gebhart/patrepeval huggingface dataset:
A Simple Mouse Model for the Study of Human Immunodeficiency Virus (2015)

Humanized mouse models derived from immune-deficient mice have been the primary tool for studies of human infectious viruses, such as human immunodeficiency virus (HIV). However, the current protocol for constructing humanized mice requires elaborate procedures and complicated techniques, limiting the supply of such mice for viral studies. Here, we report a convenient method for constructing a simple HIV-1 mouse model. Without prior irradiation, NOD/SCID/IL2Rγ-null (NSG) mice were intraperitoneally injected with 1 × 10(7) adult human peripheral blood mononuclear cells (hu-PBMCs). Four weeks after PBMC inoculation, human CD45(+) cells, and CD3(+)CD4(+) and CD3(+)CD8(+) T cells were detected in peripheral blood, lymph nodes, spleen, and liver, whereas human CD19(+) cells were observed in lymph nodes and spleen. To examine the usefulness of hu-PBMC-inoculated NSG (hu-PBMC-NSG) mice as an HIV-1 infection model, we intravenously injected these mice with dual-tropic HIV-1DH12 and X4-tropic HIV-1NL4-3 strains. HIV-1-infected hu-PBMC-NSG mice showed significantly lower human CD4(+) T cell counts and high HIV viral loads in the peripheral blood compared with noninfected hu-PBMC-NSG mice. Following highly active antiretroviral therapy (HAART) and neutralizing antibody treatment, HIV-1 replication was significantly suppressed in HIV-1-infected hu-PBMC-NSG mice without detectable viremia or CD4(+) T cell depletion. Moreover, the numbers of human T cells were maintained in hu-PBMC-NSG mice for at least 10 weeks. Taken together, our results suggest that hu-PBMC-NSG mice may serve as a relevant HIV-1 infection and pathogenesis model that could facilitate in vivo studies of HIV-1 infection and candidate HIV-1 protective drugs.
Immunological characterization of a 17-kDa antigen from Cryptosporidium parvum recognized early by mucosal IgA antibodies (1992)

Cryptosporidium parvum antigens were characterized by immunoblot analysis of sera and intestinal secretions of BALB/c mice orally infected with 105 oocysts. A major band at 17 kDa under non-reduced conditions and at 18 kDa under reduced conditions was recognized by anti-C. parvum IgA and IgG in serum and intestinal secretions from day 15 post-infection. This recognition persisted throughout the experiment (day 30). Mouse-serum antibodies raised against the 17-kDa purified antigen (P17) showed no cross-reactivity with other C. parvum antigens. Immunofluorescence study revealed that this antigen is located on the sporozoite. It is suggested that this antigen could be a good candidate for studies of mucosal immune response to C. parvum and for vaccination.
A minimum decap allocation technique based on simultaneous switching for nanoscale SoC (2009)

In this paper, we propose a novel decoupling capacitance (decap) optimization technique based on simultaneous cell switching activity at the pre-layout stage. White space in the form of cell padding for the required quantity of decap is added to cells which simultaneously switch during the peak noise period, which is quickly estimated using initial timing information and the current waveforms for each cell instance, without the need to reference the power grid. The method is applied to an actual 45nm LSI and results show a 35% decap area reduction or 21.9% peak noise reduction compared with conventional decap insertion flows. The technique can improve the reliability of SoC with a runtime overhead of only 1% at the P&R stage in existing nanoscale SoC EDA design flows.
Magnetic-field-induced crossover from 2<i>e</i>to<i>e</i>periodicity in the superconducting single-electron transistor (1996)

We present extensive experimental data on the gate-charge-periodic current I(${\mathit{Q}}_{\mathit{o}}$) through a single-electron transistor as a function of the applied magnetic field. This device consists of a mesoscopic superconducting island which is coupled to two macroscopic superconducting leads through small tunnel junctions and to a capacitive gate. The behavior of the system exhibits two separate transitions as the magnetic field is increased. In the first, the I-${\mathit{Q}}_{\mathit{o}}$ curves cross from 2e to e periodicity in ${\mathit{Q}}_{\mathit{o}}$ while two-electron tunneling is still the dominant charge transport mechanism. In a second transition that occurs at higher magnetic fields, single-electron tunneling becomes the dominant mechanism. This transition from two-electron to single-electron tunneling shifts the maxima of the I-${\mathit{Q}}_{\mathit{o}}$ curves by e/2 in ${\mathit{Q}}_{\mathit{o}}$, and results in a significant increase in the current magnitude. Both transitions can be understood by considering how superconductivity in the leads and the island is affected by an increasing magnetic field. \textcopyright{} 1996 The American Physical Society.
[The organization and modern principles of the treatment of periodontitis in the Armed Forces]. (1995)

The article deals with the questions of spreading and the structure of periodontitis among servicemen, as well as the peculiarities of prophylaxis and medical care in military units and medical institution. The authors show the priority of surgical methods of treatment (curettage, flap operation). Characteristic features of pre-operational preparation are described, as well as methods of conservative treatment (general and local), and professional hygiene of the oral cavity.
Extended Macroscopic Study of Dilute Gas Flow within a Microcavity (2016)

The behaviour of monatomic and dilute gas is studied in the slip and early transition regimes using the extended macroscopic theory. The gas is confined within a two-dimensional microcavity where the longitudinal sides are in the opposite motion with constant velocity <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:msub><mml:mrow><mml:mo>±</mml:mo><mml:mi>U</mml:mi></mml:mrow><mml:mrow><mml:mi>w</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>. The microcavity walls are kept at the uniform and reference temperature <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:msub><mml:mrow><mml:mi>T</mml:mi></mml:mrow><mml:mrow><mml:mn mathvariant="normal">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>. Thus, the gas flow is transported only by the shear stress induced by the motion of upper and lower walls. From the macroscopic point of view, the regularized 13-moment equations of Grad, R13, are solved numerically. The macroscopic gas proprieties are studied for different values of the so-called Knudsen number (Kn), which gives the gas-rarefaction degree. The results are compared with those obtained using the classical continuum theory of Navier-Stokes and Fourier (NSF).
Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR) (2017)

Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we present methods to determine the limit of detection (LoD) and the limit of quantification (LoQ) as applicable to qPCR. These are based on standard statistical methods as recommended by regulatory bodies adapted to qPCR and complemented with a novel approach to estimate the precision of LoD.
Identification and Functional Requirement of Cu(I) and Its Ligands within Coagulation Factor VIII (1997)

Coagulation factor VIII (FVIII) is a heterodimer consisting of a light chain of 80 kDa (domains A3-C1-C2) in a metal ion-dependent association with a 220-kDa heavy chain (domains A1-A2-B). The nature of the metal ion-dependent association between the heavy and light chains was investigated using atomic absorption spectroscopy, electron paramagnetic resonance spectroscopy (EPR), and site-directed mutagenesis and expression of the FVIII cDNA. Whereas copper ion was not detected in intact recombinant FVIII, EDTA dissociation of the chains yielded an EPR signal consistent with 1 mol of Cu(I)/mol of active protein, supporting the hypothesis that a single molecule of reduced copper ion is buried within intact FVIII and is released and oxidized upon treatment with EDTA. Cu(I), and not Cu(II), was able to reconstitute FVIII activity from dissociated chains, demonstrating a requirement for Cu(I) in FVIII function. Three potential copper ion binding sites exist within FVIII: one type-2 site and two type-1 sites. The importance of these potential copper ion ligands was tested by studying the effect of site-directed mutants. Of the two histidines that compose the type-2 binding site, the His-1957 --> Ala mutant displayed secretion, light and heavy chain assembly, and activity similar to wild-type FVIII, while mutant His-99 --> Ala was partially defective for secretion and had low levels of heavy and light chain association and activity. In contrast, FVIII having the mutation Cys-310 --> Ser within the type-1 copper binding site in the A1 domain was inactive and partially defective for secretion from the cell, and the heavy and light chains of the secreted protein were not associated. Mutant Cys-2000 --> Ser within the A3 domain displayed secretion, assembly, and activity similar to that for wild-type FVIII. These results support the hypothesis that Cu(I) is buried within the type-1 copper binding site within the A1 domain and is required for FVIII chain association and activity.
Two‐dimensional RFLP analyses reveal megabase‐sized clusters of rRNA gene variants in <i>Arabidopsis thaliana</i>, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution (1996)

Eukaryotic genes encoding the precursor of 18S, 5.8S and 25S ribosomal RNA (rRNA genes or rDNA) are virtually identical within a species, yet they evolve rapidly between species, a phenomenon known as concerted evolution. The mechanisms by which sequence homogenization and fixation of new rRNA gene variants occurs within a genome are not clear. In diploid Arabidopsis thaliana, approximately 1500 rRNA genes are tandemly arrayed at two nucleolus organizer regions, one on chromosome 2 (NOR2), the other on chromosome 4 (NOR4). This paper shows that NOR2 and NOR4 are similar in size, each spanning approximately 3.5-4.0 Mbp. Using two-dimensional mapping techniques involving a combination of pulsed-field and conventional gel electrophoresis, the distributions of four distinct rRNA gene variants at NOR2 and NOR4 have been determined. rRNA genes at NOR4 are homogeneous with respect to a HindIII site occurring once per gene. In contrast, fewer than 10% of the rRNA genes at NOR2 are HindIII-bearing variants. A single intergenic spacer length is found among rRNA genes at NOR2 but three classes of spacer length variants are present at NOR4. The NOR4 variants are not intermingled with one another; instead, they are highly clustered over distances as large as 1.5 Mbp. These data suggest that in the concerted evolution of rRNA genes, homogenization is a consequence of local spreading of new rRNA gene variants.
Recapitulation of oral mucosal tissues in long‐term organotypic culture (2003)

To test the influence of fibroblasts on epithelial morphology and expression of keratinocyte proteins and barrier lipids, we bioengineered homotypic and heterotypic oral mucosae and skin using cultured adult human cells. Fibroblasts were allowed to modify collagen type I gels for 2 weeks before keratinocytes were added. The organotypic cultures were then grown at the air-liquid interface for 4 weeks. In homotypic combinations, epithelial morphology and protein expression closely mimicked those in vivo. In heterotypic combinations, the morphology resembled that in vivo and keratinocytes expressed their typical markers, except when skin keratinocytes were recombined with alveolar fibroblasts; they expressed K19, K4, and K13, which is similar to oral mucosal epithelia rather than to the epidermis. Morphologically, the stratum corneum layers were typical for the epithelial tissues. Grafting the bioengineered cultures to the backs of Nude mice did not change the results, suggesting that our findings are not merely a culture phenomenon. Lipid profiles of the homotypic combinations mimicked the profiles found in the normal epithelial tissues, except that the engineered alveolar epithelium expressed more ceramide 2 than that in vivo. In the heterotypic combinations, keratinocytes appeared to control the lipid profile, except in the combination of skin keratinocytes with alveolar fibroblasts, wherein the ceramide profile appeared to be partly that of alveolar epithelium and partly that of epidermis. These results suggest that cultured adult fibroblasts and keratinocytes are sufficient to recapitulate graftable oral tissues, and, except for alveolar fibroblasts, the type of fibroblast had little influence on keratinocyte differentiation.
Nutrient sensing by the mitochondrial transcription machinery dictates oxidative phosphorylation (2014)

Sirtuin 3 (SIRT3), an important regulator of energy metabolism and lipid oxidation, is induced in fasted liver mitochondria and implicated in metabolic syndrome. In fasted liver, SIRT3-mediated increases in substrate flux depend on oxidative phosphorylation (OXPHOS), but precisely how OXPHOS meets the challenge of increased substrate oxidation in fasted liver remains unclear. Here, we show that liver mitochondria in fasting mice adapt to the demand of increased substrate oxidation by increasing their OXPHOS efficiency. In response to cAMP signaling, SIRT3 deacetylated and activated leucine-rich protein 130 (LRP130; official symbol, LRPPRC), promoting a mitochondrial transcriptional program that enhanced hepatic OXPHOS. Using mass spectrometry, we identified SIRT3-regulated lysine residues in LRP130 that generated a lysine-to-arginine (KR) mutant of LRP130 that mimics deacetylated protein. Compared with wild-type LRP130 protein, expression of the KR mutant increased mitochondrial transcription and OXPHOS in vitro. Indeed, even when SIRT3 activity was abolished, activation of mitochondrial transcription and OXPHOS by the KR mutant remained robust, further highlighting the contribution of LRP130 deacetylation to increased OXPHOS in fasted liver. These data establish a link between nutrient sensing and mitochondrial transcription that regulates OXPHOS in fasted liver and may explain how fasted liver adapts to increased substrate oxidation.
Solid lipid nanoparticles (SLN) : an alternative colloidal carrier system for controlled drug delivery (1995)

Solid lipid nanoparticles of a quality acceptable for i.v. administration were produced by high pressure homogenization. Dispersion at increased temperature (melted lipids) was performed to yield SLN loaded with lipophilic drugs (e.g. tetracaine base), incorporation of the hydrophilic drug iotrolan was achieved by homogenization of the drug-loaded lipid in its solid state. Recrystallization of the SLN after production was investigated using differential scanning calorimetry. Drug loading capacities of up to 9.8% of the lipid matrix were obtained, prolonged in vitro drug release was achieved over 5 weeks (prednisolone). SLN of optimized composition proved to be physically stable during sterilization (autoclaving) and on long-term as aqueous dispersion. Alternatively dry products were produced by lyophilization or spray-drying. SLN were surface-modified for drug targeting purposes using poloxamer 407 and poloxamine 908 polymers as surfactants in the production process. Production parameters were optimized to obtain nanoparticle sizes required for the envisaged targets, e.g. <150 nm for endothelial cells
H.264/AVC improvement based on adaptive motion vector coding (2009)

We propose a new method for improving motion vector coding. The coding efficiency of the H.264/AVC standard is significantly degraded for video sequences that include irregular motions. The degradation is caused by the fact that the correlations among the motion vectors on adjacent blocks get to be small when motions are irregular. Our method solves this problem by two schemes. First, the predictive motion vector (PMV) is adaptively coded with additional bits based on the distribution pattern of reference vectors. Second, an appropriate code table for the motion vector difference (MVD) is adaptively selected out of a couple of tables defined in advance. These schemes enable the appropriate methodologies for the motion vector coding to be adaptively selected according to the motion vector diversity. Experimental results show the effectiveness and potentiality of our approach for high coding efficiency.
Nigeria and the World Bank : learning from the past, looking to the future (1995)

To assist in efforts to improve the lives of Nigerians, the bank is currently funding 32 projectsacross the country -making it one the Bank's largest portfolio- in agriculture and rural development, education, health, environment, water supply, transportation, energy and private sector development, among others. In these operations the goal is to reach Nigerian's poorest and most vulnerable groups, particularly women and children. However these projects are no substitute for the immense task of forming the economy, and returning to the path of steady growth. This booklet reviews the course of Nigeria's economic development, the Bank's lending program from 1958 to 1994, and responds to frequent asked questions about Nigeria's partnership with the World Bank.
Multi-channel speech enhancement in a car environment using Wiener filtering and spectral subtraction (2002)

This paper presents a multichannel-algorithm for speech enhancement for hands-free telephone systems in cars. This new algorithm takes advantage of the special noise characteristics in fast driving cars. The incoherence of the noise allows to use adaptive Wiener filtering in the frequencies above a theoretically determined frequency. Below this frequency a smoothed spectral subtraction (SSS) is used to get an improved noise suppression. The algorithm yields better results in noise reduction with significantly less distortions and artificial noise than spectral subtraction or Wiener filtering alone.
Morphology and morphometrics of six species of pratylenchus. (1969)

Six species of Pratylenchus (P. penetrans, P. vulnus, P. coffeae, P. scribneri, P. zeae and P. brachyurus) were propagated aseptically on alfalfa callus tissue at 27 C and in greenhouse pot culture on suitable hosts. Morphological and morphometric comparisons revealed a high degree of variability of most taxonomic characters studied. The number of annules in the lip region, the number and arrangement of incisures in the lateral field, the shape of stylet knobs and tail varied considerably within most of the species. Of 20 morphometric characters, vulva percent and stylet length had the lowest coefficients of variability and were found to be of diagnostic value. A slightly greater morphometric variability was encountered in P. vulnus females and males from greenhouse than from callus cultures. A small spermatotheca containing no spermatozoa was present in the monosexual species P. scribneri, P. zeae and P. brachyurus. A few males were found only in P. brachyurus. The distal part of the uterus was composed of 12 cells arranged in three rows of four cells each (tricolumella). A detailed description of each species is given.
The Response to Nitric Oxide of the Nitrogen-Fixing Symbiont <i>Sinorhizobium meliloti</i> (2010)

Nitric oxide (NO) is crucial in animal- and plant-pathogen interactions, during which it participates in host defense response and resistance. Indications for the presence of NO during the symbiotic interaction between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti have been reported but the role of NO in symbiosis is far from being elucidated. Our objective was to understand the role or roles played by NO in symbiosis. As a first step toward this goal, we analyzed the bacterial response to NO in culture, using a transcriptomic approach. We identified approximately 100 bacterial genes whose expression is upregulated in the presence of NO. Surprisingly, most of these genes are regulated by the two-component system FixLJ, known to control the majority of rhizobial genes expressed in planta in mature nodules, or the NO-dedicated regulator NnrR. Among the genes responding to NO is hmp, encoding a putative flavohemoglobin. We report that an hmp mutant displays a higher sensitivity toward NO in culture and leads to a reduced nitrogen fixation efficiency in planta. Because flavohemoglobins are known to detoxify NO in numerous bacterial species, this result is the first indication of the importance of the bacterial NO response in symbiosis.
Improving branch prediction by understanding branch behavior (2000)

Accurate branch prediction can be seen as a mechanism for enabling design decisions. When short pipelines were the norm, accurate branch prediction was not as important. However, having accurate branch prediction enables technologies like wide-issue deeply pipelined superscalar processors. If branch predictors can be improved further, we can more successfully use more aggressive speculation techniques. Accurate branch prediction enables larger scheduling windows, out-of-order fetch, deeper pipelines etc. It is therefore likely that there will be a growing demand for more accurate predictors beyond today's prediction technology. Previous studies have shown which branch predictors and configurations best predict the branches in a given set of benchmarks. Some studies have also investigated effects, such as pattern history table interference, that can be detrimental to the performance of these branch predictors. However, little research has been done on which characteristics of branch behavior make branches predictable. This dissertation approaches the branch problem in a different way from previous studies. The focus is on understanding how branches behave and why they are predictable. Branches are classified based on the type of behavior, and the extent of each type of behavior is quantified. One important result is that two thirds of all branches are very predictable using a simple predictor because they follow repeating patterns. We also show how correlation between branches works, and what part of this correlation is important for branch prediction. Based on this information about branch behavior, some shortcomings of current branch predictors are identified, new branch predictors are introduced, and potential areas for future improvement are identified. One of the new predictors, Dual History Length Gshare with Selective Update is more accurate than a Gshare predictor using Branch Filtering while having a simpler implementation. Another new predictor, the Multi Hybrid, suffers 10% fewer mispredictions than a state-of-the-art PAs/Gshare hybrid predictor at an implementation cost of 100 KB.