gebhart/patrepeval huggingface dataset:
A Survey of 215 Non-Hemophilic Patients with Inhibitors to Factor VIII (1981)

Information was obtained by questionnaire about 215 non-hemophilic patients who developed inhibitors against factor VIII (antihemophilic factor). The majority of the patients were over 50 years of age, and approximately equal numbers of males and females were reported. Rheumatoid arthritis was present in 8% of the cases, 7% occurred during pregnancy or the post-partum period, and in several there was an association with allergy to penicillin, asthma, "auto-immune" diseases, or malignancy. In 46% of cases, no underlying disorders were identified. Major bleeding was observed in 87% of patients, and in 22%, death was attributed either directly or indirectly to the presence of the inhibitor. In 11 of 31 patients receiving no therapy other than supportive transfusions of blood or factor VIII concentrate, the inhibitor disappeared after being present for an average duration of 14 months. Corticosteroids were thought to be effective in abolishing the inhibitor in 22 of 45 patients in whom these were the only drugs administered. Twenty-eight patients received azathioprine as well as corticosteroids; in 19, the inhibitor declined or disappeared during treatment. Finally, 80 patients were treated with cyclophosphamide; in 37 there was a favorable outcome. Inhibitors in children and post-partum patients were more likely to disappear spontaneously or with steroid therapy, whereas those in patients with rheumatoid arthritis or other "autoimmune" disorders required treatment with alkylating agents. However, before any specific therapy can be recommended for this disorder, prospective trials of potential therapeutic agents should be conducted in selected subgroups.
Expression and Potential Roles of Pregnane X Receptor in Endometrial Cancer (2003)

Estrogen has been shown to contribute greatly to growth and development in endometrial cancer. And recent research has suggested that intratumoral production of estrogen may play important roles in this cancer tissue. On the other hand, pregnane X receptor (PXR), a new member of nuclear receptors, has been shown to mediate the genomic effects of steroid hormones, including estrogen and xenobiotics. And this receptor is thought to regulate the expression of the cytochrome P-450 3A (CYP3A) gene family, which plays important roles in the metabolism of endogenous steroids and xenobiotics. Various levels of PXR expression were found in endometrial cancer tissues but not normal tissues. Tissues showing high PXR expression showed significantly high expression of CYP3A4/7 and low expression of estrogen receptor (ER) compared with levels in tissues showing low PXR expression. In endometrial cancer cell lines, HEC-1 cells, which express high PXR and low ER and progesterone receptor, show a stronger transcriptional response of the PXR-CYP3A pathway to the PXR ligands, especially endocrine-disrupting chemical, than do Ishikawa cells. These data suggest that the steroid/xenobiotics metabolism in the tumor tissue through PXR-CYP3A pathway might play an important role, especially in alternative pathway for gonadal hormone and endocrine-disrupting chemical effects on endometrial cancer expressing low ER alpha.
Low switching current flux-closed magnetoresistive random access memory (2003)

A spin valve magnetoresistive random access memory with a flux-closed structure is presented. The flux-closed structure prevents the disruption to magnetization of the recording layer and increases the thermal stability. Simulation results show that the switching field increases under the uniform external field, however, the switching field has no change under the bit current field. Only the bit current that flows mostly at the center is used to switch the cell. Experimental results show that the bit current of 10 mA is sufficient to switch the 1 μm×4 μm cell.
Instantaneous normal mode analysis of orientational motions in liquid water: Local structural effects (2004)

We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.
Modulation of Hepatic Inflammatory Risk Markers of Cardiovascular Diseases by PPAR–α Activators (2006)

Atherosclerosis is a long-term chronic inflammatory disease associated with increased concentrations of inflammatory hepatic markers, such as CRP and fibrinogen, and of peripheral origin, such as tumor necrosis factor (TNF)-alpha and interleukin (IL)-6. Peroxisome proliferator-activated receptor (PPAR-)-alpha is a ligand-activated transcription factor that regulates expression of key genes involved in lipid homeostasis and modulates the inflammatory response both in the vascular wall and the liver. PPAR-alpha is activated by natural ligands, such as fatty acids, as well as the lipid-lowering fibrates. PPAR-alpha agonists impact on different steps of atherogenesis: (1) early markers of atherosclerosis, such as vascular wall reactivity, are improved, (2) however, reduced expression of adhesion molecules on the surface of endothelial cells, accompanied by decreased levels of inflammatory cytokines, such as TNF-alpha, IL-1, and IL-6, leads to a decreased leukocyte recruitment into the arterial wall; (3) in later stages of the atherosclerotic process, PPAR-alpha agonists may promote plaque stabilization and reduce cardiovascular events, via effects on metalloproteinases, such as MMP9. Moreover, PPAR-alpha activation by fibrates also impairs proinflammatory cytokine-signaling pathways in the liver resulting in the modulation of the acute phase response reaction via mechanisms independent of changes in lipoprotein levels. Effective coronary artery disease (CAD) prevention requires the use of agents that act beyond low-density lipoprotein cholesterol-lowering. PPAR-alpha agonists appear to comprehensively address some of the abnormalities of the most common clinical phenotypes of the high CAD risk patient of the 21st century such as in the metabolic syndrome and type 2 diabetes: low high-density lipoprotein cholesterol, high triglycerides, small, dense low-density lipoprotein, and a proinflammatory, procoagulant state.
Explaining the origins of complexity in language: A case study for agreement systems (2011)

The complexity observed in human languages (structural complexity, system complexity, size complexity, individual diversity and language diversity) can only be understood by taking a functional and evolutionary viewpoint. The functional viewpoint insists that language is a tool for communication and hence language users expand their language systems to increase expressive power, but this must be balanced with minimizing cognitive effort, e.g. by re-using existing elements for new purposes or by limiting combinatorial search. The evolutionary viewpoint emphasizes that a language community has to collectively find within the open-ended space of possible languages a candidate that satisfies their&#13;\npurposes. Nobody has a global view or telepathic insight in the brain of another person. So speakers and hearers make guesses and adjust these based on the outcome of their communications. Individual variation arises naturally and language diversity is unavoidable. I will report on a number of computational simulations and robotic experiments of language games, in which these functional and&#13;\nevolutionary viewpoints have been explored. The experiments allow us to pin down precisely the different factors contributing to the complexity of human language. I will use case studies coming from studying how (internal) agreement systems may arise.
Euskarazko denbora-egiturak. Azterketa eta etiketatze-esperimentua (2014)

Denbora-informazioa erauztea oso erabilgarria da hizkuntzaren prozesamenduan (HP), besteak beste, testuen sinplifikazioan, informazio-erauzketako eta itzulpen automatikoko sistemetan balia baitaiteke. Lan honetan, euskaraz informazio hori baliagarri bihurtzeko egin diren lehen urratsak azaltzen dira: batetik, euskaraz denbora adierazteko erabiltzen diren egiturak zein eratakoak diren aztertu da gramatiketan oinarrituta, eta bestetik, egitura horiek testuetan etiketatzeko lehen erabakiak hartu dira. Halaber, ekonomiari buruzko corpus bat osatuta egin den etiketatze-lanaren esperimentua azaltzen da.
Test of the Universality of Free Fall with Atoms in Different Spin Orientations (2016)

We report a test of the universality of free fall by comparing the gravity acceleration of the ^{87}Rb atoms in m_{F}=+1 versus those in m_{F}=-1, of which the corresponding spin orientations are opposite. A Mach-Zehnder-type atom interferometer is exploited to alternately measure the free fall acceleration of the atoms in these two magnetic sublevels, and the resultant Eötvös ratio is η_{S}=(0.2±1.2)×10^{-7}. This also gives an upper limit of 5.4×10^{-6} m^{-2} for a possible gradient field of the spacetime torsion. The interferometer using atoms in m_{F}=±1 is highly sensitive to the magnetic field inhomogeneity. A double differential measurement method is developed to alleviate the inhomogeneity influence, of which the effectiveness is validated by a magnetic field modulating experiment.
Microgrids and other Local Area Power and Energy Systems (2016)

Describing the formation, integration, planning, composition and operation of microgrids, this book explains how local power systems can address limitations in conventional electric power grids and provides insights into the practical implementation needs and outcomes of microgrid technology. All aspects of microgrid design and applications are covered, including the main technologies involved in microgrids and other local area power and energy systems. The reliability and economic characteristics of microgrid system architecture, energy storage and grid interaction are explored in depth. Over 300 illustrations and real-world application examples make this a fully self-contained resource, ideal for graduate students and professionals in electrical, mechanical and chemical engineering and materials science.
Fuzzy Rules Generation And Extraction From Support Vector Machine Based On Kernel Function Firing Signals (2010)

Our study proposes an alternative method in building Fuzzy Rule-Based System (FRB) from Support Vector Machine (SVM). The first set of fuzzy IF-THEN rules is obtained through an equivalence of the SVM decision network and the zero-ordered Sugeno FRB type of the Adaptive Network Fuzzy Inference System (ANFIS). The second set of rules is generated by combining the first set based on strength of firing signals of support vectors using Gaussian kernel. The final set of rules is then obtained from the second set through input scatter partitioning. A distinctive advantage of our method is the guarantee that the number of final fuzzy IFTHEN rules is not more than the number of support vectors in the trained SVM. The final FRB system obtained is capable of performing classification with results comparable to its SVM counterpart, but it has an advantage over the black-boxed SVM in that it may reveal human comprehensible patterns.
Protein Structural Biology Using Cell-Free Platform from Wheat Germ (2018)

Abstract One of the biggest bottlenecks for structural analysis of proteins remains the creation of high yield and high purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited many areas of genomic and proteomics research, therapeutics, vaccine development and protein chip constructions. In this work, we demonstrate a versatile and multistage eukaryotic wheat-germ cell-free protein expression pipeline to generate functional proteins of different sizes from multiple host organism and DNA source origins. We also developed a robust purification procedure, which can produce highly-pure (&gt;98%) proteins with no specialized equipment required and minimal time invested. This pipeline successfully produced and analyzed proteins in all three major geometry formats used for structural biology including single particle analysis, and both two-dimensional and three-dimensional protein crystallography. The flexibility of the wheat germ system in combination with the multiscale pipeline described here provides a new workflow for rapid generation of samples for structural characterization that may not be amenable to other recombinant approaches.
New Concepts in Genome Regulation (2016)

Abstract Manipulating gene regulation to favor gamma-globin transcription over beta-globin transcription has been a goal of research in erythropoiesis for decades because of its relevance to amelioration of the pathophysiology of sickle cell disease and beta-thalassemia. A fundamental unanswered question in biology is how the unique pattern of gene expression, the transcriptome, of the many different individual mammalian cell types arises from the same genome blueprint and changes during development and differentiation. There is a growing appreciation that genome organization and the folding of chromosomes is a key determinant of gene transcription. Within this framework, enhancers function to increase the transcription of target genes over long linear distances. To accomplish this, enhancers engage in close physical contact with target promoters through chromosome folding, or looping. These long range interactions are orchestrated by cell type specific proteins and protein complexes that bind to enhancers and promoters and stabilize their interaction with each other. We have been studying LDB1, a member of an erythroid protein complex containing GATA1, TAL1 and LMO2. The LDB1complex activates erythroid genes through occupancy of virtually all erythroid enhancers. LDB1engages in homo- and heterotypic interactions with proteins occupying the promoters of erythroid genes to bring them into proximity with their enhancers. We find that enhancer long range looping activity can be redirected. Both targeting of the beta-globin locus control region to the gamma-globin gene in adult erythroid cells by the tethering of LDB1 or epigenetic unmasking of a silenced gamma-globin gene lead to increased locus control region (LCR)/gamma-globin contact frequency and reduced LCR/beta-globin contact. The outcome of these manipulations is robust, pan-cellular gamma-globin transcription activation with a concomitant reduction in beta-globin transcription. These examples suggest that chromosome looping can be considered a therapeutic target for gene activation or gene silencing to ameliorate genetic diseases such as sickle cell disease and beta-thalassemia. Disclosures No relevant conflicts of interest to declare.
A Numerical Study of Superconducting Cavity Components (1990)

Computer programs which solve Maxwell's equations in three dimensions are becoming an invaluable tool in the design of RF structures for particle accelerators. In particular, the lack of cylindrical symmetry of superconducting cavities with waveguide couplers demands a 3-D analysis for a reasonable description of a number of important phenomena. A set of codes, collectively known as MAFIA, developed by Weiland and his collaborators, has been used at CEBAF to study its five-cell superconducting accelerating cavities. The magnitude of RF crosstalk between cavities is found to depend critically on the breaking of cylindrical symmetry by the fundamental power couplers. A model of the higher order mode coupler exhibits an unexpected mode which is in good agreement with measurement.
Low-dose imatinib mesylate leads to rapid induction of major molecular responses and achievement of complete molecular remission in FIP1L1-PDGFRA–positive chronic eosinophilic leukemia (2007)

The FIP1L1-PDGFRA fusion gene is a recurrent molecular lesion in eosinophilia-associated myeloproliferative disorders, predicting a favorable response to imatinib mesylate. To investigate its prevalence, 376 patients with persistent unexplained hypereosinophilia were screened by the United Kingdom reference laboratory, revealing 40 positive cases (11%). To determine response kinetics following imatinib, real-time quantitative-polymerase chain reaction (RQ-PCR) assays were developed and evaluated in samples accrued from across the European LeukemiaNet. The FIP1L1-PDGFRA fusion transcript was detected at a sensitivity of 1 in 10(5) in serial dilution of the EOL-1 cell line. Normalized FIP1L1-PDGFRA transcript levels in patient samples prior to imatinib varied by almost 3 logs. Serial monitoring was undertaken in patients with a high level of FIP1L1-PDGFRA expression prior to initiation of imatinib (100 mg/d-400 mg/d). Overall, 11 of 11 evaluable patients achieved at least a 3-log reduction in FIP1L1-PDGFRA fusion transcripts relative to the pretreatment level within 12 months, with achievement of molecular remission in 9 of 11 (assay sensitivities 1 in 10(3)-10(5)). In 2 patients, withdrawal of imatinib was followed by a rapid rise in FIP1L1-PDGFRA transcript levels. Overall, these data are consistent with the exquisite sensitivity of the FIP1L1-PDGFRalpha fusion to imatinib, as compared with BCR-ABL, and underline the importance of RQ-PCR monitoring to guide management using molecularly targeted therapies.
Sorafenib-Induced Mitochondrial Complex I Inactivation and Cell Death in Human Neuroblastoma Cells (2012)

Sorafenib is a multikinase inhibitor that is approved for use against renal cell and hepatocellular carcinoma. We found that sorafenib potently induced cell death in human neuroblastoma cells. To understand the molecular basis of sorafenib-mediated cell death in human SH-SY5Y cells, we performed a temporal quantitative proteome analysis. The results showed significant quantitative changes of 193 unique proteins. Bioinformatics-assisted pathway analysis of the regulated proteins revealed that mitochondrial proteins, especially components of the electron transport chain and the mitochondrial ribosomes, were significantly affected upon exposure to sorafenib. The observed down-regulation of the respiratory chain complex I (NADH dehydrogenase) was accompanied with loss of mitochondrial transmembrane potential (Δψm) and complete impairment of complex I enzyme activity. The destabilization of complex I subunits was consistent, rapid, and independent of caspase activation as well as Bcl-2 overexpression. This study provides an overview of the molecular machinery driving sorafenib-mediated cell death in neuroblastoma cells and suggests that sorafenib could be a potential therapeutic drug for the treatment of neuroblastoma.
Dynamic Load Balancing for Real-Time Video Encoding on Heterogeneous CPU+GPU Systems (2013)

The high computational demands and overall encoding complexity make the processing of high definition video sequences hard to be achieved in real-time. In this manuscript, we target an efficient parallelization and RD performance analysis of H.264/AVC inter-loop modules and their collaborative execution in hybrid multi-core CPU and multi-GPU systems. The proposed dynamic load balancing algorithm allows efficient and concurrent video encoding across several heterogeneous devices by relying on realistic run-time performance modeling and module-device execution affinities when distributing the computations. Due to an online adjustment of load balancing decisions, this approach is also self-adaptable to different execution scenarios. Experimental results show the proposed algorithm's ability to achieve real-time encoding for different resolutions of high-definition sequences in various heterogeneous platforms. Speed-up values of up to 2.6 were obtained when compared to the video inter-loop encoding on a single GPU device, and up to 8.5 when compared to a highly optimized multi-core CPU execution. Moreover, the proposed algorithm also provides an automatic tuning of the encoding parameters, in order to meet strict encoding constraints.
Transient expression of the neurofilament proteins NF‐L and NF‐M by Schwann cells is regulated by axonal contact (1997)

Expression of the genes that encode neurofilament proteins is considered to be confined normally to neurons. However, in demyelinating peripheral nerves Schwann cells upregulate the mRNA for the medium-sized neurofilament protein (NF-M), and cultured Schwann cells of the myelin-forming phenotype can also synthesize and incorporate NF-M protein into their intermediate filament (IF) cytoskeleton. The purpose of this study was to establish how axonal contact might influence glial neurofilament gene expression and regulate the synthesis of neurofilament proteins. We show that the gene encoding NF-M is expressed at early stages of differentiation in myelin-forming Schwann cells in vivo; nevertheless, little NF-M protein can be detected in these cells. The transient induction of NF-M mRNA is also apparent in dedifferentiating Schwann cells during Wallerian degeneration. In these Schwann cells the mRNAs for NF-M and NF-L (the smallest polypeptide), but not NF-H (the largest neurofilament subunit), are coordinately expressed. In contrast to differentiating myelin-forming Schwann cells, the cells of degenerating nerves express both NF-M and NF-L polypeptides. Restoration of axonal contact in the growing nerve stimulates the recapitulation of Schwann cell differentiation including the elevation of NF-M and NF-L mRNA expression. These results demonstrate that the transient induction of neurofilament mRNAs in Schwann cells is a feature of both differentiation and dedifferentiation. However translation of these mRNAs is confined to Schwann cells deprived of axonal contact either by nerve injury or by culture in the absence of axons. These findings suggest that the expression of the NF-M and NF-L polypeptides is an important characteristic of those Schwann cells that will contribute to the repair of damaged peripheral nerves. J. Neurosci. Res. 50:291–299, 1997. © 1997 Wiley-Liss, Inc.