gebhart/patrepeval huggingface dataset:
Optimizing microfluidic ink delivery for dip pen nanolithography (2004)

This work demonstrates the design optimization, fabrication process development, process optimization and testing of a microfluidic ink delivery apparatus (called "Inkwells") for simultaneously coating an array of DPN pens with different inks. The objective of this work is to deliver between 4 and 10 different inks from reservoirs into appropriately spacd microwell array. A tips of the multi-pen array are coated with different inks by dipping them into the microwell array. The reservoirs, microwells and their connecting micro-channels were etched in silicon wafers using Deep Reactive Ion Etching (DRIE). Fluid actuation was achieved by capillary wicking. The optimum layouts for different applications were selected with respect to the volume requirement of inks, the efficacy of ink-well filling, to obviate the problem of bubble formation, and to test the operations of dipping and writing with a parallel array of pens.
Secondary and ectopic lymphoid tissue responses in rheumatoid arthritis: from inflammation to autoimmunity and tissue damage/remodeling (2009)

Rheumatoid arthritis is a chronic systemic inflammatory disease primarily affecting the synovium of diarthrodial joints. Despite the currently unknown etiology, overwhelming evidence indicates that both innate and adaptive immunity play a central role in disease pathogenesis. In this review, we consider recent evidence examining the mechanisms of lymphoid tissue reactivity in rheumatoid arthritis with a focus on the dynamics controlling secondary and ectopic lymphoid tissue response. We then examine the cellular and molecular mechanisms regulating the biopathology of these processes with specific emphasis on cell trafficking, contribution to autoimmunity, and joint damage-repair. We finally provide a brief overview of the most recent studies addressing the clinical relevance of synovial lymphoid tissue analysis as a diagnostic and prognostic tool as well as its response to current biological therapies.
[Genetic polymorphisms as risk factors for coronary artery disease]. (1998)

The acute myocardial infarction is a multi factor disease, and various risk factors participate in its occurrence and progression. Recently, many investigators have paid their attention to the genetic polymorphisms as new risk factors for coronary artery disease. These include the polymorphisms or mutations of the gene which relates to hypertension, diabetes, the platelet function, the property of the blood vessel, the blood coagulation fibrinogenolysis system, and serum lipids. The tendency toward the occurrence and progression of coronary artery disease might be decided genetically by combining these genetic polymorphisms.
Clonal Deletion of Autospecific B Lymphocytes (1991)

Using mice transgenic for functional, rearranged immunoglobulin heavy and light chain genes, it can be demonstrated that B lymphocytes reactive with cell surface-bound class I MHC antigen can be controlled by clonal elimination. Even low-affinity cell-bound ligands can induce deletion. Deletion can occur in the pre-B to B cell transitional stage or after the B cells exist the bone marrow, depending on where the cells first encounter autoantigen. IgD appears to play no role in protecting cells from deletion. It is argued that defects in B-cell tolerance alone may be sufficient to lead to systemic autoimmunity.
Multilingual Question Answering from Formatted Text applied to Conversational Agents (2019)

Recent advances with language models (e.g. BERT, XLNet, ...), have allowed surpassing human performance on complex NLP tasks such as Reading Comprehension. However, labeled datasets for training are available mostly in English which makes it difficult to acknowledge progress in other languages. Fortunately, models are now pre-trained on unlabeled data from hundreds of languages and exhibit interesting transfer abilities from one language to another. In this paper, we show that multilingual BERT is naturally capable of zero-shot transfer for an extractive Question Answering task (eQA) from English to other languages. More specifically, it outperforms the best previously known baseline for transfer to Japanese and French. Moreover, using a recently published large eQA French dataset, we are able to further show that (1) zero-shot transfer provides results really close to a direct training on the target language and (2) combination of transfer and training on target is the best option overall. We finally present a practical application: a multilingual conversational agent called Kate which answers to HR-related questions in several languages directly from the content of intranet pages.
Differential Dynamics of α5 Integrin, Paxillin, and α-Actinin during Formation and Disassembly of Adhesions in Migrating Cells (2001)

To investigate the mechanisms by which adhesions form and disperse in migrating cells, we expressed alpha 5 integrin, alpha-actinin, and paxillin as green fluorescent protein (GFP) fusions. All localized with their endogenous counterparts and did not perturb migration when expressed at moderate levels. alpha 5-GFP also rescued the adhesive defects in CHO B2 cells, which are alpha 5 integrin deficient. In ruffling cells, alpha 5-GFP and alpha-actinin--GFP localized prominently at the leading edge in membrane protrusions. Of the three GFP fusion proteins that we examined, paxillin was the first component to appear visibly organized in protrusive regions of the cell. When a new protrusion formed, the paxillin appeared to remodel from older to newer adhesions at the leading edge. alpha-Actinin subsequently entered adhesions, which translocated toward the cell center, and inhibited paxillin turnover. The new adhesions formed from small foci of alpha-actinin--GFP and paxillin-GFP, which grew in size. Subsequently, alpha 5 integrin entered the adhesions to form visible complexes, which served to stabilize the adhesions. alpha 5-GFP also resided in endocytic vesicles that emanated from the leading edge of protrusions. Integrin vesicles at the cell rear moved toward the cell body. As cells migrated, alpha 5 vesicles also moved from a perinuclear region to the base of the lamellipodium. The alpha 5 vesicles colocalized with transferrin receptor and FM 4-64 dye. After adhesions broke down in the rear, alpha 5-GFP was found in fibrous structures behind the cell, whereas alpha-actinin--GFP and paxillin-GFP moved up the lateral edge of retracting cells as organized structures and then dissipated.
An MM-based algorithm for L<inf>1</inf>-regularized least squares estimation in GPR image reconstruction (2013)

We present a regularized Least-Squares (LS) method for estimating subsurface reflection coefficients from ground penetrating radar (GPR) measurements. The expected sparsity of the reflection coefficients induced via L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -regularization. The majorize-minimize (MM) framework is used to develop a novel iterative algorithm for solving the L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -regularized LS problem in a straightforward and effective manner. The proposed L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -regularized Least-Squares (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -LS) algorithm is amenable to parallel implementation since the MM procedure decouples the estimation of the individual reflection coefficients. In order to work toward an extended algorithm that would be suited for real-time implementations, we investigate an online strategy for choosing the regularization parameter. The L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -LS algorithm is validated using simulated GPR datasets.
Psychiatric applications of bromocriptine therapy. (1990)

Bromocriptine, an ergot alkaloid derivative that possesses both dopamine agonist and antagonist activity, has been studied in a broad spectrum of psychiatric illnesses. The literature consists primarily of case reports and small trials limited by methodological shortcomings. The authors critically review these reports, focusing on efficacy, mechanistic issues, dosing, side effects, predictors of response, monitoring parameters, and practical guidelines. Preliminary data suggest bromocriptine may have promise in the treatment of neuroleptic malignant syndrome, cocaine withdrawal, and depression. At present, the agent appears less efficacious in the treatment of tardive dyskinesia, mania, and schizophrenia; however, doses in these trials may have been excessive, producing primarily postsynaptic agonist effects. More extensive clinical trials are required to clearly define the role of bromocriptine in psychiatry.
A novel gene, MEL1, mapped to 1p36.3 is highly homologous to the MDS1/EVI1 gene and is transcriptionally activated in t(1;3)(p36;q21)-positive leukemia cells (2000)

The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), which is frequently characterized by trilineage dysplasia, in particular dysmegakaryocytopoiesis, and poor prognosis. Previously, the breakpoint cluster region (BCR) at 3q21 was identified within a 60-kilobase (kb) region centromeric to the BCR of 3q21q26 syndrome and that at 1p36.3 within a 90-kb region. In this study, genes were searched near the breakpoints at 1p36.3, and a novel gene was isolated that encoded a zinc finger protein with a PR domain, which is highly homologous to theMDS1/EVI1 gene. The novel gene, designated asMEL1(MDS1/EVI1-like gene 1), with 1257 amino acid residues is 64% similar in nucleotide and 63% similar in amino acid sequences to MDS1/EVI1 with the same domain structure. The MEL1 gene is expressed in leukemia cells with t(1;3) but not in other cell lines or bone marrow, spleen, and fetal liver, suggesting that MEL1 is specifically in the t(1;3)(p36;q21)-positive MDS/AML. On the basis of the positional relationship between the EVI1 and MEL1 genes in each translocation, it was suggested that both genes are transcriptionally activated by the translocation of the 3q21 region with the Ribophorin I gene. Because of the transcriptional activation of the EVI1 family genes in both t(1;3)(p36;q21)-positive MDS/AML and 3q21q26 syndrome, it is suggested that they share a common molecular mechanism for the leukemogenic transformation of the cells.
Local glutamate release in the rat ventral lateral thalamus evoked by high-frequency stimulation (2010)

Thalamic deep brain stimulation (DBS) is proven therapy for essential tremor, Parkinson's disease and Tourette's syndrome. We tested the hypothesis that high-frequency electrical stimulation results in local thalamic glutamate release. Enzyme-linked glutamate amperometric biosensors were implanted in anesthetized rat thalamus adjacent to the stimulating electrode. Electrical stimulation was delivered to investigate the effect of frequency, pulse width, voltage-controlled or current-controlled stimulation, and charge balancing. Monophasic electrical stimulation-induced glutamate release was linearly dependent on stimulation frequency, intensity and pulse width. Prolonged stimulation evoked glutamate release to a plateau that subsequently decayed back to baseline after stimulation. Glutamate release was less pronounced with voltage-controlled stimulation and not present with charge balanced current-controlled stimulation. Using fixed potential amperometry in combination with a glutamate bioprobe and adjacent microstimulating electrode, the present study has shown that monophasic current-controlled stimulation of the thalamus in the anesthetized rat evoked linear increases in local extracellular glutamate concentrations that were dependent on stimulation duration, frequency, intensity and pulse width. However, the efficacy of monophasic voltage-controlled stimulation, in terms of evoking glutamate release in the thalamus, was substantially lower compared to monophasic current-controlled stimulation and entirely absent with biphasic (charge balanced) current-controlled stimulation. It remains to be determined whether similar glutamate release occurs with human DBS electrodes and similar charge balanced stimulation. As such, the present results indicate the importance of evaluating local neurotransmitter dynamics in studying the mechanism of action of DBS.
Selective Visualization of Cyclooxygenase-2 in Inflammation and Cancer by Targeted Fluorescent Imaging Agents (2010)

Effective diagnosis of inflammation and cancer by molecular imaging is challenging because of interference from nonselective accumulation of the contrast agents in normal tissues. Here, we report a series of novel fluorescence imaging agents that efficiently target cyclooxygenase-2 (COX-2), which is normally absent from cells, but is found at high levels in inflammatory lesions and in many premalignant and malignant tumors. After either i.p. or i.v. injection, these reagents become highly enriched in inflamed or tumor tissue compared with normal tissue and this accumulation provides sufficient signal for in vivo fluorescence imaging. Further, we show that only the intact parent compound is found in the region of interest. COX-2-specific delivery was unambiguously confirmed using animals bearing targeted deletions of COX-2 and by blocking the COX-2 active site with high-affinity inhibitors in both in vitro and in vivo models. Because of their high specificity, contrast, and detectability, these fluorocoxibs are ideal candidates for detection of inflammatory lesions or early-stage COX-2-expressing human cancers, such as those in the esophagus, oropharynx, and colon.
Intermittent peripheral tissue ischemia during coronary ischemia reduces myocardial infarction through a KATP-dependent mechanism: first demonstration of remote ischemic perconditioning (2006)

Remote ischemic preconditioning reduces myocardial infarction (MI) in animal models. We tested the hypothesis that the systemic protection thus induced is effective when ischemic preconditioning is administered during ischemia (PerC) and before reperfusion and examined the role of the K(+)-dependent ATP (K(ATP)) channel. Twenty 20-kg pigs were randomized (10 in each group) to 40 min of left anterior descending coronary artery occlusion with 120 min of reperfusion. PerC consisted of four 5-min cycles of lower limb ischemia by tourniquet during left anterior descending coronary artery occlusion. Left ventricular (LV) function was assessed by a conductance catheter and extent of infarction by tetrazolium staining. The extent of MI was significantly reduced by PerC (60.4 +/- 14.3 vs. 38.3 +/- 15.4%, P = 0.004) and associated with improved functional indexes. The increase in the time constant of diastolic relaxation was significantly attenuated by PerC compared with control in ischemia and reperfusion (P = 0.01 and 0.04, respectively). At 120 min of reperfusion, preload-recruitable stroke work declined 38 +/- 6% and 3 +/- 5% in control and PerC, respectively (P = 0.001). The force-frequency relation was significantly depressed at 120 min of reperfusion in both groups, but optimal heart rate was significantly lower in the control group (P = 0.04). There were fewer malignant arrhythmias with PerC during reperfusion (P = 0.02). These protective effects of PerC were abolished by glibenclamide. Intermittent limb ischemia during myocardial ischemia reduces MI, preserves global systolic and diastolic function, and protects against arrhythmia during the reperfusion phase through a K(ATP) channel-dependent mechanism. Understanding this process may have important therapeutic implications for a range of ischemia-reperfusion syndromes.
<title>Solid state volumetric display projecting 3D objects in space</title> (2001)

My prototype 3D display shows that 3D objects can be projected in space in color without moving parts by using a scalable high-resolution screen, 10 micrometer pixels, that combines up to 100 views. The patented high-resolution screen uses coherent optical fiber bundles to combine the images of many spatial light modulators together. The straightforward modular approach makes it easy to: scale the screen up; adjust light output and change 2D and 3D resolution. Depending on the computer used refresh rates go from 0.1 up to real-time. The volume of the apparatus is comparable to an ordinary TV set. The paper will include concepts, theory, experiments, proof of concept and configurations for different uses. The flexibility of the system allows you to make curved 3D screens, live size 3D screens and even the possibility to reproduce the 'Princess Leia it's a hologram' of Star Wars effect.
Characterization of Aspen Isoprene Synthase, an Enzyme Responsible for Leaf Isoprene Emission to the Atmosphere (1995)

Isoprene (2-methyl-1,3-butadiene) is a volatile hydrocarbon emitted from many plant species to the atmosphere, where it plays an important role in atmospheric chemistry. An enzyme extracted from aspen (Populus tremuloides) leaves was previously found to catalyze the Mg(2+)-dependent elimination of pyrophosphate from dimethylallyl diphosphate (DMAPP) to form isoprene (Silver, G. M., and Fall, R. (1991) Plant Physiol. 97, 1588-1591). This enzyme, isoprene synthase, has now been purified 4000-fold to near homogeneity. The enzyme had a native molecular mass of 98-137 kDa and isoelectric point of 4.7 and contained 58- and 62-kDa subunits, implying that it is a heterodimer. Partial amino acid sequences of the two subunits indicated they are closely related to each other and that they do not share a strong homology with any other reported proteins. The isoprene synthase reaction was dependent on Mg2+ or Mn2+, and the reaction products were shown to be isoprene and pyrophosphate with a stoichiometry close to 1:1. The Km for DMAPP was high at 8 mM, and the kcat of 1.7 s-1 was low, but similar to those of other allylic diphosphate-utilizing enzymes. It is argued that the isoprene synthase reaction may be much more efficient in vivo, where it is under light-dependent control. It seems probable that this unique enzyme, rather than non-enzymatic reactions, can account for the emission of hundreds of millions of metric tons of isoprene from plants to the global atmosphere each year.
Flexible frequency control of cortical oscillations enables computations required for working memory (2013)

Cognitive effort leads to a seeming cacophony of brain oscillations. For example, during tasks engaging working memory (WM), specific oscillatory frequency bands modulate in space and time. Despite ample data correlating such modulation to task performance, a mechanistic explanation remains elusive. We propose that flexible control of neural oscillations provides a unified mechanism for the rapid and controlled transitions between the computational operations required by WM. We show in a spiking network model that modulating the input oscillation frequency sets the network in different operating modes: rapid memory access and load is enabled by the beta-gamma oscillations, maintaining a memory while ignoring distractors by the theta, rapid memory clearance by the alpha. The various frequency bands determine the dynamic gating regimes enabling the necessary operations for WM, whose succession explains the need for the complex oscillatory brain dynamics during effortful cognition.
Recombinant human IgG molecules lacking Fcγ receptor I binding and monocyte triggering activities (1999)

Subclasses of human IgG have a range of activity levels with different effector systems but each triggers at least one mechanism of cell destruction. We are aiming to engineer non-destructive human IgG constant regions for therapeutic applications where depletion of cells bearing the target antigen is undesirable. The attributes required are a lack of killing via Fcgamma receptors (R) and complement but retention of neonatal FcR binding to maintain placental transport and the prolonged half-life of IgG. Eight variants of human IgG constant regions were made with anti-RhD and CD52 specificities. The mutations, in one or two key regions of the CH2 domain, were restricted to incorporation of motifs from other subclasses to minimize potential immunogenicity. IgG2 residues at positions 233 - 236, substituted into IgG1 and IgG4, reduced binding to FcgammaRI by 10(4)-fold and eliminated the human monocyte response to antibody-sensitized red blood cells, resulting in antibodies which blocked the functions of active antibodies. If glycine 236, which is deleted in IgG2, was restored to the IgG1 and IgG4 mutants, low levels of activity were observed. Introduction of the IgG4 residues at positions 327, 330 and 331 of IgG1 and IgG2 had no effect on FcgammaRI binding but caused a small decrease in monocyte triggering.
Veto-Like Activity of Mesenchymal Stem Cells: Functional Discrimination Between Cellular Responses to Alloantigens and Recall Antigens (2003)

Trans-differentiation of stem cells shows promise for use in tissue repair medicine. Although poorly defined, mesenchymal stem cells (MSC) appear useful for applications in repair medicine. Despite the low frequency of MSC, they are relatively easy to expand. The expression of MHC class II on MSC, however, could deter their use in repair medicine, since these molecules could stimulate an allogeneic host response. This study sought to compare the immune stimulatory and suppressive effects of MSC. Primary human MSC were cultured from bone marrow aspirates and then passaged at least three times before use in assays. Morphologically, MSC were symmetrical; were SH2(+), MHC class II(+), CD45(-), CD44(+), CD31(-), CD14(-), proly-4-hydroxylase(-); and showed normal karyotype patterns and elevated telomerase activities. MSC elicited significant stimulatory responses when cocultured with allogeneic PBMC. Despite the production of different types of growth factors, allogeneic effects of MSC could not be explained by the production of these growth factors. One-way MLR reactions were significantly blunted by third-party MSC. Similar suppression was not observed for responses to three different recall Ags. Based on these functional differences by MSC in responses to allo- and recall Ags, we examined whether MSC could exert veto-like functions. We showed that MSC could blunt the cytotoxic effects of allogeneic-induced effectors to mitogen-activated targets. The results showed that although MSC elicited allogeneic responses in a model that mimics a graft-vs-host reaction, they also exerted veto-like activity, but caused no effect on responses to recall Ags.
Turbulence-free ghost imaging (2011)

Atmospheric turbulence is a serious problem for satellite and aircraft-to-ground based classical imaging. Taking advantage of the natural, nonfactorizable, point-to-point correlation of thermal light, this experiment demonstrated turbulence-free ghost imaging, which will be extremely useful for these applications. In addition, this observation suggests that the nontrivial intensity-intensity correlation of thermal light cannot be caused by the statistical correlation of intensity fluctuations.
Synergistic use of direct manipulation and natural language (1989)

This paper shows how the integration of natural language with direct manipulation produces a multimodal interface that overcomes limitations of these techniques when used separately. Natural language helps direct manipulation in being able to specify objects and actions by description, while direct manipulation enables users to learn which objects and actions are available in the system. Furthermore, graphical rendering and manipulation of context provides a partial solution to difficult problems of natural language anaphora.