gebhart/patrepeval huggingface dataset:
Using Acoustics to Study and Stimulate the Coalescence of Oil Drops Surrounded by Water (1993)

The coalescence of oil drops in water is studied using acoustic levitation and stimulated with acoustic cavitation. Unlike most earlier studies, which investigate the coalescence of a single drop with an initially plannar interface, the use of acoustic radiation forces allows two drops to be brought into contact and allowed to coalesce. This acoustic technique has the advantage over other drop-drop coalescence systems in that the drops remain in contact until they coalesce without the use of solid supports to control them. Additionally, acoustic cavitation is observed to deposit sufficient energy in the oil-water interface to trigger the coalescence of a pair of 2-mm-diameter drops. This stimulation mechanism could have application to emulsion breaking. Some of the factors that affect spontaneous and stimulated coalescence are investigated.
The Amino-terminal Immunoglobulin-like Domain of Sialoadhesin Contains the Sialic Acid Binding Site (1995)

Sialoadhesin and CD22 are members of a recently characterized family of sialic acid-dependent adhesion molecules belonging to the immunoglobulin superfamily. Sialoadhesin is a macrophage-restricted receptor containing 17 extracellular Ig-like domains which recognizes oligosaccharides terminating in NeuAc alpha 2-3Gal in N- and O-linked glycans. CD22 is a B cell-restricted receptor with seven Ig-like domains which selectively recognizes oligosaccharides terminating in NeuAc alpha 2-6Gal in N-glycans. Sequence similarity between these proteins is highest within their first four amino-terminal Ig-like domains. Here we identify the domain(s) containing the binding sites of both molecules by generating a series of extracellular domain deletion mutants fused to the Fc portion of human IgG1. Binding activity was analyzed by solid phase cell adhesion assays and also by surface plasmon resonance using purified glycophorin and CD45 as ligands for sialoadhesin and CD22, respectively. For sialoadhesin, the amino-terminal V-set Ig-like domain was both necessary and sufficient to mediate sialic acid-dependent adhesion of the correct specificity. In contrast, for murine CD22, only constructs containing both the V-set domain and the adjacent C2-set domain were able to mediate sialic acid-dependent binding. These results are consistent with the sialic acid binding site for both proteins residing in the membrane distal V-set domain, but for CD22 a direct contribution in binding from the neighboring C2-set domain cannot be excluded.
Auto- and alloimmune reactivity to human islet allografts transplanted into type 1 diabetic patients. (1999)

Allogeneic islet transplantation can restore an insulin-independent state in C-peptide-negative type 1 diabetic patients. We recently reported three cases of surviving islet allografts that were implanted in type 1 diabetic patients under maintenance immune suppression for a previous kidney graft. The present study compares islet graft-specific cellular auto- and alloreactivity in peripheral blood from those three recipients and from four patients with failing islet allografts measured over a period of 6 months after portal islet implantation. The three cases that remained C-peptide-positive for >1 year exhibited no signs of alloreactivity, and their autoreactivity to islet autoantigens was only marginally increased. In contrast, rapid failure (<3 weeks) in three other cases was accompanied by increases in precursor frequencies of graft-specific alloreactive T-cells; in one of them, the alloreactivity was preceded by a sharply increased autoreactivity to several islet autoantigens. One recipient had a delayed loss of islet graft function (33 weeks); he did not exhibit signs of graft-specific alloimmunity, but developed a delayed increase in autoreactivity. The parallel between metabolic outcome of human beta-cell allografts and cellular auto- and alloreactivity in peripheral blood suggests a causal relationship. The present study therefore demonstrates that T-cell reactivities in peripheral blood can be used to monitor immune mechanisms, which influence survival of beta-cell allografts in diabetic patients.
Pathophysiologic mechanisms of acute ischemic stroke: An overview with emphasis on therapeutic significance beyond thrombolysis (2010)

Stroke is a serious neurological disease, and constitutes a major cause of death and disability throughout the world. The pathophysiology of stroke is complex, and involves excitotoxicity mechanisms, inflammatory pathways, oxidative damage, ionic imbalances, apoptosis, angiogenesis and neuroprotection. The ultimate result of ischemic cascade initiated by acute stroke is neuronal death along with an irreversible loss of neuronal function. Therapeutic strategies in stroke have been developed with two main aims: restoration of cerebral flow and the minimization of the deleterious effects of ischemia on neurons. Intense research spanning over the last two decades has witnessed significant therapeutic advances in the form of carotid endarterectomy, thrombolytics, anticoagulant therapy, antiplatelet agents, neuroprotective agents, and treating associated risk factors such as hypertension and hyperlipidemia. However, the search for an effective neuroprotectant remains frustrating, and the current therapeutic protocols remain suboptimal. Till date only one FDA-approved drug is available for ischemic stroke; i.e., the serine protease tissue-type plasminogen activator (tPA), utility of which is limited by short therapeutic window. The objective of this review is to critically evaluate the major mechanisms underlying stroke pathophysiology, with emphasis on potential novel targets for designing newer therapeutic modalities.
Letter-Based Speech Recognition with Gated ConvNets (2017)

In the recent literature, "end-to-end" speech systems often refer to letter-based acoustic models trained in a sequence-to-sequence manner, either via a recurrent model or via a structured output learning approach (such as CTC). In contrast to traditional phone (or senone)-based approaches, these "end-to-end'' approaches alleviate the need of word pronunciation modeling, and do not require a "forced alignment" step at training time. Phone-based approaches remain however state of the art on classical benchmarks. In this paper, we propose a letter-based speech recognition system, leveraging a ConvNet acoustic model. Key ingredients of the ConvNet are Gated Linear Units and high dropout. The ConvNet is trained to map audio sequences to their corresponding letter transcriptions, either via a classical CTC approach, or via a recent variant called ASG. Coupled with a simple decoder at inference time, our system matches the best existing letter-based systems on WSJ (in word error rate), and shows near state of the art performance on LibriSpeech.
Functional analysis of the 3' control region of the potato wound-inducible proteinase inhibitor II gene. (1989)

Proteinase inhibitor genes are expressed strongly in specific plant tissues under both developmental and environmental regulation. We have studied the role of the 3' control region of the potato proteinase inhibitor II gene (PI-II) that is inducible in leaves in response to herbivore attacks or other severe wounding. Comparison of the terminator from the PI-II gene with two different terminators from the 6b and 7 genes, driven by a common PI-II promoter-cat fusion molecule, indicated that the PI-II terminator provided the most efficient expression of cat. The PI-II terminator also caused a significantly elevated cat gene expression driven by the cauliflower mosaic virus 35S promoter. The increase in the level of expression is probably not due to the presence of an enhancer element in the PI-II terminator region, but to cis-acting elements involved in mRNA processing or stability. Both transient and stable transformation analyses of the deletion mutants in the 3'-flanking sequence indicated that about a 100-base pair DNA fragment surrounding the polyadenylation site is essential for the efficient gene expression. This region seems to consist of several regulatory elements, including the conserved sequence, CGTGTCTT, which is located 9 bases downstream from the polyadenylation site. The elements appear to contribute to the increased stability of mRNAs containing the PI-II terminator.
Chemokine Receptor Antagonists (2000)

Chemokines belong to a large family of chemoattractant molecules involved in the directed migration of immune cells. They achieve their cellular effects by direct interaction with cell surface receptors. Chemokines appear to be involved in a variety of proinflammatory and autoimmune diseases and this makes them and their receptors very attractive therapeutic targets. This review highlights current efforts toward obtaining highly specific chemokine receptor antagonists and discusses their chemistry and potential role as disease modifiers.
Centralized packet radio network (1993)

Thii paper presents the development of a centralized multihop packet rado networkusedtotransfer information ina real time flash flood prediction system.The limitations imposedby the environment of the flashfloodreporting system,alongwhh thehiddenterminals problemand theoverheadintroduced by theacknowledgement tJaftlc, carried on themessagechannel, arestudied. The approachtotheproblemcombinestheresults of a mathematical and a simulation models to arrive at a feasible solution. The main results of both models, obtained through a worst case analysis, were found to coinci& with a high degree of accuracy.
Bicontinuous Cubic Block Copolymer Photonic Crystals (2002)

Three‐dimensional photonic crystals are fabricated from block copolymers, forming a double gyroid network structure. Further processing produces three‐dimensionally nanoporous, freestanding materials (see Figure), and allows dielectric enhancement and infiltration, which dramatically improve optical and material properties. These etched materials provide a path to highly effective photonic crystals via self‐assembly.
Movelets: A dictionary of movement (2012)

Recent technological advances provide researchers with a way of gathering real-time information on an individual's movement through the use of wearable devices that record acceleration. In this paper, we propose a method for identifying activity types, like walking, standing, and resting, from acceleration data. Our approach decomposes movements into short components called "movelets", and builds a reference for each activity type. Unknown activities are predicted by matching new movelets to the reference. We apply our method to data collected from a single, three-axis accelerometer and focus on activities of interest in studying physical function in elderly populations. An important technical advantage of our methods is that they allow identification of short activities, such as taking two or three steps and then stopping, as well as low frequency rare(compared with the whole time series) activities, such as sitting on a chair. Based on our results we provide simple and actionable recommendations for the design and implementation of large epidemiological studies that could collect accelerometry data for the purpose of predicting the time series of activities and connecting it to health outcomes.
Structural basis of antigenic specificity and design of new vaccines (1992)

This manuscript describes the design of new vaccines based on synthetic peptides. To this end, we first analyze the structural basis of antigenic reactivity and specificity and the various types of epitopes that form the mosaics of macromolecular antigens, as well as the regulatory mechanisms involved in immune recognition. A distinction is made between sequential or continuous epitopes, and discontinuous or conformational ones, which are the majority of epitopes in globular proteins. In this context it is of particular interest to identify epitopes reacting with B cells and T cells, respectively, or with cytotoxic T cells, in association with the major histocompatibility cell-surface antigens, and the role of these interactions in protective immunity. Identification of such epitopes in proteins of viral, bacterial, or parasitic organisms led to the synthesis of peptides, which when used in conjunction with appropriate carriers and/or adjuvants induced neutralizing antibodies. Particular examples are described, including: bacterial epitopes and mainly those of toxins of diphtheria, cholera, and shigella, leading not only to neutralizing antibodies but also to protective immunity against the deleterious effects of the respective toxins; parasite epitopes, such as those leading to anti-malaria vaccine, based on either the sporozoite or the merozoite stage antigens; viral epitopes leading to protective immunity, with special emphasis on influenza virus where induction of CTL is crucial; and finally, synthetic peptide vaccines against HIV, which should lead to broad specificity protective immunity while avoiding the risks of a vaccine based on the infectious agent. The rapid recent progress in this field, as described in this review, increases the prospect of constructing successful synthetic peptide vaccines in the not too distant future.
Targeting diphtheria toxin to growth factor receptors (1995)

Biochemical, genetic and X-ray crystallographic analysis of diphtheria toxin have demonstrated that the native toxin is composed of three structural domains that function in an ordered fashion to intoxicate a eukoryotic cell. With the knowledge that, if delivered to the cytosol, a single molecule of the catalytic domain is lethal for the cell, we have used recombinant DNA methods to genetically replace the native toxin receptor binding domain with a series of growth factors. The resulting diphtheria toxin-related cytokine fusion proteins, or fusion toxins bind to their respective receptors, are internalized by receptor-mediated endocytosis, and efficiently eliminate target cell populations by the adenosine diphosphate ribosylation of elongation factor 2. Based upon the results of preclinical studies, DAB486IL-2, DAB389IL-2 and DAB389EGF have, or are in the process of being evaluated in Phase I/II clinical trials. To date, administration of the diphtheria toxin-based fusion proteins targeted toward the high affinity IL-2 receptor have been found to be safe, well tolerated, and capable of inducing remission in refractory hematologic malignancies.
Immunosuppression with mammalian target of rapamycin inhibitor and incidence of post-transplant cancer in kidney transplant recipients (2016)

De novo mTOR inhibition was associated with a substantially and significantly reduced risk of basal cell carcinoma of the skin after kidney transplantation. A significant reduction of the incidence of other cancers was not found.
Differences in sensitivity to vasoconstrictor drugs within the wall of the sheep carotid artery (1972)

1. Controlled heat damage was used to separate the responses of the outer innervated smooth muscle from those of the inner nerve-free smooth muscle of the sheep carotid artery.2. Preparations of smooth muscle from the inner part of the media gave 50% maximal contractions in response to approximately 1/15 the concentration of noradrenaline needed to produce similar responses from outer smooth muscle. The difference in sensitivity was greater in the lower than the upper parts of the dose-response curves.3. Much of the difference in sensitivity was still seen in the presence of Desipramine and after chronic denervation, and so could not be attributed to uptake of noradrenaline by the nerve fibres in the outer smooth muscle; disappearance of the fibres after denervation was confirmed by fluorescence microscopy.4. Similar but generally smaller differences in sensitivity between inner and outer smooth muscle were seen with respect to histamine, angiotensin II and 5-hydroxytryptamine.5. Sympathetic denervation 10-14 days previously increased the sensitivity of outer strips to noradrenaline; it usually also increased their sensitivity to histamine, suggesting that the change largely represented non-specific denervation super-sensitivity.6. The high sensitivity of the inner smooth muscle is likely to be of value in enabling it to respond to the relatively low concentration of noradrenaline reaching it in life.
Vaccine protection against Staphylococcus aureus pneumonia (2008)

Staphylococcus aureus pneumonia causes significant mortality in hospitalized or healthy individuals, and recent increases in morbidity are attributed to the rapid spread of methicillin-resistant S. aureus (MRSA) strains, which are often not susceptible to antibiotic therapy. Alpha-hemolysin (Hla), a secreted pore-forming toxin, is an essential virulence factor of MRSA in a mouse model of S. aureus pneumonia. We show that the level of Hla expression by independent S. aureus strains directly correlates with their virulence. Active immunization with a mutant form of Hla (Hla(H35L)), which cannot form pores, generates antigen-specific immunoglobulin G responses and affords protection against staphylococcal pneumonia. Moreover, transfer of Hla-specific antibodies protects naive animals against S. aureus challenge and prevents the injury of human lung epithelial cells during infection. Thus, Hla vaccination or immunotherapy may prevent S. aureus pneumonia in humans.
Phase I Trial of Multiple Large Doses of Murine Monoclonal Antibody CO17-1A. II. Pharmacokinetics and Immune Response1 (1988)

Twenty-five patients with metastatic gastrointestinal adenocarcinoma received one to four infusions of large doses (400 mg) of murine monoclonal antibody CO17-1A (17-1A). The pharmacokinetics of 17-1A at the time of first, second, third, or fourth infusion were not statistically different; plasma half-lives were 15.0 +/- 1.7 hours (n = 5), 15.1 +/- 1.8 (n = 10), 25.3 +/- 6.2 (n = 3), and 14.4 +/- 1.8 (n = 5), respectively. Most patients had an antibody response to 17-1A, with peak levels occurring 15-22 days after infusion. The presence of serum antibody to 17-1A at the time of the second or third infusion did not significantly alter the pharmacokinetics of this large dose of antibody. Four of 25 patients failed to develop an antibody response, but this did not correlate with the amount of 17-1A administered. The administration of four doses of 400 mg over 1 week provided continuously circulating 17-1A for 10 days.
Theory and Practice in Applied Probability (1975)

J. Gani, Theory and Practice in Applied Probability, Advances in Applied Probability, Vol. 7, Supplement: Proceedings of the Conference on Directions for Mathematical Statistics (Sep., 1975), pp. 38-49
Carbon nanotube based electromechanical probes (2007)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2007.
Association of Inflammation-Related and microRNA Gene Expression with Cancer-Specific Mortality of Colon Adenocarcinoma (2009)

IRS and miR-21 expression are independent predictors of colon cancer prognosis and may provide a clinically useful tool to identify high-risk patients.
The Rationale for Banning Human Chorionic Gonadotropin and Estrogen Blockers in Sport (2006)

In men undergoing potential stimulation of endogenous blood testosterone concentrations, blood testosterone concentration is a reasonable surrogate measure for muscle growth and increased strength in men. Because hCG and estrogen blockers produce marked increase in blood testosterone concentration in men, this provides strong evidence to support the banning of hCG and estrogen blockers in men. In women, however, the negligible effect on blood testosterone suggests that drug-induced performance enhancement by hCG or estrogen blockers is highly unlikely. Furthermore, routine urinary hCG testing in young women risks invasion of privacy by detecting unrecognized pregnancy. These considerations suggest that prohibition of hCG and estrogen blockers should be restricted to men in which they are well justified.
Combination therapy with AG-490 and interleukin 12 achieves greater antitumor effects than either agent alone. (2002)

Constitutive activation of Janus kinases (JAKs) and signal transducers and activators of transcription (STAT) occurs at very high frequency in various hematopoietic malignancies and solid tumors. It has been demonstrated that the tyrosine kinase inhibitor, AG-490, selectively blocks JAK activity and completely eliminates leukemia cells in a severe combined immunodeficient (SCID) mouse model. Because many cytokines, including interleukin (IL)-12, have been shown to signal through JAK/STAT pathways, AG-490 may inhibit cytokine-based cancer therapy. In this study, we evaluated the effects of AG-490 on IL-12 functional signaling and IL-12-mediated antitumor response in vivo. Previous studies have established the critical roles of macrophages and IFN-gamma in mediating IL-12-induced antitumor effects. Our results show that in vivo administration of AG-490 causes tumor cell apoptosis but does not inhibit IL-12-mediated macrophage activation and IFN-gamma production by lymphocytes. Furthermore, our data indicate that combined therapy with AG-490 and IL-12-induces greater antitumor effects than either agent alone in a murine myeloma tumor model. These results suggest that JAK/STAT inhibitors deserve further investigation for use with IL-12 therapy in treating human cancers with elevated JAK/STAT activity.
A Suicide Gene Therapy Combining the Improvement of Cyclophosphamide Tumor Cytotoxicity and the Development of an Anti-Tumor Immune Response (2014)

Gene-directed enzyme prodrug therapy (GDEPT) consists in targeted delivery to tumor cells of a suicide gene responsible for in situ conversion of a prodrug into cytotoxic metabolites. One of the major limitations of this strategy in clinical application was the poor prodrug activation capacity of suicide gene. We built a highly efficient suicide gene capable of bioactivating the prodrug cyclophosphamide (CPA) by fusing a CYP2B6 triple mutant with NADPH cytochrome P450 reductase (CYP2B6TM-RED). Expression of this fusion gene via a recombinant lentivirus (LV) vector converted resistant human (A549) and murine (TC1) pulmonary cell lines into CPA-susceptible cell lines. We tested the efficiency of our GDEPT strategy in C57Bl/6 immunocompetent mice, using TC1 cells expressing the HPV-16 E6/E7 oncoproteins. In mice bearing tumors composed only of TC1-CYP2B6TM-RED cells, four CPA injections (140 mg/Kg once a week) completely eradicated the tumors for more than two months. Tumors having only 25% of TC1-CYP2B6TM-RED cells were also completely eradicated by five CPA injections, demonstrating a major in vivo bystander effect. Moreover, surviving mice were rechallenged with parental TC1 cells. The tumors regressed spontaneously 7 days after cell inoculation or grew more slowly than in control naive mice due to a strong immune response mediated by anti-E7CD8(+)T cells. These data suggest that combining the CYPB6TM-RED gene with CPA may hold promise as a highly effective treatment for solid tumors in humans.