gebhart/patrepeval huggingface dataset:
The Ensemble Kalman Filter: Theoretical formulation and practical implementation (2003)

The purpose of this paper is to provide a comprehensive presentation and interpretation of the Ensemble Kalman Filter (EnKF) and its numerical implementation. The EnKF has a large user group, and numerous publications have discussed applications and theoretical aspects of it. This paper reviews the important results from these studies and also presents new ideas and alternative interpretations which further explain the success of the EnKF. In addition to providing the theoretical framework needed for using the EnKF, there is also a focus on the algorithmic formulation and optimal numerical implementation. A program listing is given for some of the key subroutines. The paper also touches upon specific issues such as the use of nonlinear measurements, in situ profiles of temperature and salinity, and data which are available with high frequency in time. An ensemble based optimal interpolation (EnOI) scheme is presented as a cost-effective approach which may serve as an alternative to the EnKF in some applications. A fairly extensive discussion is devoted to the use of time correlated model errors and the estimation of model bias.
The Mentor I Never Met (2006)

Abstract Donald Wood writes from a unique perspective in his tribute to Neil Postman. Although he never had the opportunity to meet Postman in person, Wood traces the overwhelming influence the godfather of media ecology has had on his own professional career over a 40-year span. Through his books, some correspondence, and a few phone conversations, Postman shaped Wood's professional career and strongly determined the direction of two of his books—including writing the foreword to one of them.
Technical Aspects in Studying Peritoneal Morphology in Animal Models of Peritoneal Dialysis (2009)

Our results suggest that peritoneum obtained from the anterior abdominal wall is the most affected area and therefore the most suitable site to investigate peritoneal changes in the experimental rat PD model. There were no significant differences between fixation with 4% formaldehyde and B5 solution. Abdominal wall samples should be of the same direction of inner abdominal muscle, that is, horizontal sectioning should be used for measurements of the submesothelial area.
HPV in Head and Neck Cancer: Treatment (2012)

과거 20~30년간 미국 및 북유럽에서 두경부암의 발생 빈도는 흡연율이 감소함에 따라 조금씩 낮아지고 있지만， 두경부암 중 구인두암은 이와 반대로 그 빈도가 매년 2% 가량 증가하고 있으며 특히 흡연과 음주를 하지 않는 젊은 남자들에서 구인두암의 발생 증가가 뚜렷이 관찰되고 있 다. 최근，이러한 구인두암의 발생 빈도의 증가가 인간유두 종바이러스(Human papillomavirus，HPV)의 감염 증가와 관련이 있음이 확인되었으며，이에 따라 HPV는 전통적인 두경부암의 원인 인자들인 술，담배와 함께 두경부암을 일 으키는 중요한 원인 중 하나로 여겨지게 되었다. 비흡연자 의 경우 구강 내에 HPV 가 감염된 경우，감염이 되지 않 은 경우보다 두경부암의 발생 확율이 15~200배 가량 높 아지는 것으로 알려져 있다.1–5)
Pressure/photo sensor utilizing polymer magnetic composite (1993)

A polymer magnetic composite (PMC) is a flexible thick film and is composed of a ferrite powder with variable possible Curie temperatures, polymer and solvent. It is found that high and low Curie temperature PMCs can be used for pressure and photosensors, respectively. The set up combined with the PMC and a pressure element acts as a pressure sensor. The device, painted with a radiant flux absorbent on the surface of the PMC, responds to the visible rays. The pressure and light signals are read out by a Hall element in noncontact with the PMC.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Role of Avian Pathogenic <i>Escherichia coli</i> Virulence Factors in Bacterial Interaction with Chicken Heterophils and Macrophages (2002)

Avian pathogenic Escherichia coli (APEC) cause extraintestinal disease in avian species via respiratory tract infection. Virulence factors associated with APEC include type 1 and P fimbriae, curli, aerobactin, lipopolysaccharide (LPS), K1 capsular antigen, temperature-sensitive hemagglutinin (Tsh), and an uncharacterized pathogen-specific chromosomal region (the 0-min region). The role of these virulence factors in bacterial interaction with phagocytes was investigated by using mutants of three APEC strains, each belonging to one of the most predominant serogroups O1, O2, and O78. Bacterial cell interaction with avian phagocytes was tested with primary cultures of chicken heterophils and macrophages. The presence of type 1 fimbriae and, in contrast, the absence of P fimbriae, K1 capsule, O78 antigen, and the 0-min region promoted bacterial association with chicken heterophils and macrophages. The presence of type 1 and P fimbriae, O78 antigen, and the 0-min region seemed to protect bacteria against the bactericidal effect of phagocytes, especially heterophils. The tested virulence factors seemed to have a limited role in intracellular survival for up to 48 h in macrophages. Generally, opsonized and nonopsonized bacteria were eliminated to the same extent, but in some cases, unopsonized bacteria were eliminated to a greater extent than opsonized bacteria. These results confirm the important role of type 1 fimbriae in promotion of initial phagocytosis, but nevertheless indicate a role for type 1 fimbriae in the protection of bacteria from subsequent killing, at least in heterophils. The results also indicate a role for K1 capsule, O78 antigen, P fimbriae, and the 0-min region in initial avoidance of phagocytosis, but demonstrate an additional role for O78 antigen, P fimbriae, and the 0-min region in subsequent protection against the bactericidal effects of phagocytes after bacterial association has occurred.
Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C‐dependent activation of nuclear genes: repression by guanosine‐3′‐5′‐bisdiphosphate and activation by sigma factor 5 (2015)

Abscisic acid (ABA) represses the transcriptional activity of chloroplast genes (determined by run-on assays), with the exception of psbD and a few other genes in wild-type Arabidopsis seedlings and mature rosette leaves. Abscisic acid does not influence chloroplast transcription in the mutant lines abi1-1 and abi2-1 with constitutive protein phosphatase 2C (PP2C) activity, suggesting that ABA affects chloroplast gene activity by binding to the pyrabactin resistance (PYR)/PYR1-like or regulatory component of ABA receptor protein family (PYR/PYL/RCAR) and signaling via PP2Cs and sucrose non-fermenting protein-related kinases 2 (SnRK2s). Further we show by quantitative PCR that ABA enhances the transcript levels of RSH2, RSH3, PTF1 and SIG5. RelA/SpoT homolog 2 (RSH2) and RSH3 are known to synthesize guanosine-3'-5'-bisdiphosphate (ppGpp), an inhibitor of the plastid-gene-encoded chloroplast RNA polymerase. We propose, therefore, that ABA leads to an inhibition of chloroplast gene expression via stimulation of ppGpp synthesis. On the other hand, sigma factor 5 (SIG5) and plastid transcription factor 1 (PTF1) are known to be necessary for the transcription of psbD from a specific light- and stress-induced promoter (the blue light responsive promoter, BLRP). We demonstrate that ABA activates the psbD gene by stimulation of transcription initiation at BLRP. Taken together, our data suggest that ABA affects the transcription of chloroplast genes by a PP2C-dependent activation of nuclear genes encoding proteins involved in chloroplast transcription.
Influence of Hydrophobicity on Polyelectrolyte Complexation (2017)

Polyelectrolyte complexes are a fascinating class of soft materials that can span the full spectrum of mechanical properties from low-viscosity fluids to glassy solids. This spectrum can be accessed by modulating the extent of electrostatic association in these complexes. However, to realize the full potential of polyelectrolyte complexes as functional materials, their molecular level details need to be clearly correlated with their mechanical response. The present work demonstrates that by making simple amendments to the chain architecture, it is possible to affect the salt responsiveness of polyelectrolyte complexes in a systematic manner. This is achieved by quaternizing poly(4-vinylpyridine) (QVP) with methyl, ethyl, and propyl substituents—thereby increasing the hydrophobicity with increasing side chain length—and complexing them with a common anionic polyelectrolyte, poly(styrenesulfonate). The mechanical behavior of these complexes is compared to the more hydrophilic system of poly(styrenesulfonate) and poly(diallyldimethylammonium) by quantifying the swelling behavior in response to salt stimuli. More hydrophobic complexes are found to be more resistant to doping by salt, yet the mechanical properties of the complex remain contingent on the overall swelling ratio of the complex itself, following near universal swelling–modulus master curves that are quantified in this work. Furthermore, the rheological behaviors of QVP complex coacervates are found to be approximately the same, only requiring higher salt concentrations to overcome strong hydrophobic interactions, demonstrating that hydrophobicity can be used as an important parameter for tuning the stability of polyelectrolyte complexes in general, while still preserving the ability to be processed “saloplastically”.
Deciphering targeting rules of splicing modulator compounds: case of TG003 (2015)

In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators.
Repair of Abdominal Aortic Aneurysm by Transfemoral Endovascular Graft Placement (1994)

Transfemoral repair is safe and appears to be effective. Phase II study currently is appropriate, with need for long-term follow-up.
Regenerated Marine Gas Turbines: Part I — Cycle Selection and Performance Estimation (1982)

Analytical studies are currently being conducted by the David Taylor Naval Ship R&D Center to assess the suitability of regenerative-cycle and intercooled, regenerative-cycle gas turbines for naval applications. This paper, which is presented in two parts, discusses results of initial investigations to identify attractive engine concepts based on existing turbomachinery and to consider the regenerator technology required to develop these engine concepts. Part I of the paper deals with the attractive engine concepts. A survey of simple-cycle engines rated from 2500 to 50,000 hp (2 to 37 MW) was conducted to determine the cycle conditions, performance characteristics, and mechanical configurations of current marine gas turbines. Comparative cycle studies were performed to establish the performance trends of the simple, regenerative, intercooled-simple, and intercooled-regenerative cycles. Hypothetical engine concepts are described which illustrate the improved performance obtained by adding heat exchangers for regeneration and intercooling to today’s simple-cycle marine engines.
Dendrite Remodeling and Other Abnormalities in the Retinal Ganglion Cells of Ins2<sup>Akita</sup>Diabetic Mice (2008)

The data show that retinal ganglion cells are lost from the peripheral retina of mice within the first 3 months of diabetes and that the dendrites of surviving large ON-type cells undergo morphologic changes. These abnormalities may explain some of the early anomalies in visual function induced by diabetes.
Production and characterization of a monoclonal antibody reactive with a specific neoantigenic determinant (comprising B beta 54-118) in degradation products of fibrin and of fibrinogen (1986)

Balb/c mice were immunized with a mixture of fibrin degradation products (XDPs) prepared by complete lysis of a human blood clot by tissue-type plasminogen activator and purified by immunoaffinity chromatography. Spleen cells of the mice were fused with P3 X 63 Ag 8653 myeloma cells. A clone (FDP 14) was selected that produces monoclonal antibodies (MoAbs) of the IgG1 kappa type that react with a neoantigenic determinant exposed in these XDPs, but not in intact fibrinogen or in fibrin monomers. Furthermore, the MoAb is reactive with some pure, individual degradation products of fibrinogen (fragments X, Y, E, and the N-terminal disulphide knot) and with the fibrinogen B beta-chain but not with A alpha- and gamma-chains or with fragments D, FCB-2 and FCB-3. Comparison of the known primary structures of these fibrinogen fragments indicates that the stretch B beta 54–118 comprises at least an important part of the epitope recognized by FDP-14. Apparently, this stretch contributes importantly to a neoantigenic determinant that is not functional in intact fibrinogen and fibrin monomer and that can be made functional by reduction of fibrinogen, or by digestion with plasmin or CNBr.
DNA synthesis and DNA polymerase activity of herpes simplex virus type 1 temperature-sensitive mutants (1975)

Fifteen temperature-sensitive mutants of herpes simplex virus type 1 were studied with regard to the relationship between their ability to synthesize viral DNA and to induce viral DNA polymerase (DP) activity at permissive (34 C) and nonpermissive (39 C) temperatures. At 34 C, all mutants synthesized viral DNA, while at 39 C four mutants demonstrated a DNA+ phenotype, three were DNA+/-, and eight were DNA-. DNA+ mutants induced levels of DP activity similar to thhose of the wild-type virus at both temperatures, and DNA+/- mutants induced reduced levels of DP activity at 39 C but not at 34 C. Among the DNA- mutants three were DP+, two were DP+/-, and three showed reduced DP activity at 34 C with no DP activity at 39 C. DNA-, DP- mutants induced the synthesis of a temperature-sensitive DP as determined by in vivo studies.
Mobile Terminal Capability Management for Services Enabling (2006)

The innovation of mobile communications is driving the emergence of new and exciting services. Some killer applications, such as 3 GPP streaming service, need a functionality of mobile terminal capability exchange for services enabling, which requires a mechanism to manage terminal capabilities. This paper presents the mobile terminal capability management (MTCM) architecture allowing to collect, update, store, and provide terminal capabilities dynamically. The proposed architecture leverages open mobile alliance (OMA) Device Management enabler and provides a uniform interface to various service platforms and enabling protocols. The implementation approach of this architecture could be centralized, distributed or mixed. The possible approaches that leverage the Internet Protocol Multimedia Subsystem (IMS) capabilities are also considered.
A possible ligand of serum origin for the kidney autoantigen of Heymann nephritis. (1988)

Earlier studies have localized the Heymann nephritis (HN) autoantigen (gp330) in the coated pits of the plasma membrane and multivesicular bodies of the glomerular epithelial cell. Because of these locations in the glomerular epithelial cells, it has been suggested that the HN Ag may be a receptor. The aim of our study was to search for a ligand which can bind the HN autoantigen. Normal rat serum was subjected to SDS-PAGE under reducing and non-reducing conditions followed by Western analysis of the separated polypeptides. A reaction was revealed directly by autoradiography using 125I labeled HN autoantigen as a probe and indirectly by enzyme immunodetection using unlabeled nephritogenic autoantibody (anti-gp330) eluted from glomeruli of diseased rats followed by biotinylated rabbit anti-rat IgG avidin-peroxidase complex. A polypeptide of 76 kDa Mr was identified under non-reducing conditions as a serum protein reacting with the HN autoantigen. Reactivity of the 76-kDa polypeptide was lost when serum was electrophoresed under reducing conditions. Direct binding of the 76-kDa polypeptide obtained from serum to the HN autoantigen obtained from kidney suggests that the 76-kDa polypeptide may be a ligand for the autoantigen. This is the first documentation of a possible ligand for the HN autoantigen. Not only does this polypeptide bind to the HN autoantigen but it also shows direct binding with the nephritogenic autoantibody eluted from glomerular deposits. This characteristic of the 76-kDa polypeptide indicates that this serum protein may potentially play a role in the development of the glomerular lesion of active HN. Further analysis of this serum component should assist in understanding the normal function of the HN autoantigen.
Modulation of arterial baroreflex dynamic response during mild orthostatic stress in humans (2004)

We tested the hypothesis that in humans, carotid-baroreflex dynamic responses (evaluated by examining the time course of the carotid-baroreflex-induced alterations in muscle sympathetic nerve activity (MSNA), mean arterial blood pressure (MAP) and heart rate (HR)) would be altered during mild orthostatic stress in ways that serve to limit orthostatic hypotension. In 12 healthy subjects (10 male, 2 female), 5-s periods of neck pressure (NP) (50 mmHg) and neck suction (NS) (-60 mmHg) were used to evaluate carotid baroreflex function at rest (CON) and during lower body negative pressure (LBNP) (-15 mmHg). During LBNP (as compared with CON) (a) the augmentations in MSNA and MAP elicited by NP were greater, (b) the NS-induced period of MSNA suppression was, if anything, shorter, (c) the peak decrement in MAP elicited by NS, although not different in amplitude, occurred earlier and recovered to its initial level more quickly after NS, and (d) the HR responses to NP and NS were greater. These results suggest that during mild orthostatic stress, carotid-baroreflex dynamic responses are modulated in ways that should help maintain blood pressure and limit orthostatic hypotension.
Preparation and analgesic activity of 3,6-diacetylnormorphine and 6-acetylnormorphine (1975)

3,6-Diacetylnormorphine (norheroin) and 6-acetylnormorphine have been prepared in excellent yield through the 3,N-bis(tert-butoxycarbonyl) derivative of normorphine via acetylation and selective removal of protecting groups. This general procedure would be applicable to the preparation of various 3,6-diesters or 6-monoesters of normorphine. The analgesic potency of norheroin was found to be the same as that of 6-acetylnormorphine, about 0.05 that of heroin. The onset, peak, and duration of action of these compounds were nearly identical and comparable with morphine.
Modeling and rendering of weathered stone (2006)

Stone is widespread in its use as a building material and artistic medium. One of its most remarkable qualities is that it changes appearance as it interacts with the environment. These changes are mainly confined to the surface but involve complex volumetric effects such as erosion and mineral dissolution. This paper presents an approach for the modeling and rendering of changes in the shape and appearance of stone.To represent stone, we introduce a slab data structure, which is a surface-aligned volume confined to a narrow region around the boundary of the stone. Our weathering model employs a simulation of the flow of moisture and the transport, dissolution, and recrystallization of minerals within the porous stone volume. In addition, this model governs the erosion of material from the surface. To render the optical effects of translucency and coloration due to the composition of minerals near the surface, we simulate the scattering of light inside the stone using a general subsurface Monte Carlo ray tracer. These techniques can capture many aspects of the time-dependent appearance of stone. We demonstrate the approach with models of granite and marble statues, as well as a sandstone column.
A Nonimmunoglobulin Transgene and the Endogenous Immunoglobulin μ Gene Are Coordinately Regulated by Alternative RNA Processing during B-Cell Maturation (1998)

The immunoglobulin (Ig) genes have been extensively studied as model systems for developmentally regulated alternative RNA processing. Transcripts from these genes are alternatively processed at their 3' ends to yield a transcript that is either cleaved and polyadenylated at a site within an intron or spliced to remove the poly(A) site and subsequently cleaved and polyadenylated at a downstream site. Results obtained from expressing modified genes in established tissue culture cell lines that represent different stages of B-lymphocyte maturation have suggested that the only requirement for regulation is that a pre-mRNA contain competing cleavage-polyadenylation and splice reactions whose efficiencies are balanced. Since several non-Ig genes modified to have an Ig gene-like structure are regulated in cell lines, Ig-specific sequences are not essential for this control. This strongly implies that changes in the amounts or activities of general RNA processing components mediate the processing regulation. Despite numerous studies in cell lines, this model of Ig gene regulation has never been tested in vivo during normal lymphocyte maturation. We have now introduced a non-Ig gene with an Ig gene-like structure into the mouse germ line and demonstrate that RNA from the transgene is alternatively processed and regulated in murine splenic B cells. This establishes that the balance and arrangement of competing cleavage-polyadenylation reactions are sufficient for RNA processing regulation during normal B-lymphocyte development. These experiments also validate the use of tissue culture cell lines for studies of Ig processing regulation. This is the first transgenic mouse produced to test a specific model for regulated mRNA processing.
New design and application of high efficiency LED driving system for RGB-LED backlight in LCD display (2006)

Novel RGB-LED driving system for LED backlight in LCD display have been developed and demonstrated. The driving system consists of the non-isolation type high efficiency constant current DC-DC converter and the dynamic controller with microcontroller. The efficiency of driver is up to 94.4% and the maximum color deviation, Δu'v', from the target is 0.002.
Sonar target discrimination by instrumented human divers (1976)

A series of sonar discrimination experiments has been performed using instrumented human divers wearing a helmet with a sending and two receiving transducers. Porpoiselike broad-band clicks, with energy centered about 60 kHz, were projected and the returning echoes stretched electronically in time by a factor of 128 to enable the divers to hear them. Data were collected using metallic plate targets and targets of different geometrical shapes that were previously used in experiments with a porpoise. A comparison of scores indicated that the instrumented divers performed as well as, and in some cases better than, the porpoise. Subject Classification: [43]65.62; [43]30.82.
Inorganic polyphosphate in the origin and survival of species (2004)

Inorganic polyphosphate (poly P), in chains of tens to hundreds of phosphate residues, linked by high-energy bonds, is environmentally ubiquitous and abundant. In prebiotic evolution it could have provided a flexible, polyanionic scaffold to assemble macromolecules. It has been conserved in every cell in nature. In prokaryotes, a major poly P synthetic enzyme is poly P kinase 1 (PPK1), which is found in 100 bacterial genomes, including numerous pathogens. Null mutants of PPK1, with low poly P levels, are defective in survival: namely, they show defective responses to physical/chemical stresses and predation. Pathogens with a PPK1 deletion are defective in biofilm formation, quorum sensing, general stress and stringent responses, motility, and other virulence properties. With the exception of Dictyostelium, PPK1 is absent in eukaryotes and provides a novel target for chemotherapy that would affect both virulence and susceptibility to antibacterial compounds. Remarkably, another PPK in Dictyostelium discoideum (PPK2) is an actin-related protein (Arp) complex that is polymerized into an actin-like filament, concurrent with its reversible synthesis of a poly P chain from ATP.