gebhart/patrepeval huggingface dataset:
Spatial and temporal depletion of ions from noncrosslinked denaturing polyacrylamide in capillary electrophoresis (1994)

Electrical conductivity across a polyacrylamide-filled capillary decreases during the separation of DNA sequencing fragments. This conductivity decrease is localized to the first few centimeters at the injection (negative) end of the capillary; no conductivity change is noted at the detection (positive) end of the capillary. The zone of decreased conductivity extends further into the capillary as the separation proceeds. The zone is most important for freshly prepared capillaries; capillaries used nine days after polymerization generate an insignificant current drop. The data are consistent with ionic depletion due to differences in transport numbers between the separation medium and the buffer reservoirs.
Bandwidth efficient trellis-coded modulation with prescribed decoding delay - new interpretations and results (2001)

Motivated by previous work of Li and Rimoldi for obtaining bandwidth efficient TCM signals with finite decoding delay, we present an alternative representation for their encoder/signal mapper transmitter structure which merely consists of a single filter having an input equal to the equivalent of the inoput data bits in their implementation.
Cloning and characterization of exodus, a novel beta-chemokine. (1997)

Chemokines are a family of related proteins that regulate leukocyte infiltration into inflamed tissue. Some chemokines such as MIP-1 alpha also inhibit hematopoietic progenitor cell proliferation. Recently, three chemokines, MIP-1 alpha, MIP-1 beta, and RANTES, have been found to significantly decrease human immunodeficiency virus production from infected T cells. We report here the cloning and characterization of a novel human chemokine termed Exodus for its chemotactic properties. This novel chemokine is distantly related to other chemokines (28% homology with MIP-1 alpha) and shares several biological activities. Exodus is expressed preferentially in lymphocytes and monocytes, and its expression is markedly upregulated by mediators of inflammation such as tumor necrosis factor or lipopolysaccharide. Purified synthetic Exodus was found to inhibit proliferation of myeloid progenitors in colony formation assays. Exodus also stimulated chemotaxis of peripheral blood mononuclear cells. The sequence homology, expression, and biological activity indicate that Exodus represents a novel divergent beta-chemokine.
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes (1997)

Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3-140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http:(/)/www.welch.jhu.edu/approximately devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.
Prodrug converting enzyme gene delivery by L. monocytogenes (2008)

These experiments open the way for bacterium mediated tumor specific activation of prodrugs in live animals with tumors.
Identification of a new fimbrial structure in enterotoxigenic Escherichia coli (ETEC) serotype O148:H28 which adheres to human intestinal mucosa: a potentially new human ETEC colonization factor (1987)

Three important fimbrial colonization factor antigens (CFAs) designated CFA/I, CFA/II, and E8775 were identified originally in some human enterotoxigenic Escherichia coli (ETEC) strains because of their mannose-resistant hemagglutination properties. To identify CFA, in strains lacking mannose-resistant hemagglutination properties we exploited the ability of human ETEC strains to adhere to human proximal small intestinal mucosa. ETEC strain B7A (O148:H28) was selected for study because it belongs to an epidemiologically important serotype and does not produce a known CFA, and yet it is known to be pathogenic and cause diarrheal disease in human volunteers. Results of an human enterocyte adhesion assay indicated that some bacteria in cultures of B7A produced adhesive factors. To select for such bacteria, cultured human duodenal mucosal biopsy samples were infected with B7A for up to 12 h, after which time a large percentage of the mucosal surface became colonized by bacteria. A new fimbrial structure morphologically distinct from CFA/I, CFA/II, and E8775 fimbriae and consisting of curly fibrils (approximately 3 nm in diameter) was readily identified when bacteria were subcultured from the mucosa and examined by electron microscopy. Identical fimbriae were produced by ETEC strain 1782-77 of the same serotype. Identification of these fimbriae only on bacteria subcultured from human intestinal mucosa strongly suggests that they promote mucosal adhesion of ETEC serotype O148:H28 and thus represent a potentially new human ETEC CFA.
Carbon dioxide and formic acid—the couple for environmental-friendly hydrogen storage? (2010)

In search for future energy supplies the application of hydrogen as an energy carrier is seen as a prospective issue. However, the implementation of a hydrogen economy is suffering from several unsolved problems. Particularly challenging is the storage of appropriate amounts of hydrogen. In this context the utilization of carbon dioxide–formic acid for hydrogen storing is discussed.
ATP Citrate Lyase (ACLY): A Promising Target for Cancer Prevention and Treatment (2015)

ATP citrate lyase (ACLY), an important enzyme involved in lipid biogenesis linked with glucose metabolism, catalyzes the conversion of citrate to oxaloacetic acid (OAA) and acetyl-CoA. The obtained acetyl-CoA is required for lipid synthesis during membrane biogenesis, as well as for histone acetylation reactions to regulate the expression of certain proteins in aberrantly proliferating cancer cells. Studies have shown a role for ACLY in tumorigenesis whereby increased levels of the enzyme leads to increased metabolic activity via activation of Akt signaling. Increasing lines of evidence suggest that enzymes involved in lipid biogenesis play a significant role in cancer cell proliferation and progression. In many cancer types such as glioblastoma, colorectal cancer, breast cancer, non-small cell lung cancer, hepatocellular carcinoma etc., the level of ACLY has been found to be quite high as compared to normal cells. Cancer cell growth related to overexpression of ACLY can be inhibited by using chemical inhibitors or by the knockdown of ACLY gene. Inhibition of ACLY leads to changes in cancer cell metabolism that promotes tumor growth and proliferation. This review summarizes the role of ACLY in cancer development and its inhibitors in cancer treatment.
Nanowire-based very-high-frequency electromechanical resonator (2003)

Fabrication and readout of devices with progressively smaller size, ultimately down to the molecular scale, is critical for the development of very-high-frequency nanoelectromechanical systems (NEMS). Nanomaterials, such as carbon nanotubes or nanowires, offer immense prospects as active elements for these applications. We report the fabrication and measurement of a platinum nanowire resonator, 43 nm in diameter and 1.3 μm in length. This device, among the smallest NEMS reported, has a fundamental vibration frequency of 105.3 MHz, with a quality factor of 8500 at 4 K. Its resonant motion is transduced by a technique that is well suited to ultrasmall mechanical structures.
The development of a MEMS gyroscope for absolute angle measurement (2005)

Microelectromechanical systems (MEMS) gyroscopes are typically designed to measure angular rate of rotation. A measurement of the angle itself is useful in many applications but cannot be obtained by integrating the angular rate due to the presence of bias errors which cause a drift. This paper presents an innovative design for a vibrating gyroscope that can directly measure both angle and angular rate. The design is based on the principle of measuring the angle of free vibration of a suspended mass with respect to the casing of the gyroscope. Several critical challenges have to be handled before the theoretical sensing concept can be converted into a reliable practical sensor. These include compensating for the presence of dissipative forces, mismatched springs, cross-axis stiffness and transmission of rotary torque. These challenges are addressed by the development of a composite nonlinear feedback control system that compensates for each of the above effects and ensures that the mass continues to behave as a freely vibrating structure. Theoretical analysis and simulation results presented in the paper show that the gyroscope can accurately measure both angle and angular rate for low-bandwidth applications.
Characterization of the Twin-Arginine Translocase Secretion System of Mycobacterium smegmatis (2006)

The twin-arginine translocation (TAT) system secretes fully folded proteins that contain a twin-arginine motif within their signal sequence across the cytoplasmic membrane in bacteria. Using a green fluorescent protein fused with a TAT signal sequence, we demonstrated that Mycobacterium smegmatis contains a TAT system. By inactivating individual genes, we showed that three genes (tatA, tatB, and tatC) are required for a functional TAT system in M. smegmatis. The tat mutants exhibited a decreased growth rate and altered colony morphology compared to the parent strain. Comparison of the secreted proteins of the deltatatC and parent strain by two-dimensional polyacrylamide gel electrophoresis revealed an alteration in the secretion of at least five proteins, and one of the major TAT-dependent secreted proteins was identified as beta-lactamase (BlaS). The genome of M. smegmatis was analyzed with the TATFIND program, and 49 putative TAT substrates were identified, including the succinate transporter DctP. Because disruption of the TAT secretion system has a direct effect on the physiology of M. smegmatis and homologs of the TAT proteins are also present in the genome of Mycobacterium tuberculosis, the TAT secretion system or its substrates may be good candidates for drug or vaccine development.
Efficacy assessment in trials of combination therapy for rheumatoid arthritis. (1996)

The comparison of a combination disease modifying antirheumatic drug (DMARD) regimen with a single DMARD, or one combination with another, raises the same issues encountered when studying rheumatoid arthritis: how to design, conduct, and analyze randomized controlled trials. However, these claims of comparison are unique in that the setting to show primary efficacy is the same as that showing the primary therapeutic placement relative to standard therapy. Ordinarily standard therapy is not determined prior to approval. Accordingly, any combination DMARD trial presupposes agreement on what constitutes standard therapy and, if the intent is to show equivalence, on what (small) difference can be condoned to grant the claim. I address some important considerations regarding the rigor and credibility of designs for these claims, problems far less significant with simple drug vs placebo strategies. These can be grouped into 3 categories: (1) choice of controls/designs/patients to ensure a fair comparison; (2) sufficiently broad design formulations to yield controlled assessments of safety that are as thorough as those for efficacy in the past, and (3) maintaining blinding despite new design features that threaten it.
Misincorporation of free m-tyrosine into cellular proteins: a potential cytotoxic mechanism for oxidized amino acids (2006)

In vitro studies demonstrate that the hydroxyl radical converts L-phenylalanine into m-tyrosine, an unnatural isomer of L-tyrosine. Quantification of m-tyrosine has been widely used as an index of oxidative damage in tissue proteins. However, the possibility that m-tyrosine might be generated oxidatively from free L-phenylalanine that could subsequently be incorporated into proteins as an L-tyrosine analogue has received little attention. In the present study, we demonstrate that free m-tyrosine is toxic to cultured CHO (Chinese-hamster ovary) cells. We readily detected radiolabelled material in proteins isolated from CHO cells that had been incubated with m-[14C]tyrosine, suggesting that the oxygenated amino acid was taken up and incorporated into cellular proteins. m-Tyrosine was detected by co-elution with authentic material on HPLC and by tandem mass spectrometric analysis in acid hydrolysates of proteins isolated from CHO cells exposed to m-tyrosine, indicating that free m-tyrosine was incorporated intact rather than being metabolized to other products that were subsequently incorporated into proteins. Incorporation of m-tyrosine into cellular proteins was sensitive to inhibition by cycloheximide, suggesting that protein synthesis was involved. Protein synthesis using a cell-free transcription/translation system showed that m-tyrosine was incorporated into proteins in vitro by a mechanism that may involve L-phenylalanine-tRNA synthetase. Collectively, these observations indicate that m-tyrosine is toxic to cells by a pathway that may involve incorporation of the oxidized amino acid into proteins. Thus misincorporation of free oxidized amino acids during protein synthesis may represent an alternative mechanism for oxidative stress and tissue injury during aging and disease.
Shape Stability of Octahedral PtNi Nanocatalysts for Electrochemical Oxygen Reduction Reaction Studied by in situ Transmission Electron Microscopy (2018)

Octahedral faceted nanoparticles are highly attractive fuel cell catalysts as a result of their activity for the oxygen reduction reaction (ORR). However, their surface compositional and morphological stability currently limits their long-term performance in real membrane electrode assemblies. Here, we perform in situ heating of compositionally segregated PtNi<sub>1.5</sub> octahedral nanoparticles inside a transmission electron microscope, in order to study their compositional and morphological changes. The starting PtNi<sub>1.5</sub> octahedra have Pt-rich edges and concave Ni-rich {111} facets. We reveal a morphological evolution sequence, which involves transformation from concave octahedra to particles with atomically flat {100} and {111} facets, ideally representing truncated octahedra or cuboctahedra. The flat {100} and {111} facets are thought to comprise a thin Pt layer with a Ni-rich subsurface, which may boost catalytic activity. However, the transformation to truncated octahedra/cuboctahedra also decreases the area of the highly active {111} facets. The morphological and surface compositional evolution, therefore, results in a compromise between catalytic activity and morphological stability. Our findings are important for the design of more stable faceted PtNi nanoparticles with high activities for the ORR.
¿Gramaticalización o desgramaticalización? El reanálisis y subjetivación de verbos como marcadores discursivos en la historia del español (2004)

El trabajo analiza las propiedades sintácticas y semánticas que caracterizan los procesos de gramaticalización por subjetivización, y plantea el problema teórico de si la subjetivización es una gramaticalización, entendida de la manera tradicional, o es una desgramaticalización, o de qué manera participa de uno u otro tipo de cambio. Se muestra que el empobrecimiento sintáctico y en general la pérdida de relacionalidad sintáctica es una propiedad inherente de las expresiones subjetivas. La evidencia empírica base del planteamiento teórico son los verbos que, vía reanálisis, se descategorizaron como verbos plenos y se recategorizaron como marcadores discursivos en la historia del español; el análisis llama la atención sobre la enorme flexibilidad que tiene el español para este tipo de recategorizaciones. Se analizan las características sintácticas y semánticas comunes a los verbos que dan lugar a marcadores, así como las frecuencias relativas de uso y los contextos sintácticos que permitieron ese deslizamiento diacrónico, desde un empleo objetivo' referencial hacia un uso fuertemente valorativo subjetivo y/o intersubjetivo.
Efficacy of Liposomal Bismuth-Ethanedithiol-Loaded Tobramycin after Intratracheal Administration in Rats with Pulmonary Pseudomonas aeruginosa Infection (2012)

We sought to investigate alterations in quorum-sensing signal molecule N-acyl homoserine lactone secretion and in the release of Pseudomonas aeruginosa virulence factors, as well as the in vivo antimicrobial activity of bismuth-ethanedithiol incorporated into a liposome-loaded tobramycin formulation (LipoBiEDT-TOB) administered to rats chronically infected with P. aeruginosa. The quorum-sensing signal molecule N-acyl homoserine lactone was monitored by using a biosensor organism. P. aeruginosa virulence factors were assessed spectrophotometrically. An agar beads model of chronic Pseudomonas lung infection in rats was used to evaluate the efficacy of the liposomal formulation in the reduction of bacterial count. The levels of active tobramycin in the lungs and the kidneys were evaluated by microbiological assay. LipoBiEDT-TOB was effective in disrupting both quorum-sensing signal molecules N-3-oxo-dodeccanoylhomoserine lactone and N-butanoylhomoserine lactone, as well as significantly (P < 0.05) reducing lipase, chitinase, and protease production. At 24 h after 3 treatments, the CFU counts in lungs of animals treated with LipoBiEDT-TOB were of 3 log(10) CFU/lung, comparated to 7.4 and 4.7 log(10) CFU/lung, respectively, in untreated lungs and in lungs treated with free antibiotic. The antibiotic concentration after the last dose of LipoBiEDT-TOB was 25.1 μg/lung, while no tobramycin was detected in the kidneys. As for the free antibiotic, we found 6.5 μg/kidney but could not detect any tobramycin in the lungs. Taken together, LipoBiEDT-TOB reduced the production of quorum-sensing molecules and virulence factors and could highly improve the management of chronic pulmonary infection in cystic fibrosis patients.
Xenotransplantation—the current status and prospects (2017)

Most of the advances required to justify a clinical trial have now been met.
Performance Analysis of Volume-Based Spectrum Sensing for Cognitive Radio (2014)

In this work, the volume-based method for spectrum sensing is analyzed, which is able to provide the desirable properties of constant false-alarm rate, robustness against deviation from independent and identically distributed (IID) noise and being free of noise uncertainty. By computing the first and second moments for the signal-absence and signal-presence hypotheses together with using the Gamma distribution approximation, we derive accurate analytic formulae for the false-alarm and detection probabilities for IID noise situations. This enables us to develop theoretical decision threshold as well as receiver operating characteristic. Numerical results are presented to validate our theoretical findings.
Deep Compositional Captioning: Describing Novel Object Categories without Paired Training Data (2016)

While recent deep neural network models have achieved promising results on the image captioning task, they rely largely on the availability of corpora with paired image and sentence captions to describe objects in context. In this work, we propose the Deep Compositional Captioner (DCC) to address the task of generating descriptions of novel objects which are not present in paired imagesentence datasets. Our method achieves this by leveraging large object recognition datasets and external text corpora and by transferring knowledge between semantically similar concepts. Current deep caption models can only describe objects contained in paired image-sentence corpora, despite the fact that they are pre-trained with large object recognition datasets, namely ImageNet. In contrast, our model can compose sentences that describe novel objects and their interactions with other objects. We demonstrate our model's ability to describe novel concepts by empirically evaluating its performance on MSCOCO and show qualitative results on ImageNet images of objects for which no paired image-sentence data exist. Further, we extend our approach to generate descriptions of objects in video clips. Our results show that DCC has distinct advantages over existing image and video captioning approaches for generating descriptions of new objects in context.
High-speed video analysis system using multiple shuttered charge-coupled device imagers and digital storage (1992)

A fully solid state high-speed video analysis system is presented. It is based on the use of several independent charge-coupled device (CCD) imagers, each shuttered by a liquid crystal light valve. The imagers are exposed in rapid succession and are then read out sequentially at standard video rate into digital memory, generating a time-resolved sequence with as many frames as there are imagers. This design allows the use of inexpensive, consumer-grade camera modules and electronics. A microprocessor-based controller, designed to accept up to ten imagers, handles all phases ofthe recording from exposure timing to image capture and storage to playback on a standard video monitor. A prototype with three CCD imagers and shutters has been built. It has allowed successful three-image video recordings of phenomena such as the action of an air rifle pellet shattering a piece of glass, using a high-intensity pulsed light emitting diode as the light source. For slower phenomena, recordings in continuous light are also possible by using the shutters themselves to control the exposure time. The system records full-screen black and white images with spatial resolution approaching that of standard television, at rates up to 5000 images per second.