gebhart/patrepeval huggingface dataset:
Poly(oxyethylene)−Water Interactions:  A Molecular Dynamics Study (1996)

Molecular dynamics simulations of a poly(oxyethylene) (POE) chain with 15 ethylene oxide (EO) units have been performed in an aqueous solution for 2 ns at 300 K and for 1 ns at 373 K, a cloud point for POE. The conformation and the hydration structure of POE and the structure and the dynamics of water molecules in the vicinity of POE were examined. The conformation of POE was transformed from a collapsed chain in the gas phase to a helix in water which was maintained for 2 ns. After a simulated annealing at 1000 K, POE still showed a preference for a helix. An extended network of POE−water and water−water hydrogen bonds was found throughout inside the helix, stabilizing the helix backbone. The same helical conformation was maintained even at 373 K. The pair distribution functions for water oxygen atoms near POE indicated significantly enhanced water structures in the hydrophilic region of POE, and to a lesser extent in the hydrophobic region, at both 300 and 373 K. Considerably reduced translational movements of water molecules near POE were also observed at both temperatures. All the results obtained from the simulation are in good agreement with experiments. We discuss the solubility and the phase behavior of POE in water, based on the observation from the simulations.
Assessment of epidermal growth factor receptor with 99mTc–ethylenedicysteine–C225 monoclonal antibody (2003)

Epidermal growth factor receptor (EGFR) plays an important role in cell division and cancer progression, as well as angiogenesis and metastasis. Since many tumor cells exhibit the EGFR on their surface, functional imaging of EGFR provides not only a non-invasive, reproducible, quantifiable alternative to biopsies, but it also greatly complements pharmacokinetic studies by correlating clinical responses with biological effects. Moreover, molecular endpoints of anti-EGFR therapy could be assessed effectively. C225 is a chimeric monoclonal antibody that targets the human extracellular EGFR and inhibits the growth of EGFR-expressing tumor cells. Also, it has been demonstrated that C225, in combination with chemotherapeutic drugs or radiotherapy, is effective in eradicating well-established tumors in nude mice. We have developed 99mTc-labeled C225 using ethylenedicysteine (EC) as a chelator. This study aimed at measuring uptake of 99mTc-EC-C225 in EGFR+ tumor-bearing animal models and preliminary feasibility of imaging patients with head and neck carcinomas. In vitro Western blot analysis and cytotoxicity assays were used to examine the integrity of EC-C225. Tissue distribution studies of 99mTc-EC-C225 were evaluated in tumor-bearing rodents at 0.5-4 h. In vivo biodistribution of 99mTc-EC-C225 in tumor-bearing rodents showed increased tumor-to-tissue ratios as a function of time. In vitro and biodistribution studies demonstrated the possibility of using 99mTc-EC-C225 to assess EGFR expression. SPECT images confirmed that the tumors could be visualized with 99mTc-EC-C225 from 0.5 to 4 h in tumor bearing rodents. We conclude that 99mTc-EC-C225 may be useful to assess tumor EGFR expression. This may be useful in the future for selecting patients for treatment with C225.
Evaluation of Replication and Pathogenicity of Avian Influenza A H7 Subtype Viruses in a Mouse Model (2007)

Avian influenza A H7 subtype viruses pose a significant threat to human health because of their ability to transmit directly from domestic poultry to humans and to cause disease and, sometimes, death. Although it is important to develop vaccines against viruses of this subtype, very limited information is available on the immune response and pathogenesis of H7 viruses in animal models such as mice and ferrets. Ten H7 viruses were selected for possible vaccine development on the basis of their phylogenetic relationships and geographical locations. The virulence of the 10 viruses for mice and the immunogenicity of the viruses in mice and ferrets were evaluated to study the extent of antigenic relatedness and the level of cross-reactivity of antibodies. Most of the viruses showed similar patterns of cross-reactivity with mouse and ferret antisera. The Eurasian viruses elicited broadly cross-reactive antibodies that neutralized viruses from both Eurasian and North American lineages, but the converse was not true. A subset of the viruses was also evaluated for the ability to replicate and cause disease in BALB/c mice following intranasal administration. H7 subtype viruses were able to infect mice without adaptation and manifested different levels of lethality and kinetics of replication. On the basis of phylogenetic data, induction of broadly cross-neutralizing antibodies in mouse and ferret antisera, and their ability to replicate in mice, we have selected A/Netherlands/219/03 (subtype H7N7) and A/chicken/BC/CN-7/04 (subtype H7N3) viruses for vaccine development. The mouse model can be used for the preclinical evaluation of these vaccines against H7 subtype viruses.
Frontal brain electrical activity (EEG) distinguishes valence and intensity of musical emotions (2001)

Using recent regional brain activation/emotion models as a theoretical framework, we examined whether the pattern of regional EEG activity distinguished emotions induced by musical excerpts which were known to vary in affective valence (i.e., positive vs. negative) and intensity (i.e., intense vs. calm) in a group of undergraduates. We found that the pattern of asymmetrical frontal EEG activity distinguished valence of the musical excerpts. Subjects exhibited greater relative left frontal EEG activity to joy and happy musical excerpts and greater relative right frontal EEG activity to fear and sad musical excerpts. We also found that, although the pattern of frontal EEG asymmetry did not distinguish the intensity of the emotions, the pattern of overall frontal EEG activity did, with the amount of frontal activity decreasing from fear to joy to happy to sad excerpts. These data appear to be the first to distinguish valence and intensity of musical emotions on frontal electrocortical measures.
Stopped-Flow Enzyme Assays on a Chip Using a Microfabricated Mixer (2003)

This paper describes a microfabricated enzyme assay system including a micromixer that can be used to perform stopped-flow reactions. Samples and reagents were transported into the system by electroosmotic flow (EOF). Streams of reagents were merged and passed through the 100-pL micromixer in < 1 s. The objective of the work was to perform kinetically based enzyme assays in the stopped-flow mode using a system of roughly 6 nL volume. Beta-galactosidase (beta-Gal) was chosen as a model enzyme for these studies and was used to convert the substrate fluorescein mono-beta-D-galactopyranoside (FMG) into fluorescein. Results obtained with microfabricated systems using the micromixer compared well to those obtained with an external T mixing device. In contrast, assays performed in a microfabricated device by merging two streams and allowing mixing to occur by lateral diffusion did not compare well. Using the microfabricated mixer, Km and kcat values of 75 +/- 13 microM and 44 +/- 3 s(-1) were determined. These values compare well to those obtained with the conventional stopped-flow apparatus for which Km was determined to be 60 +/- 6 microM and kcat was 47 +/- 4 s(-1). Enzyme inhibition assays with phenylethyl-beta-D-thiogalactoside (PETG) were also comparable. It was concluded that kinetically based, stopped-flow enzyme assays can be performed in 60 s or less with a miniaturized system of roughly 6 nL liquid volume when mixing is assisted with the described device.
The Accurate Measurement Of Small Rotations By Modulating Polarization (1986)

An instrument developed to accurately measure small rotations (twist about an optical axis) uses a Faraday rotator to modulate the polarization of a HeNe laser beam. Twist sensors located in the beam path consist of a calcite polarizer (analyzer), a silicon detector and associated electronics. The sensors measure relative changes of the sensor analyzer and the null position of the modulated source beam. Reference measurements of the laser intensity and beam modulation are made to avoid accurately characterizing the modulation amplitude. This instrument has a sensitivity of 0.2 microradians at 5 Hz bandwidths over a 17.5 milliradians measuring range. This is accomplished by controlling the beam wander, reducing the laser divergence, and utilizing synchronous detection.
Biomarkers for Hepatocellular Carcinoma (2017)

Hepatocellular carcinoma (HCC) is the third leading cause of cancer deaths worldwide. The HCC diagnosis is usually achieved by biomarkers, which can also help in prognosis prediction. Furthermore, it might represent certain therapeutic interventions through some combinations of biomarkers. Here, we review on our current understanding of HCC biomarkers.
Prevention and reduction of scarring in the skin by Transforming Growth Factor beta 3 (TGFβ3): from laboratory discovery to clinical pharmaceutical (2008)

Scarring in the skin after trauma, surgery, burn or sports injury is a major medical problem, often resulting in adverse aesthetics, loss of function, restriction of tissue movement and/or growth and adverse psychological effects. Current treatments are empirical and unpredictable, and there are no prescription drugs for the prevention or treatment of dermal scarring. We have investigated the cellular and molecular differences between scar-free healing in embryonic wounds and scar-forming healing in adult wounds. We have identified Transforming Growth Factor beta 3 (TGFbeta3) as a key regulator of the scar-free phenotype in embryonic healing. Exogenous addition of TGFbeta3 to cutaneous wounds in pre-clinical (adult) in vivo models reduces early extracellular matrix deposition and these molecules are deposited with a markedly improved architecture in the neodermis, resembling that of normal skin. This improvement of structural organisation in the healing wound is self-propagating and leads to a reduction of subsequent scarring. TGFbeta3 has completed safety studies and entered human clinical trials. Data from these studies have demonstrated that TGFbeta3 (Juvista) in humans is safe and well tolerated. Acute, local administration of TGFbeta3 (Juvista) significantly reduces dermal scarring in a dose responsive manner resulting in the regeneration of a skin structure that is permanently improved.
Nanoparticles as structural and functional units in surface-confined architectures. (2001)

The nanoscale engineering of functional chemical assemblies has attracted recent research effort to provide dense information storage, miniaturized sensors, efficient energy conversion, light-harvesting, and mechanical motion. Functional nanoparticles exhibiting unique photonic, electronic and catalytic properties provide invaluable building blocks for such nanoengineered architectures. Metal nanoparticle arrays crosslinked by molecular receptor units on electrodes act as selective sensing interfaces with controlled porosity and tunable sensitivity. Photosensitizer/electron-acceptor bridged arrays of Au-nanoparticles on conductive supports act as photoelectrochemically active electrodes. Semiconductor nanoparticle composites on surfaces act as efficient light collecting systems, and nanoengineered semiconductor 'core-shell' nanocrystal assemblies reveal enhanced photoelectrochemical performance due to effective charge separation. Layered metal and semiconductor nanoparticle arrays crosslinked by nucleic acids find applications in the optical, electronic and photoelectrochemical detection of DNA. Metal and semiconductor nanoparticles assembled on DNA templates may be used to generate complex electronic circuitry. Nanoparticles incorporated in hydrogel matrices yield new composite materials with novel magnetic, optical and electronic properties.
Improved methods for hiding latency in high bandwidth networks (extended abstract) (1996)

Article Improved methods for hiding latency in high bandwidth networks (extended abstract) Share on Authors: Matthew Andrews Department of Mathematics and Laboratory for Computer Science, MIT Department of Mathematics and Laboratory for Computer Science, MITView Profile , Tom Leighton Department of Mathematics and Laboratory for Computer Science, MIT Department of Mathematics and Laboratory for Computer Science, MITView Profile , P. Takis Metaxas Department of Computer Science, Wellesley College Department of Computer Science, Wellesley CollegeView Profile , Lisa Zhang Department of Mathematics and Laboratory for Computer Science, MIT Department of Mathematics and Laboratory for Computer Science, MITView Profile Authors Info & Claims SPAA '96: Proceedings of the eighth annual ACM symposium on Parallel Algorithms and ArchitecturesJune 1996 Pages 52–61https://doi.org/10.1145/237502.237507Online:24 June 1996Publication History 6citation193DownloadsMetricsTotal Citations6Total Downloads193Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Pulmonary Edema Develops after Recurrent Obstructive Apneas (1999)

There are anecdotal reports of pulmonary edema after a night of recurrent obstructive apneas (OAs) in humans, but no data on lung water, gas exchange, filling pressure, or cardiac output (Q) exist in these patients. By clamping the endotracheal tube of eight intubated, anesthesized dogs, we created repetitive OAs of 45-s duration at 30-s intervals, for 8 h. Five additional dogs without apneas, but identically instrumented, were studied simultaneously, serving as nonapneic controls. Sa (O(2)) was measured by intraarterial catheter, pulmonary capillary wedge pressure (Pcw), continuous cardiac output (Q), and mixed venous oxygen saturation (Sv(O(2))) were measured by flotation catheter. Basal and hourly hemodynamics and blood gases (arterial and venous) under steady state respiration were measured. Venous admixture (Q S/Q T) was calculated by standard equations. Pa(O(2)) from the beginning to the end of the experiment fell from 89.6 to 82.8 mm Hg in apneic animals and from 92.2 to 85.5 mm Hg in controls. The Q S/Q T increased in both groups but more so in the apnea group (3.3 to 19.4%) than in nonapneic controls (3.1 to 7.9%). Neither Q nor Pcw changed significantly in either group. Lung wet/dry weight was 5.40 +/- 0.93 in apneic animals and 5.00 +/- 0.67 in controls. Light microscopy showed gross alveolar fluid in three apneic dogs, and electron microscopy showed interstitial fluid in two additional apneic dogs. One of the lung edema dogs expired of acute heart failure in the seventh hour of the experiment. Worsening of gas exchange and histology suggest that lung edema can result from recurrent OAs.
Passive immunization to prevent mother-infant transmission of human immunodeficiency virus (1991)

A definitive conclusion regarding the potential for the presence of neutralizing antibody to epitopes of the V3 loop to attenuate or prevent vertical transmission of HIV infection cannot be made based on the results of these four studies. However, the studies provide an intriguing suggestion that it may be possible to identify an epitope or array of epitopes from the V3 loop of judiciously selected HIV isolates that could induce protective immunity against HIV. Future collaborative studies are needed to standardize and independently validate the various assays. A recent conference, Early Diagnosis of HIV Infection in Infants, sponsored by the National Institute of Child Health and Human Development, the National Institute of Allergy and Infectious Diseases and the Centers for Disease Control, provided a forum to facilitate exchange of information among researchers in this field, and encourage future collaborative efforts. If one or more subpopulations of anti-gp120/V3 loop or other neutralizing antibodies are indeed associated with a decreased risk of maternal-infant transmission, it becomes important to determine whether these antibodies are protective per se or are merely surrogate markers of a different mechanism. The former conclusion seems to be supported by the finding of HIV-specific antibodies in seropositive persons' saliva and breast milk, both of which have relatively low infectivity, although the potential neutralizing activities of these antibodies have not been adequately evaluated. The development and testing of a highly specific (monoclonal antibody-derived) passive immunotherapy will probably be required to answer this question.(ABSTRACT TRUNCATED AT 250 WORDS)
Smooth skinning decomposition with rigid bones (2012)

This paper introduces the Smooth Skinning Decomposition with Rigid Bones (SSDR), an automated algorithm to extract the linear blend skinning (LBS) from a set of example poses. The SSDR model can effectively approximate the skin deformation of nearly articulated models as well as highly deformable models by a low number of rigid bones and a sparse, convex bone-vertex weight map. Formulated as a constrained optimization problem where the least squared error of the reconstructed vertices by LBS is minimized, the SSDR model can be solved by a block coordinate descent-based algorithm to iteratively update the weight map and the bone transformations. By employing the sparseness and convex constraints on the weight map, the SSDR model can be used for traditional skinning decomposition tasks such as animation compression and hardware-accelerated rendering. Moreover, by imposing the orthogonal constraints on the bone rotation matrices (rigid bones), the SSDR model can also be applied in motion editing, skeleton extraction, and collision detection tasks. Through qualitative and quantitative evaluations, we show the SSDR model can measurably outperform the state-of-the-art skinning decomposition schemes in terms of accuracy and applicability.
Rothmund - Thomson Syndrome (2003)

Rothmund-Thomson syndrome is a rare geno-photodermatosis of children. Poikilodermatous cutaneous changes, growth retardation, juvenile cataract and high incidence of malignancy are its classical features. A Thomson type of Rothmund-Thomson syndrome with characteristic poikiloderma congenitale, growth retardation, absence of juvenile cataract and parental non-consanguinity is described in an 8 year old Indian girl.
Animal Models For The Study Of Drugs In Ischemic Stroke (1989)

Heme oxygenases (HO) catabolize free heme, that is, iron (Fe) protoporphyrin (IX), into equimolar amounts of Fe2+, carbon monoxide (CO), and biliverdin. The stress-responsive HO-1 isoenzyme affords protection against programmed cell death. The mechanism ...Read More
Enhancing subbasalt reflections using parabolic τ-p transformation (2003)

Potential hydrocarbon-bearing sediment structures in the Faroe-Shetland Basin are often overlain by basaltic sequences of stacked flows up to several kilometers thick. With conventional seismic acquisition and processing methods, it is difficult to image the internal (intrabasalt) and underlying (subbasalt) structures. Scattering from the highly reflective top of the basalt and short-period multiples from intrabasalt boundaries may completely mask reflections from the base of the basalt and below. High attenuation of seismic energy in the basaltic sequence due to its complex internal structure generally causes a weak subbasalt signal. Long-period multiples, such as those generated between the sea bottom and the top-basalt boundary, may obscure subbasalt reflections and energy reflected from the basement.
Integrin-linked kinase (ILK) and its interactors (2001)

How intracellular cytoskeletal and signaling proteins connect and communicate with the extracellular matrix (ECM) is a fundamental question in cell biology. Recent biochemical, cell biological, and genetic studies have revealed important roles of cytoplasmic integrin-linked kinase (ILK) and its interactive proteins in these processes. Cell adhesion to ECM is an important process that controls cell shape change, migration, proliferation, survival, and differentiation. Upon adhesion to ECM, integrins and a selective group of cytoskeletal and signaling proteins are recruited to cell matrix contact sites where they link the actin cytoskeleton to the ECM and mediate signal transduction between the intracellular and extracellular compartments. In this review, we discuss the molecular activities and cellular functions of ILK, a protein that is emerging as a key component of the cell-ECM adhesion structures.
Impact of pre-transplant disease burden on the outcome of allogeneic hematopoietic stem cell transplant in refractory and relapsed acute myeloid leukemia: a single-center study (2014)

Patients with refractory or relapsed acute myeloid leukemia (AML) receiving allogeneic hematopoietic stem cell transplant (HSCT) were retrospectively assessed to evaluate the effect of disease burden on outcomes and to identify predictive variables. Of all patients, 53 achieved a complete morphological remission (CR-AML) before transplant, while 48 failed to do so (NR-AML). In the CR-AML group, 32 patients displayed minimal residual disease (MRDpos). Estimated 5-year overall survival (5-OS) and disease-free survival of all patients was 37% and 29%, respectively. The 5-OS was significantly different between patients with CR-AML and NR-AML (46% vs. 18%). However, pre-transplant MRD status did not affect 5-OS (51% in MRDneg vs. 41% in MRDpos). Using multivariate analysis, we identified patient's physical condition and risk stratification as additional prognostic factors. Our findings suggest that NR status influences the outcomes of HSCT while pre-transplant MRD does not. HSCT needs to be optimized accordingly to treat high risk AML.
Hybrid silicon evanescent laser fabricated with a silicon waveguide and III-V offset quantum wells (2005)

A novel laser that utilizes a silicon waveguide bonded to AlGaInAs quantum wells is demonstrated. This wafer scale fabrication approach allows the optical waveguide to be defined by CMOS-compatible silicon processing while optical gain is provided by III-V materials. The AlGaInAs quantum well structure is bonded to the silicon wafer using low temperature oxygen plasma-assisted wafer bonding. The optically pumped 1538 nm laser has a pulsed threshold of 30 mW and an output power of 1.4 mW.