 and 110 pC/N for the (100)‐and (111)‐oriented films, respectively.
Comparison of the phenotypes of the lpxA and lpxD mutants of Escherichia coli (1995)

We compared the phenotype of two thermosensitive Escherichia coli mutants defective in lipid A biosynthesis i.e. SM101 (lpxA) and CDH23-213 (lpxD). More than 40% of the periplasmic 27-kDa marker enzyme β-lactamase was released from SM101 at 28°C. At this temperature, the mutant still grew with a generation time (67 min), not much longer than that of the parent control strain (57 min). CDH23-213 released β-lactamase only at higher temperatures. SM101 and CDH23-213 were both unable to grow in hypo-osmotic conditions. Derivatives of SM101 and CDH23-213 with mdoA::Tn 10 had identical phenotypes (including thermosensitivity and defective outer membrane permeability barrier to hydrophobic probes) to those of SM101 and CDH23-213, indicating that the potential loss of membrane-derived oligosaccharides (MDO) did not explain these phenotypic properties. A method for the estimation of lipid A synthesis rate was developed.
Defective prohormone processing and altered pancreatic islet morphology in mice lacking active SPC2 (1997)

The prohormone convertase SPC2 (PC2) participates in the processing of proinsulin, proglucagon, and a variety of other neuroendocrine precursors, acting either alone or in conjunction with the structurally related dense-core granule convertase SPC3 (PC3/PC1). We have generated a strain of mice lacking active SPC2 by introducing the neomycin resistance gene (Neor) into the third exon of the mSPC2 gene. This gene insertion results in the synthesis of an exon 3-deleted form of SPC2 that does not undergo autoactivation and is not secreted. The homozygous mutant mice appear to be normal at birth. However, they exhibit a small decrease in rate of growth. They also have chronic fasting hypoglycemia and a reduced rise in blood glucose levels during an intraperitoneal glucose tolerance test, which is consistent with a deficiency of circulating glucagon. The processing of proglucagon, prosomatostatin, and proinsulin in the alpha, delta, and beta cells, respectively, of the pancreatic islets is severely impaired. The islets in mutant mice at 3 months of age show marked hyperplasia of alpha and delta cells and a relative diminution of beta cells. SPC2-defective mice offer many possibilities for further delineating neuroendocrine precursor processing mechanisms and for exploring more fully the physiological roles of many neuropeptides and peptide hormones.
Intravenous levodopa in hallucinating Parkinson's disease patients (1998)

In five nondemented Parkinson9s disease patients with daily visual hallucinations, we tested whether high-dose IV levodopa (LD) infusions precipitated hallucinations. Two infusion paradigms were studied, each with 1.5—mg/kg hourly dose for 4 hours—steady infusion and pulse infusion of the full hour dose over 5 minutes each hour. In both protocols, plasma LD levels changed significantly during the infusion protocol. The cumulative area under the curve was equivalent for the two infusions. All patients remained alert, and none developed visual hallucinations. The two patients with peak-dose dyskinesias on oral LD developed prominent dyskinesias during the infusion. Visual hallucinations do not relate simply to high levels of LD or to sudden changes in plasma levels.
Quantum Dot Image Sensors (2012)

Colloidal quantum dots are semiconductors synthesized in, and applied from, the solution phase. They enable wide tuning of their sharp spectral response via the quantum size effect. I will present advances in colloidal quantum dot light sensing materials and devices and their application in imaging.
Sensing of RNA Viruses: a Review of Innate Immune Receptors Involved in Recognizing RNA Virus Invasion (2012)

Our knowledge regarding the contribution of the innate immune system in recognizing and subsequently initiating a host response to an invasion of RNA virus has been rapidly growing over the last decade. Descriptions of the receptors involved and the molecular mechanisms they employ to sense viral pathogen-associated molecular patterns have emerged in great detail. This review presents an overview of our current knowledge regarding the receptors used to detect RNA virus invasion, the molecular structures these receptors sense, and the involved downstream signaling pathways.
A 250-622 MHz deskew and jitter-suppressed clock buffer using a frequencyand delay-locked two-loop architecture (2002)

Recently, several delay-locked loop (DLL) circuits for on-chip clock supply have been reported. In this paper a new 2-loop circuit has been designed for on-chip clock-supply applications which require a quick pull-in, suppressed jitter in a wide operating frequency range. The design technologies included are: 1) A 2-loop architecture in which a frequency-locked loop (FLL) is provided separately from a DLL for quick pull-in over a wide frequency range; 2) A current-mode phase detector (CMPD) used in the DLL, which makes use of a flip-flop metastability for increasing the phase-difference detecting sensitivity.
A GaAs MESFET Mixer with Very Low Intermodulation (1987)

This paper describes the design and performance of a new type of resistive mixer, which uses the channel resistance of a GaAs MESFET to achieve frequency mixing. Because this resistance is highly linear, very low intermodulation results. The mixer can be analyzed via existing mixer theory, with good agreement with measured performance. At 10 dBm LO power, the X-band mixer achieves 6.5 dB conversion loss, 6.6 dB noise figure, 21.5 dBm output third-order intermodulation intercept point, and 9.1 dBm 1-dB compression point.
Centers for Oceans and Human Health: a unified approach to the challenge of harmful algal blooms (2008)

Along the way, many challenges have been encountered that are common to the OHH Centers and also echo those of the wider HAB community. Long-term field data and basic biological information are needed to develop accurate models. Sensor development is hindered by the lack of simple and rapid assays for algal cells and especially toxins. It is also critical to adequately understand the human health effects of HAB toxins. Currently, we understand best the effects of acute toxicity, but almost nothing is known about the effects of chronic, subacute toxin exposure. The OHH initiatives have brought scientists together to work collectively on HAB issues, within and across regions. The successes that have been achieved highlight the value of collaboration and cooperation across disciplines, if we are to continue to advance our understanding of HABs and their relationship to human health.
Modification of the N-Glycosylation Pathway to Produce Homogeneous, Human-Like Glycans Using GlycoSwitch Plasmids (2007)

Glycosylation is an important issue in heterologous protein production for therapeutic applications. Glycoproteins produced in Pichia pastoris contain high mannose glycan structures that can hamper downstream processing, might be immunogenic, and cause rapid clearance from the circulation. This chapter describes a method that helps solving these glycosylation-related problems by inactivation of OCH1, overexpression of an HDEL-tagged mannosidase, and overexpression of a Kre2/GlcNAc-transferase I chimeric enzyme. Different plasmids are described as well as glycan analysis methods.
Nucleotide Biosynthesis Is Critical for Growth of Bacteria in Human Blood (2008)

Proliferation of bacterial pathogens in blood represents one of the most dangerous stages of infection. Growth in blood serum depends on the ability of a pathogen to adjust metabolism to match the availability of nutrients. Although certain nutrients are scarce in blood and need to be de novo synthesized by proliferating bacteria, it is unclear which metabolic pathways are critical for bacterial growth in blood. In this study, we identified metabolic functions that are essential specifically for bacterial growth in the bloodstream. We used two principally different but complementing techniques to comprehensively identify genes that are required for the growth of Escherichia coli in human serum. A microarray-based and a dye-based mutant screening approach were independently used to screen a library of 3,985 single-gene deletion mutants in all non-essential genes of E. coli (Keio collection). A majority of the mutants identified consistently by both approaches carried a deletion of a gene involved in either the purine or pyrimidine nucleotide biosynthetic pathway and showed a 20- to 1,000-fold drop in viable cell counts as compared to wild-type E. coli after 24 h of growth in human serum. This suggests that the scarcity of nucleotide precursors, but not other nutrients, is the key limitation for bacterial growth in serum. Inactivation of nucleotide biosynthesis genes in another gram-negative pathogen, Salmonella enterica, and in the gram-positive pathogen Bacillus anthracis, prevented their growth in human serum. The growth of the mutants could be rescued by genetic complementation or by addition of appropriate nucleotide bases to human serum. Furthermore, the virulence of the B. anthracis purE mutant, defective in purine biosynthesis, was dramatically attenuated in a murine model of bacteremia. Our data indicate that de novo nucleotide biosynthesis represents the single most critical metabolic function for bacterial growth in blood and reveal the corresponding enzymes as putative antibiotic targets for the treatment of bloodstream infections.
New results in subband/wavelet image coding (2002)

A novel technique for redundancy removal of quantized coefficents of a wavelet transform is discussed. This technique rests on the coding of the address of nonzero coefficients using blocks in both lossy and lossless approach. Simulations show that the proposed technique performs better than classical methods, while maintaining an efficient implementation complexity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>