gebhart/patrepeval huggingface dataset:
CROSS-SPECTRAL ANALYSIS OF TREMOR TIME SERIES (2000)

We discuss cross-spectral analysis and report applications for the investigation of human tremors. For the physiological tremor in healthy subjects, the analysis enables to determine the resonant contribution to the oscillation and allows to test for a contribution of reflexes to this tremor. Comparing the analysis of the relation between the tremor of both hands in normal subjects and subjects with a rare abnormal organization of certain neural pathways proves the involvement of central structures in enhanced physiological tremor. The relation between the left and the right side of the body in pathological tremor shows a specific difference between orthostatic and all other forms of tremor. An investigation of EEG and tremor in patients suffering from Parkinson's disease reveals the tremor-correlated cortical activity. Finally, the general issue of interpreting the results of methods designed for the analysis of bivariate processes when applied to multivariate processes is considered. We discuss and apply partial cross-spectral analysis in the frame of graphical models as an extention of bivariate cross-spectral analysis for the multivariate case.
Chimeric Antigen Receptors in Cancer Immuno-Gene Therapy: Current Status and Future Directions (2011)

The concept of chimeric antigen receptors (CARs) as molecules able to redirect T lymphocytes toward tumor cells is currently being exploited in the field of cancer immunotherapy. Despite promising preliminary results, some clinical trials evidenced limitations for this technology that must be overcome for more extensive application of CARs in tumor immunotherapy. We describe here the fundaments of these molecules in terms of structure, function, possible targets and pre-clinical and clinical applications. We also discuss strategies that can potentially overcome the limitations seen so far, paving the road to a wider application of this exciting new technology.
Periplasmic Cytochrome c 3 of Desulfovibrio vulgaris Is Directly Involved in H 2 -Mediated Metal but Not Sulfate Reduction (2004)

Kinetic parameters and the role of cytochrome c(3) in sulfate, Fe(III), and U(VI) reduction were investigated in Desulfovibrio vulgaris Hildenborough. While sulfate reduction followed Michaelis-Menten kinetics (K(m) = 220 micro M), loss of Fe(III) and U(VI) was first-order at all concentrations tested. Initial reduction rates of all electron acceptors were similar for cells grown with H(2) and sulfate, while cultures grown using lactate and sulfate had similar rates of metal loss but lower sulfate reduction activities. The similarities in metal, but not sulfate, reduction with H(2) and lactate suggest divergent pathways. Respiration assays and reduced minus oxidized spectra were carried out to determine c-type cytochrome involvement in electron acceptor reduction. c-type cytochrome oxidation was immediate with Fe(III) and U(VI) in the presence of H(2), lactate, or pyruvate. Sulfidogenesis occurred with all three electron donors and effectively oxidized the c-type cytochrome in lactate- or pyruvate-reduced, but not H(2)-reduced cells. Correspondingly, electron acceptor competition assays with lactate or pyruvate as electron donors showed that Fe(III) inhibited U(VI) reduction, and U(VI) inhibited sulfate loss. However, sulfate reduction was slowed but not halted when H(2) was the electron donor in the presence of Fe(III) or U(VI). U(VI) loss was still impeded by Fe(III) when H(2) was used. Hence, we propose a modified pathway for the reduction of sulfate, Fe(III), and U(VI) which helps explain why these bacteria cannot grow using these metals. We further propose that cytochrome c(3) is an electron carrier involved in lactate and pyruvate oxidation and is the reductase for alternate electron acceptors with higher redox potentials than sulfate.
Ester Formation by Alcohol Acetyltransferase from Brewers’ Yeast (1981)

Alcohol acetyltransferase responsible for the formation of acetate esters during beer fermentation was found to be localized at the cell membrane of brewers’ yeast. This cell membrane-bound enzyme was purified 120-fold by solubilization with Triton X-100, gel filtration on a Sepharose 6B column and chromatography on a DEAE-Sephadex A-50 column. The enzyme was most active at 30°C at pH 7 ˜ 8. It was least active against C3 alcohol among C1 ˜ C6 alcohols, and slightly more active against straight-chain alcohols than against branched-chain alcohols with the same carbon number. The enzyme was strongly inhibited by unsaturated fatty acids, heavy metal ions and sulfhydryl reagents.
Molecular Cloning of a Defense-Response-Related Cytochrome P450 Gene from Tobacco (1999)

Plant defenses against pathogen attack involve a series of inducible responses that contribute to resistance. Tobacco leaves injected with HWC (hyphal wall components prepared from Phytophthora infestans) elicitor showed typical defense responses, including the induction of localized necrosis and the accumulation of pathogenesis-related proteins. In order to elucidate the molecular mechanisms by which plant defense systems are activated, we screened tobacco plants for genes differentially expressed in response to HWC. We performed differential screening by RT-PCR with random primers and obtained PCR products specific to HWC-treated leaf RNA. Northern hybridization using the PCR products as probes confirmed that one transcript was actually induced by HWC treatment. As the deduced amino acid sequence of this clone showed the highest degree of similarity to elicitor-induced soybean cytochrome P450 CYP82A4, it was designated CYP82E1. The expression of CYP82E1 was strongly induced in tobacco by the soybean pathogen Pseudomonas syringae pv. glycinea (nonpathogenic on tobacco), but it was activated only slightly and in a delayed fashion by the tobacco pathogen P. syringae pv. tabaci (pathogenic on tobacco), implying that the product of CYP82E1 may be involved in disease resistance in tobacco.
Direct three-dimensional ultrasound-to-video registration using photoacoustic markers (2013)

Modern surgical procedures often have a fusion of video and other imaging modalities to provide the surgeon with information support. This requires interventional guidance equipment and surgical navigation systems to register different tools and devices together, such as stereoscopic endoscopes and ultrasound (US) transducers. In this work, the focus is specifically on the registration between these two devices. Electromagnetic and optical trackers are typically used to acquire this registration, but they have various drawbacks typically leading to target registration errors (TRE) of approximately 3 mm. We introduce photoacoustic markers for direct three-dimensional (3-D) US-to-video registration. The feasibility of this method was demonstrated on synthetic and ex vivo porcine liver, kidney, and fat phantoms with an air-coupled laser and a motorized 3-D US probe. The resulting TRE for each experiment ranged from 380 to 850 μm with standard deviations ranging from 150 to 450 μm. We also discuss a roadmap to bring this system into the surgical setting and possible challenges along the way.
The SF-36 Health Survey: Development and Use in Mental Health Research and the IQOLA Project (1994)

(1994). The SF-36 Health Survey: Development and Use in Mental Health Research and the IQOLA Project. International Journal of Mental Health: Vol. 23, Quality of Life Assessment Cross-cultural Issues—1, pp. 49-73.
BMI Affects the Relationship between Long Chain N-3 Polyunsaturated Fatty Acid Intake and Stroke Risk: a Meta-Analysis (2015)

We performed a meta-analysis to clarify the relationship between long chain n-3 polyunsaturated fatty acid (PUFA) intake and stroke risk. Relevant studies were identified by searching online databases through May 2015. Log relative risks (RRs) of the highest versus the lowest for cohort studies were weighed by the inverse variance method to obtain pooled RRs. Fourteen prospective cohort studies including 514,483 individuals and 9,065 strokes were included. The pooled RR of overall stroke risk for long chain n-3 PUFA intake was 0.87 [95% confidence interval (CI), 0.79-0.95]. Stratification analysis showed that higher long chain n-3 PUFAs intake was associated with reduced fatal stroke risk (RR = 0.84; 95% CI, 0.73-0.97), reduced stroke risk for BMI < 24 (RR = 0.86; 95% CI, 0.75-0.98) and reduced stroke risk for females (RR = 0.81; 95% CI, 0.71-0.92), but was not associated with stroke risk for either BMI ≥ 24 or men. This meta-analysis reveals that higher long chain n-3 PUFA intake is inversely associated with risk of stroke morbidity and mortality with BMI and sex as key factors influencing this risk. Individuals should be encouraged to manage their body weight while increasing their intake of long chain n-3 PUFAs.
Trastuzumab and interleukin-2 in HER2-positive metastatic breast cancer: a pilot study. (2003)

Trastuzumab + IL-2 is a well-tolerated outpatient regimen that results in NK cell expansion with enhanced in vitro targeted killing of HER2-expressing cells. These preliminary data suggest that this strategy may benefit heavily pretreated metastatic breast cancer patients.
Molecular breeding of a novel herbicide‐tolerant rice by gene targeting (2007)

We have previously reported the production of a rice cell line tolerant to the acetolactate synthase (ALS)-inhibiting herbicide bispyribac (BS), and demonstrated that the BS-tolerant phenotype was due to a double mutation in the rice ALS gene. We further indicated that while changing either of the two amino acids (W548 L or S627I) individually resulted in a BS-tolerant phenotype, conversion of both amino acids simultaneously conferred increased tolerance to BS. As the BS-tolerant cell line had lost the ability to regenerate during two years of tissue culture selection, we attempted to introduce these two point mutations into the rice ALS gene via gene targeting (GT). Using our highly efficient Agrobacterium-mediated transformation system in rice, we were able to regenerate 66 independent GT rice plants from 1500 calli. Furthermore, two-thirds of these plants harbored the two point mutations exclusively, without any insertion of foreign DNA such as border sequences of T-DNA. The GT plants obtained in the present study are therefore equivalent to non-GM herbicide-tolerant rice plants generated by conventional breeding approaches that depend on spontaneous mutations. Surprisingly, GT rice homozygous for the modified ALS locus showed hyper-tolerance to BS when compared to BS-tolerant plants produced by a conventional transgenic system; ALS enzymatic activity in plants homozygous for the mutated ALS gene was inhibited only by extremely high concentrations of BS. These results indicate that our GT method has successfully created novel herbicide-tolerant rice plants that are superior to those produced by conventional mutation breeding protocols or transgenic technology.
Microfluidic Production of Biopolymer Microcapsules with Controlled Morphology (2006)

We report a microfluidic approach to generating capsules of biopolymer hydrogels. Droplets of an aqueous solution of a biopolymer were emulsified in an organic phase comprising a cross-linking agent. Polymer gelation was achieved in situ (on a microfluidic chip) by diffusion-controlled ionic cross-linking of the biopolymer, following the transfer of the cross-linking agent from the continuous phase to the droplets. Gelation was quenched by collecting particles in a large pool of cross-linking agent-free liquid. The structure of microgels (from capsules to gradient microgels to particles with a uniform structure) was controlled by varying the time of residence of droplets on the microfluidic chip and the concentration of the cross-linking agent in the continuous phase. We demonstrated the encapsulation of a controlled number of polystyrene beads in the microgel capsules. The described approach was applied to the preparation of capsules of several polysaccharides such as alginate, kappa-carrageenan, and carboxymethylcellulose.
Emissions from Charbroiling and Grilling of Chicken and Beef (2003)

Emission rates for fine particle (<2.5 microm) mass (PM2.5), carbon (organic/elemental), inorganic ions (SO4(2-), NO3-, NH4+), elements (primarily metals), and speciated organic compounds are reported for charbroiling hamburger, steak, and chicken. The PM2.5 rates for charbroiling meats ranged from 4.4 to 11.6 g/kg of uncooked meat in this study. No mass-emission rates are available from grilling, but the speciated organic data are available for these samples. Emission rates varied by type of appliance, meat, meat-fat content, and cooking conditions. High-fat hamburger cooked on an underfired charbroiler emitted the highest amount of PM2.5. The emissions were almost exclusively composed of organic carbon, with small amounts of elements and inorganic ions. Water-soluble K+ and Cl-, which are used as indicators of wood smoke in source apportionment studies, were also present in meat-cooking emissions. The speciated organic compounds that were measured include polycyclic aromatic hydrocarbons (PAHs), cholesterol, and the long-chain gamma-lactones. Charbroiling emissions yielded an average of approximately 3-5 times more PAHs, approximately 20 times more cholesterol, and approximately 10 times more lactones than grilling. These data were utilized in the ambient source apportionment analysis for the 1997 Northern Front Range Air Quality Study source apportionment.
Receptor-Directed Therapy of T-Cell Leukemias and Lymphomas (2008)

T-Cell leukemias and lymphomas represent a less common and heterogeneous group of lymphoid neoplasms. Overall, they respond less well to chemotherapy and have a poorer prognosis than their B-cell counterparts. T-Cell tumors express a number of potential targets for receptor-directed antibody therapy; however, there is no available therapeutic monoclonal antibody for these diseases with comparable activity to that of rituximab in B-cell disorders. Despite this, alemtuzumab, a humanized anti-CD52 monoclonal antibody has demonstrated meaningful anti-tumor activity in a variety of T-cell malignancies. A number of other antibodies, modified antibodies and immunotoxins directed against targets such as CD2, CD4, CD5, CD25, CD30 and CD122 expressed on malignant T-cells are under investigation. The current status of receptor-directed antibody therapy for T-cell leukemia and lymphoma is reviewed.
<title>Evaluation of complex elementary functions: a new version of BKM</title> (1999)

We present an improvement of BKM: a shift-and-add algorithm based on the CORDIC that allows fast computation of complex exponential and logarithm functions. BKM is accelerated by the use of a redundant binary number system. Unlike the previous redundant CORDIC methods, we do not need neither to calculate the scale factor during the computation, nor to double the number of iterations. So our algorithm is suitable for an efficient hardware implementation.
Estimating Dependency Structure as a Hidden Variable (1997)

This publication can be retrieved by anonymous ftp to publications.ai.mit.edu. This paper introduces a probability model,themixture oftrees that can account for sparse, dynamically changing dependence relationships. We present a family of e cient algorithms that use EM and the Minimum Spanning Tree algorithm to nd the ML and MAP mixture of trees for a variety of priors, including the Dirichlet and the MDL priors.
The Alpha Chain of the Nascent Polypeptide-Associated Complex Functions as a Transcriptional Coactivator (1998)

We report the characterization of clone 1.9.2, a gene expressed in mineralizing osteoblasts. Remarkably, clone 1.9.2 is the murine homolog of the alpha chain of the nascent polypeptide-associated complex (alpha-NAC). Based on sequence similarities between alpha-NAC/1.9.2 and transcriptional regulatory proteins and the fact that the heterodimerization partner of alpha-NAC was identified as the transcription factor BTF3b (B. Wiedmann, H. Sakai, T. A. Davis, and M. Wiedmann, Nature 370:434-440, 1994), we investigated a putative role for alpha-NAC/ 1.9.2 in transcriptional control. The alpha-NAC/1.9.2 protein potentiated by 10-fold the activity of the chimeric activator GAL4/VP-16 in vivo. The potentiation was shown to be mediated at the level of gene transcription, because alpha-NAC/1.9.2 increased GAL4/VP-16-mediated mRNA synthesis without affecting the half-life of the GAL4/VP-16 fusion protein. Moreover, the interaction of alpha-NAC/1.9.2 with a transcriptionally defective mutant of GAL4/VP-16 was severely compromised. Specific protein-protein interactions between alpha-NAC/1.9.2 and GAL4/VP-16 were demonstrated by gel retardation, affinity chromatography, and protein blotting assays, while interactions with TATA box-binding protein (TBP) were detected by immunoprecipitation, affinity chromatography, and protein blotting assays. Based on these interactions that define the coactivator class of proteins, we conclude that the alapha-NAC/1.9.2 gene product functions as a transcriptional coactivator.
Comparison of analgesic efficacy of flupirtine maleate and ibuprofen in gynaecological ambulatory surgeries: A randomized controlled trial (2015)

Analgesic efficacy of flupirtine maleate was comparable with ibuprofen in patients in ambulatory gynaecological patients up to 48 h postoperatively with superior satisfaction scores.
Reducing uncertainties in volumetric image based deformable organ registration (2003)

Applying volumetric image feedback in radiotherapy requires image based deformable organ registration. The foundation of this registration is the ability of tracking subvolume displacement in organs of interest. Subvolume displacement can be calculated by applying biomechanics model and the finite element method to human organs manifested on the multiple volumetric images. The calculation accuracy, however, is highly dependent on the determination of the corresponding organ boundary points. Lacking sufficient information for such determination, uncertainties are inevitable-thus diminishing the registration accuracy. In this paper, a method of consuming energy minimization was developed to reduce these uncertainties. Starting from an initial selection of organ boundary point correspondence on volumetric image sets, the subvolume displacement and stress distribution of the whole organ are calculated and the consumed energy due to the subvolume displacements is computed accordingly. The corresponding positions of the initially selected boundary points are then iteratively optimized to minimize the consuming energy under geometry and stress constraints. In this study, a rectal wall delineated from patient CT image was artificially deformed using a computer simulation and utilized to test the optimization. Subvolume displacements calculated based on the optimized boundary point correspondence were compared to the true displacements, and the calculation accuracy was thereby evaluated. Results demonstrate that a significant improvement on the accuracy of the deformable organ registration can be achieved by applying the consuming energy minimization in the organ deformation calculation.
Cutting Edge: Alum Adjuvant Stimulates Inflammatory Dendritic Cells through Activation of the NALP3 Inflammasome (2008)

Adjuvants are vaccine additives that stimulate the immune system without having any specific antigenic effect of itself. In this study we show that alum adjuvant induces the release of IL-1beta from macrophages and dendritic cells and that this is abrogated in cells lacking various NALP3 inflammasome components. The NALP3 inflammasome is also required in vivo for the innate immune response to OVA in alum. The early production of IL-1beta and the influx of inflammatory cells into the peritoneal cavity is strongly reduced in NALP3-deficient mice. The activation of adaptive cellular immunity to OVA-alum is initiated by monocytic dendritic cell precursors that induce the expansion of Ag-specific T cells in a NALP3-dependent way. We propose that, in addition to TLR stimulators, agonists of the NALP3 inflammasome should also be considered as vaccine adjuvants.
ABA Regulates Apoplastic Sugar Transport and is a Potential Signal for Cold-Induced Pollen Sterility in Rice (2007)

Cold temperatures cause pollen sterility and large reductions in grain yield in temperate rice growing regions of the world. Induction of pollen sterility by cold involves a disruption of sugar transport in anthers, caused by the cold-induced repression of the apoplastic sugar transport pathway in the tapetum. Here we demonstrate that the phytohormone ABA is a potential signal for cold-induced pollen sterility (CIPS). Cold treatment of the cold-sensitive cultivar Doongara resulted in increased anther ABA levels. Exogenous ABA treatment at the young microspore stage induced pollen sterility and affected cell wall invertase and monosaccharide transporter gene expression in a way similar to cold treatment. In the cold-tolerant cultivar R31, ABA levels were significantly lower under normal circumstances and remained low after cold treatment. The differences in endogenous ABA levels in Doongara and R31 correlated with differences in expression of the ABA biosynthetic genes encoding zeaxanthin epoxidase (OSZEP1) and 9-cis-epoxycarotenoid dioxygenase (OSNCED2, OSNCED3) in anthers. The expression of three ABA-8-hydroxylase genes (ABA8OX1, 2 and 3) in R31 anthers was higher under control conditions and was regulated differently by cold compared with Doongara. Our results indicate that the cold tolerance phenotype of R31 is correlated with lower endogenous ABA levels and a different regulation of ABA metabolism.
Design of ultraspherical windows with prescribed spectral characteristics (2003)

A method for designing ultraspherical windows with prescribed spectral characteristics is proposed. The characteristics considered include the ripple ratio, main-lobe width, null-to-null width, and a user defined side-lobe pattern. The method employs a variety of short algorithms that calculate the ultraspherical window's independent parameters based on the prescribed spectral characteristics.
TRANSCRIPTION FACTORS OF THE NFAT FAMILY:Regulation and Function (1997)

As targets for the immunosuppressive drugs cyclosporin A and FK506, transcription factors of the NFAT (nuclear factor of activated T cells) family have been the focus of much attention. NFAT proteins, which are expressed in most immune-system cells, play a pivotal role in the transcription of cytokine genes and other genes critical for the immune response. The activity of NFAT proteins is tightly regulated by the calcium/calmodulin-dependent phosphatase calcineurin, a primary target for inhibition by cyclosporin A and FK506. Calcineurin controls the translocation of NFAT proteins from the cytoplasm to the nucleus of activated cells by interacting with an N-terminal regulatory domain conserved in the NFAT family. The DNA-binding domains of NFAT proteins resemble those of Rel-family proteins, and Rel and NFAT proteins show some overlap in their ability to bind to certain regulatory elements in cytokine genes. NFAT is also notable for its ability to bind cooperatively with transcription factors of the AP-1 (Fos/Jun) family to composite NFAT:AP-1 sites, found in the regulatory regions of many genes that are inducibly transcribed by immune-system cells. This review discusses recent data on the diversity of the NFAT family of transcription factors, the regulation of NFAT proteins within cells, and the cooperation of NFAT proteins with other transcription factors to regulate the expression of inducible genes.