gebhart/patrepeval huggingface dataset:
Overexpression of transforming growth factor ?-type II receptor reduces tumorigenicity and metastastic potential of K-ras-transformed thyroid cells (1999)

Expression of type II receptor of transforming growth factor beta (TbetaRII) is necessary for this factor to inhibit the growth of thyroid epithelial cells. In rat thyroid transformed cells, the resistance to transforming growth factor beta (TGFbeta) is associated with a decreased expression of TbetaRII mRNA and protein. Reduced TbetaRII expression has also been found in human thyroid differentiated and undifferentiated carcinomas. To investigate the role of TbetaRII in modulating the tumorigenic potential of k-ras-transformed thyroid cells, we transfected these cells with an expression vector carrying the human TbetaRII gene, regulated by an inducible promoter. Isolated clones, overexpressing TbetaRII, showed a reduction in the anchorage-dependent and -independent cell growth, compared with control k-ras-transformed cells. When transplanted in athymic nude mice, the transfected clones presented a decrease in tumorigenicity with respect to the highly malignant parental cells. Moreover, the diminished tumorigenic ability of the clones studied was accompanied by a statistically significant reduction in spontaneous and lung artificial metastases. Taken together, our data demonstrate that TbetaRII acts as a potent tumor suppressor gene when overexpressed in malignant thyroid cells.
Ipilimumab reshapes T cell memory subsets in melanoma patients with clinical response (2016)

These results suggest that CTLA-4 blockade is able to reshape the memory subset with the potential involvement of Eomes and memory subsets including TSCM.
Convergence of Contrastive Divergence Algorithm in Exponential Family (2016)

The Contrastive Divergence (CD) algorithm has achieved notable success in training energy-based models including Restricted Boltzmann Machines and played a key role in the emergence of deep learning. The idea of this algorithm is to approximate the intractable term in the exact gradient of the log-likelihood function by using short Markov chain Monte Carlo (MCMC) runs. The approximate gradient is computationally-cheap but biased. Whether and why the CD algorithm provides an asymptotically consistent estimate are still open questions. This paper studies the asymptotic properties of the CD algorithm in canonical exponential families, which are special cases of the energy-based model. Suppose the CD algorithm runs $m$ MCMC transition steps at each iteration $t$ and iteratively generates a sequence of parameter estimates $\{θ_t\}_{t \ge 0}$ given an i.i.d. data sample $\{X_i\}_{i=1}^n \sim p_{θ_\star}$. Under conditions which are commonly obeyed by the CD algorithm in practice, we prove the existence of some bounded $m$ such that any limit point of the time average $\left. \sum_{s=0}^{t-1} θ_s \right/ t$ as $t \to \infty$ is a consistent estimate for the true parameter $θ_\star$. Our proof is based on the fact that $\{θ_t\}_{t \ge 0}$ is a homogenous Markov chain conditional on the data sample $\{X_i\}_{i=1}^n$. This chain meets the Foster-Lyapunov drift criterion and converges to a random walk around the Maximum Likelihood Estimate. The range of the random walk shrinks to zero at rate $\mathcal{O}(1/\sqrt[3]{n})$ as the sample size $n \to \infty$.
Identification of Early Interactions between Francisella and the Host (2014)

The adaptive immune response to Francisella tularensis is dependent on the route of inoculation. Intradermal inoculation with the F. tularensis live vaccine strain (LVS) results in a robust Th1 response in the lungs, whereas intranasal inoculation produces fewer Th1 cells and instead many Th17 cells. Interestingly, bacterial loads in the lungs are similar early after inoculation by these two routes. We hypothesize that the adaptive immune response is influenced by local events in the lungs, such as the type of cells that are first infected with Francisella. Using fluorescence-activated cell sorting, we identified alveolar macrophages as the first cell type infected in the lungs of mice intranasally inoculated with F. novicida U112, LVS, or F. tularensis Schu S4. Following bacterial dissemination from the skin to the lung, interstitial macrophages or neutrophils are infected. Overall, we identified the early interactions between Francisella and the host following two different routes of inoculation.
Scalable Sequential Equivalence Checking across Arbitrary Design Transformations (2006)

High-end hardware design flows mandate a variety of sequential transformations to address needs such as performance, power, post-silicon debug and test. Industrial demand for robust sequential equivalence checking (SEC) solutions is thus becoming increasingly prevalent. In this paper, we discuss the role of SEC within IBM. We motivate the need for a highly-automated scalable solution, which is robust against a variety of design transformations - including those that alter initialization sequences. This motivation has caused us to embrace the paradigm of SEC with respect to designated initial states. We furthermore describe the diverse set of algorithms comprised within our SEC framework, which we have found necessary for the automated solution of the most complex SEC problems. Finally, we provide several experiments illustrating the necessity of our diverse algorithm flow to efficiently solve difficult SEC problems involving a variety of design transformations.
Human Resources Readiness for Industry 4.0 (2019)

Industry 4.0 is related to major changes, particularly in production. As such changes might have major implications for the labour market; the paper focuses on the assumptions of the human capital and its preparedness for Industry 4.0 in the Czech Republic. The findings are based on EUROSTAT, MEYS, OECD, ISCED, CZSO, and WEF. Based on such data, twelve indicators were selected and described in the results. Subsequently, the correlation analysis was carried out, using the data of the Czech Republic in order to estimate which indicators are related and thus to obtain a more detailed view of areas that need to be improved. The level of computer skills in the Czech Republic are increasing. Internet connection is around 80%. The share of technical workers in the Czech Republic is in the range of 30&ndash;40%. In terms of expenditure on education, the Czech Republic belongs to the countries of the eastern region. The number of graduates of technical professions managed to catch up with the development of the European Union (EU). In terms of employment in High-tech and Medium-high-tech areas, the Czech Republic is one of the leaders in the EU. Czech students have great potential in basic computer skills.
Linked open data-based framework for automatic biomedical ontology generation (2018)

This paper has presented LOD-ABOG framework which shows that current LOD sources and technologies are a promising solution to automate the process of biomedical ontology generation and extract relations to a greater extent. In addition, unlike existing frameworks which require domain experts in ontology development process, the proposed approach requires involvement of them only for improvement purpose at the end of ontology life cycle.
A Prospective, Multicenter Study of Laboratory Cross-Contamination ofMycobacterium tuberculosisCultures (2002)

A prospective study of false-positive cultures of Mycobacterium tuberculosis that resulted from laboratory cross-contamination was conducted at three laboratories in California. Laboratory cross-contamination accounted for 2% of the positive cultures. Cross-contamination should be a concern when an isolate matches the genotype of another sample processed during the same period.
Costimulatory Requirements for the Expansion of Human T Regulatory Cells (2008)

We used cell‐based artificial APCs (aAPC) to explore the costimulatory requirements to expand functional T regulatory cells (Treg) enriched from human peripheral blood. Only CD28 costimulation maintained high levels of FoxP3 expression and suppressive function in enriched T regulatory cultures. Interestingly, CD4 T cells grown in the presence of CD28 costimulation and rapamycin displayed significant in vitro suppressive activity. However, when these cells were evaluated for suppressive activity in vivo, only the cultures that were initially enriched for Tregs suppressed. We investigated whether additional costimulatory pathways could augment CD28's ability to promote further Treg expansion in rapamycin. In a minority of donors OX40 costimulation was able to augment Treg expansion and maintain function; however, in the majority of donors these cultures often lost suppressive function. In contrast, we found that re‐stimulation of the Treg cultures after 8–10 days of culture with CD28 costimulation alone resulted in 1000 fold expansion of Treg in less than 3 weeks. These highly expanded Tregs retained potent in vitro and in vivo suppressive function. These studies indicate the optimal costimulatory requirements to expand Tregs differ from T effector cells and establish the feasibility of using expanded Tregs for adoptive T cell therapy. The project is supported by JDRF for Cell Therapy grant.
A two-type branching process model of gene family evolution (2021)

Abstract Phylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption of these models is the constant per-gene loss rate in any particular family. Because of the possibility of partial functional redundancy among gene family members, gene loss dynamics are however likely to be dependent on the number of genes in a family, and different variations of commonly employed BDP models indeed suggest this is the case. We propose a simple two-type branching process model to better approximate the stochastic evolution of gene families by gene duplication and loss and perform Bayesian statistical inference of model parameters in a phylogenetic context. We evaluate the statistical methods using simulated data sets and apply the model to gene family data for Drosophila , yeasts and primates, providing new quantitative insights in the long-term maintenance of duplicated genes.
Lead-free Cesium Europium Halide Perovskite Nanocrystals (2020)

Because of the toxicity of lead, searching for a lead-free halide perovskite semiconducting material with comparable optical and electronic properties is of great interest. Rare-earth-based halide perovskite represents a promising class of materials for this purpose. In this work, we demonstrate the solution-phase synthesis of single-crystalline CsEuCl<sub>3</sub> nanocrystals with a uniform size distribution centered around 15 nm. The CsEuCl<sub>3</sub> nanocrystals have photoluminescence emission centered at 435 nm, with a full width at half-maximum of 19 nm. Furthermore, CsEuCl<sub>3</sub> nanocrystals can be embedded in a polymer matrix that provides enhanced stability under continuous laser irradiation. Lead-free rare-earth cesium europium halide perovskite nanocrystals represent a promising candidate to replace lead halide perovskites.
The association of moderate renal dysfunction with impaired preference-based health-related quality of life: 3rdKorean national health and nutritional examination survey (2012)

Although age affects the association between renal dysfunction and the EQ-5D, moderate renal dysfunction seems to be an important determinant of impaired health utility in a general population and may affect the mobility and pain/discomfort dimensions of health utility.
Digital Compensation of RF Imperfections for Broadband Wireless Systems (2007)

In this paper we propose a generally applicable frequency-domain equalization and radio frequency (RF) imperfection compensation technique for orthogonal frequency division multiplexing (OFDM) transmission over frequency-selective channels. Radio frequency (RF) imperfections, such as in-phase/quadrature-phase (IQ) imbalance and carrier frequency offset (CFO) are important issues in today's wireless broadband systems. Due to component imperfections in practical analog electronics such imbalances are unavoidable, resulting in an overall performance degradation of the system. In this paper the joint effect of frequency selective IQ imbalance at both transmitter and receiver end along with CFO is studied for OFDM based transmission. We also consider the general case when the cyclic prefix is not sufficiently long to accommodate the channel impulse response combined with the transmitter and receiver filter, which results in inter-block-interference (IBI) between the OFDM symbols.
Mild and cost-effective synthesis of iron fluoride–graphene nanocomposites for high-rate Li-ion battery cathodes (2012)

Exploring high performance cathode materials is essential to realize the adoption of Li-ion batteries for application in electric vehicles and hybrid electric vehicles. FeF3, as a typical iron-based fluoride, has been attracting considerable interest due to both the high electromotive force value of 2.7 V and the high theoretical capacity of 237 mA h g−1 (1e− transfer). In this study, we report a facile low-temperature solution phase approach for synthesis of uniform iron fluoride nanocrystals on reduced graphene sheets stably suspended in ethanol solution. The resulting hybrid of iron fluoride nanocrystals and graphene sheets showed high specific capacity and high rate performance for iron fluoride type cathode materials. High stable specific capacity of about 210 mA h g−1 at a current density of 0.2 C was achieved, which is much higher than that of LiFePO4 cathode material. Notably, these iron fluoride/nanocomposite cathode materials demonstrated superior rate capability, with discharge capacities of 176, 145 and 113 mA h g−1 at 1, 2 and 5 C, respectively.
Separation of Two Salmonella O-Antigen Polysaccharides by Means of a Glutaraldehyde-Concanavalin-A Polymer. Primary Studies on the Separated Fractions (1977)

The Salmonella zuerich (1,9,12,(46),27) cell wall O-polysaccharides have been characterized as a mixture of two immunologically distinct fractions differing in the presence or absence of the antigenic determinant 1 usually carried by side chains of an alpha-D-glucosyl residue. In this paper, we describe the use of concanavalin A in separating the two O-polysaccharides. The procedure involves polymerization of concanavalin A with glutaraldehyde, followed by selective adsorption of the polysaccharide containing O factor 1 and elution with D-glucose. Immunological and chemical analyses showed that the separation was successful and demonstrated chemical differences between these two fractions in relation to their immunological behaviour.
Recovering shape from shadows in synthetic aperture radar imagery (2008)

There has been little interest in the information associated with the shadows in high resolution Synthetic Aperture Radar (SAR) images. In this paper we give an algorithm for the reconstruction of an object's shape from the shadows cast by the object in a sequence of SAR images. The algorithm is a back-projection type algorithm based on the intersection of solids. The effects of diffraction and synthetic aperture occlusion on SAR shadow resolution are also addressed.
The Study on Value-Added Information Service Modes Based on the Sci-Tech Novelty Search (2013)

The sci-tech novelty search is a kind of information consulting service, based on the manual and computer retrieval, using the method of comprehensive and contrast analysis, providing the objective facts for the novelty and advancement evaluation of research project approval, sci-tech achievement appraisal, patent application, technology consulting and other innovation activities. The sci-tech novelty search institutions have rich information resources, human resources, customer resources and brand resources to carry out innovative value-added information service. In this paper, we select some value-added information service modes which are suitable to carry out by the novelty search institutes, and make the contrastive analysis between traditional novelty search service and innovative value-added information service. Therefore we make some constructive suggestions for the sci-tech novelty search institutions to increase competitive intelligence service, specific information service, intelligence reporting service, and foreign enterprise credit investigation service basing on the traditional novelty search service.
Plasmodium berghei Purified Hemozoin Associated with DNA Strongly Inhibits P. berghei Liver-Stage Development in BALB/c Mice after Intravenous Inoculation (2023)

In the acidic lysosome-like digestive vacuole, <i>Plasmodium</i> parasites crystallize heme from hemoglobin into hemozoin, or malaria pigment. Upon release of progeny merozoites, the residual hemozoin is phagocytized by macrophages principally in the liver and spleen where the heme crystals can persist for months to years, as heme oxygenase does not readily degrade the crystal. Previous studies demonstrated hemozoin modulation of monocytes and macrophages. Hemozoin modulates immune function activity of monocytes/macrophages. Here, we used purified/washed hemozoin (W-Hz) isolated from murine Plasmodium berghei infections and intravenously (i.v.) injected it back into naive mice. We characterized the modulating effect of W-Hz on liver-stage replication. Purified washed hemozoin decreases P. berghei liver levels both at 1 week and 1 month after i.v. injection in a dose and time dependent fashion. The injected hemozoin fully protected in nine out of 10 mice given a 50 sporozoite inoculum, and in 10 out of 10 mice against 2,000 sporozoites when they were infected an hour or a day after hemozoin inoculation. DNase treatment at the hemozoin reversed the observed liver load reduction. The liver load reduction was similar in mature B- and T-cell-deficient RAG-1 knockout (KO) mice suggesting an innate immune protection mechanism. This work indicates a role for residual hemozoin in down modulation of <i>Plasmodium</i> liver stages.
Effect of Oil Content on Optimum Conditions for Cryo-Cutting of Frozen Surimi, as Estimated by DSC. (2006)

水分と油脂含量の異なる凍結すり身の破壊エネルギー（破壊強度）を0℃以下の低温下で測定し，DSC測定の結果と比較することで，凍結魚肉の低温切断加工の最適温度条件をDSC測定の結果から推定した．水分60～80％，油脂（タラ油）含量1～20％の凍結すり身を低温下で3点曲げ試験を行い，破壊エネルギーを測定した．その結果，試験片は－40℃で凍結していたが，低温切断は－80℃以下の温度で可能となった．DSC測定の結果，添加したタラ油の融解開始温度は，切断可能温度である－80℃より高温側にあった．このようにタラ油を含んだすり身は，タラ油の融解開始温度以下で切断が可能であり，その融解開始温度はDSCにより測定が可能であった．切断可能温度（温度A）以下での曲げ破壊エネルギーの急速な低下すなわち脆化は，今回測定したサンプルでは確認できなかった．これらのサンプルのDSC測定では，ガラス転移様の変化が現れておらず，タラ油の融解温度範囲が水-すり身系でのガラス転移温度範囲と重なっていたことから，すり身に添加したタラ油が低温での脆化を抑制したことが示された．これらの結果から，油脂を含む凍結すり身の低温での破壊挙動並びに低温切断に適切な凍結温度条件は，試料のDSC測定結果から予測可能であり，それは－80℃以下に存在した．
Vector-valued Lambertian fields and their sources (2016)

The electromagnetic field within an aperture in the wall of a blackbody cavity is a known example of a Lambertian source producing a far field which is unpolarized in all directions. In this work we show that in the electromagnetic context other Lambertian sources exist whose far fields, while obeying the cosine law for the radiant intensity, differ by their polarization states and degrees. For example, the far field may be azimuthally, radially, or circularly polarized, or the polarization state may vary depending on the direction. For specific Lambertian fields generated by quasihomogeneous sources it is possible to calculate explicitly the $3\ifmmode\times\else\texttimes\fi{}3$ electric cross-spectral density matrix of the nonevanescent part of the source. This enables one to assess the source's spatial coherence and partial polarization properties. In all cases, the coherence length turns out to be roughly half a wavelength, whereas the polarization characteristics of the sources may differ significantly. Our results could find uses, for instance, in radiometry and photometry, lighting applications, and remote sensing.
Recovery and Growth Potential of Listeria monocytogenes in Temperature Abused Milkshakes Prepared from Naturally Contaminated Ice Cream Linked to a Listeriosis Outbreak (2016)

The recovery and growth potential of Listeria monocytogenes was evaluated in three flavors of milkshakes (vanilla, strawberry, and chocolate) that were prepared from naturally contaminated ice cream linked to a listeriosis outbreak in the U.S. in 2015, and were subsequently held at room temperature for 14 h. The average lag phase duration of L. monocytogenes was 9.05 h; the average generation time was 1.67 h; and the average population level increase per sample at 14 h was 1.14 log CFU/g. Milkshake flavors did not significantly affect these parameters. The average lag phase duration of L. monocytogenes in milkshakes with initial contamination levels ≤ 3 CFU/g (9.50 h) was significantly longer (P < 0.01) than that with initial contamination levels > 3 CFU/g (8.60 h). The results highlight the value of using samples that are contaminated with very low levels of L. monocytogenes for recovery and growth evaluations. The behavior of L. monocytogenes populations in milkshakes prepared from naturally contaminated ice cream linked to the listeriosis outbreak should be taken into account when performing risk based analysis using this outbreak as a case study.
A method to evaluate the performance of coal fire extinguishants (1991)

A complete cytokine mix (CCM) or its individual components tumour necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta) and interferon-gamma (IFN-gamma) were used to switch resting murine astrocytes to reactive states. The transformation process was characterized by differential up-regulation of interleukin-6 (IL-6), cyclooxygenase-2 (COX-2) and inducible nitric oxide synthetase (iNOS) mRNA and protein and a subsequent release of prostaglandin E2, nitric oxide (NO) and IL-6. Both CD95L and anti-CD95 antibodies triggered caspase activation followed by apoptotic death in fully pro-inflammatory astrocytes, whereas resting cells were totally resistant. Two other death-inducing ligands, TNF and TNF-related apoptosis-inducing ligand (TRAIL) did not induce apoptosis in reactive astrocytes. The switch in astrocyte sensitivity was accompanied by up-regulation of caspase-8 and CD95 as well as the capacity to recruit Fas-associated death domain (FADD) to the activated death receptor complex. Neither CD95-mediated death, nor other inflammatory parameters were affected by inhibition of iNOS or COX, respectively. Accordingly, IFN-gamma was absolutely essential for up-regulation of iNOS, but not for the switch in apoptosis sensitivity. In contrast, p38 kinase activity was identified as an important controller of both the inflammatory reaction and apoptosis both in astrocytes stimulated with CCM and in glia exposed to TNF and IL-1 only.
Correlation-induced spectral changes in tissues (2011)

We report experimental evidence of correlation-induced spectral changes in biological tissues. The overall spectral shift in our transmission measurements is to the red and the mean wavelength of the original spectrum is up 10% larger. These results indicate that the spectral changes due to elastic scattering are significant and likely to hinder all spectroscopic measurements based on the inelastic (i.e., emission and absorption) interaction between light and tissues. Thus, simultaneous morphology and spectral measurements are required for accurate measurements spectroscopic information.