gebhart/patrepeval huggingface dataset:
Blood-pool and gated-SPECT imaging confirms enhancement of cardiovascular function by 17{beta}-estradiol (E2) following severe and prolonged hypotension even without fluid resuscitation in a rat model (2007)

181 Objectives: Although it is known that E2 administration after major blood loss significantly improves survival, the mechanism responsible for the salutary effects of E2 remains unknown. These studies evaluated E2 treatment (Tx) on cardiovascular parameters in an established rat trauma-hemorrhage model. Methods: Male SD rats (235-285 g) with laparotomy were bled over 45 min to reach maximum bleed out (MBO), then E2 or vehicle cyclodextrin (CD) at 1mg/Kg BW (in 0.4ml/Kg BW) was i.v. injected. Tc-99m-bovine serum albumin (BSA) or Tc-99m-MIBI was i.v. injected (separate groups) before bleeding for blood-pool or gated SPECT imaging, respectively. Imaging was continuous for a maximum of 3 h post-MBO; mean blood pressure (MBP) and heart rate (HR) were monitored. The % injected dose (ID) and %ID/g in heart, brain, liver, and kidney were estimated from the blood-pool imaging (n=16) at 30, 60, 90, 120, and 150 min post-MBO. Left ventricular ejection fraction (EF) was measured from the gated imaging (n=8) at 30 and 60 min post-MBO. Results: The %ID of Tc-99m-BSA after E2 Tx was significantly higher (p .05) between E2 and CD treatments. Liver %ID was higher for E2 Tx (all temporal points), but were not significantly different than CD Tx (p>.05). EF and HR were not significantly different between the two treatments. Conclusions: The significant increase of heart blood volume by E2 Tx, together with no difference in EF and HR, validates that cardiac output was significantly improved by E2. Significantly higher blood volume in kidney shows that renal blood flow was maintained by E2. These data suggest that the liver retained more blood volume after E2 Tx, perhaps by inducing vasodilation for better circulation and consequently O2 delivery. Research Support (if any): DARPA award W911NF-06-1-0219
Architecture of 3D Memory Cell Array on 3D IC (2012)

High density 3D memory cell array using SGT(Surrounding Gate Transistor) on 3D IC is proposed. SGT with 4F2 cell size shows uniform cell characteristics with a low resistive bit-line path on 3D IC. Parasitic bit-line capacitance of the structure can also be much lower compared to conventional 2D memory cell array or SGT cell array on bulk substrate, which is especially good for memory feature size at or below 10 nm cell node. A combination of 3D memory cell and 3D IC seems to be the ideal memory architecture for the low cost-per- bit of high density memories.
Novel Immunomodulatory Proteins Generated via Directed Evolution of Variant IgSF Domains (2020)

Immunoglobulin superfamily member (IgSF) proteins play a significant role in regulating immune responses with surface expression on all immune cell subsets, making the IgSF an attractive family of proteins for therapeutic targeting in human diseases. We have developed a directed evolution platform capable of engineering IgSF domains to increase affinities for cognate ligands and/or introduce binding to non-cognate ligands. Using this scientific platform, ICOSL domains have been derived with enhanced binding to ICOS and with additional high-affinity binding to the non-cognate receptor, CD28. Fc-fusion proteins containing these engineered ICOSL domains significantly attenuate T cell activation <i>in vitro</i> and <i>in vivo</i> and can inhibit development of inflammatory diseases in mouse models. We also present evidence that engineered ICOSL domains can be formatted to selectively provide costimulatory signals to augment T cell responses. Our scientific platform thus provides a system for developing therapeutic protein candidates with selective biological impact for treatments of a wide array of human disorders including cancer and autoimmune/inflammatory diseases.
Phase transition and elasticity of protein-based hydrogels (2001)

Reported are specific materials characterizations of three protein-based polymers comprised of repeating pentapeptide sequences, namely (GVGVP)251, (GVGIP)260 and (GVGVP GVGVP GEGVP GVGVP GVGVP GVGVP)n](GVGVP) where G = glycine, V = valine, P = proline, I = isoleucine, and E = glutamic acid, which had been previously prepared and gamma-irradiation cross-linked into elastic matrices. These polymers exhibit a hydrophobic folding and assembling transition on raising the temperature above a critical temperature, designated by Tt. Their equilibrium swelling ratio, uniaxial tensile and dynamic shear behavior were studied. The effect of the transition on swelling and mechanical properties was demonstrated. Equilibrium swelling ratio below the transition temperature decreased with the increase of gamma-irradiation dose. Above the transition temperature, hysteresis and frequency dependence were found in tensile loading-unloading tests and dynamic shear measurements, respectively. The rubber elasticity theory of random chain networks was applied to the data only below the transition temperature, where they may properly be considered random network hydrogels, to estimate molecular weight between cross-links and the Flory-Huggins interaction parameter.
Micro‐CT with respiratory and cardiac gating (2004)

Cardiopulmonary imaging in rodents using micro-computed tomography (CT) is a challenging task due to both cardiac and pulmonary motion and the limited fluence rate available from micro-focus x-ray tubes of most commercial systems. Successful imaging in the mouse requires recognition of both the spatial and temporal scales and their impact on the required fluence rate. Smaller voxels require an increase in the total number of photons (integrated fluence) used in the reconstructed image for constant signal-to-noise ratio. The faster heart rates require shorter exposures to minimize cardiac motion blur imposing even higher demands on the fluence rate. We describe a system with fixed tube/detector and with a rotating specimen. A large focal spot x-ray tube capable of producing high fluence rates with short exposure times was used. The geometry is optimized to match focal spot blur with detector pitch and the resolution limits imposed by the reproducibility of gating. Thus, it is possible to achieve isotropic spatial resolution of 100 microm with a fluence rate at the detector 250 times that of a conventional cone beam micro-CT system with rotating detector and microfocal x-ray tube. Motion is minimized for any single projection with 10 ms exposures that are synchronized to both cardiac and breathing motion. System performance was validated in vivo by studies of the cardiopulmonary structures in C57BL/6 mice, demonstrating the value of motion integration with a bright x-ray source.
Tumor-Induced CD8+ T-Cell Dysfunction in Lung Cancer Patients (2012)

Lung cancer is the leading cause of cancer deaths worldwide and one of the most common types of cancers. The limited success of chemotherapy and radiotherapy regimes have highlighted the need to develop new therapies like antitumor immunotherapy. CD8+ T-cells represent a major arm of the cell-mediated anti-tumor response and a promising target for developing T-cell-based immunotherapies against lung cancer. Lung tumors, however, have been considered to possess poor immunogenicity; even so, lung tumor-specific CD8+ T-cell clones can be established that possess cytotoxicity against autologous tumor cells. This paper will focus on the alterations induced in CD8+ T-cells by lung cancer. Although memory CD8+ T-cells infiltrate lung tumors, in both tumor-infiltrating lymphocytes (TILs) and malignant pleural effusions, these cells are dysfunctional and the effector subset is reduced. We propose that chronic presence of lung tumors induces dysfunctions in CD8+ T-cells and sensitizes them to activation-induced cell death, which may be associated with the poor clinical responses observed in immunotherapeutic trials. Getting a deeper knowledge of the evasion mechanisms lung cancer induce in CD8+ T-cells should lead to further understanding of lung cancer biology, overcome tumor evasion mechanisms, and design improved immunotherapeutic treatments for lung cancer.
MT-III, a brain-specific member of the metallothionein gene family. (1992)

A third member of the metallothionein (MT) gene family, designated MT-III, was cloned by virtue of its homology to a human protein that was shown previously to inhibit neuronal survival in culture and to be deficient in the brains of people with Alzheimer disease. Human and mouse MT-IIIs have two insertions relative to all other known mammalian MTs: a threonine after the fourth amino acid and a block of six amino acids near the carboxyl terminus. The genes encoding MT-III resemble all other mammalian MT genes in their small size and exon/intron organization. The MT-III genes are closely linked to the other functional MT genes on human chromosome 16 and mouse chromosome 8. Mouse MT-III gene expression appears to be restricted to brain; in addition, it fails to respond to zinc, cadmium, dexamethasone, or bacterial endotoxin in vivo, thereby distinguishing MT-III from other known MTs.
Soft, Skin‐Interfaced Microfluidic Systems with Passive Galvanic Stopwatches for Precise Chronometric Sampling of Sweat (2019)

Comprehensive analysis of sweat chemistry provides noninvasive health monitoring capabilities that complement established biophysical measurements such as heart rate, blood oxygenation, and body temperature. Recent developments in skin-integrated soft microfluidic systems address many challenges associated with standard technologies in sweat collection and analysis. However, recording of time-dependent variations in sweat composition requires bulky electronic systems and power sources, thereby constraining form factor, cost, and modes of use. Here, presented are unconventional design concepts, materials, and device operation principles that address this challenge. Flexible galvanic cells embedded within skin-interfaced microfluidics with passive valves serve as sweat-activated "stopwatches" that record temporal information associated with collection of discrete microliter volumes of sweat. The result allows for precise measurements of dynamic sweat composition fluctuations using in situ or ex situ analytical techniques. Integrated electronics based on near-field communication (NFC) protocols or docking stations equipped with standard electronic measurement tools provide means for extracting digital timing results from the stopwatches. Human subject studies of time-stamped sweat samples by in situ colorimetric methods and ex situ techniques based on inductively coupled plasma mass spectroscopy (ICP-MS) and chlorodimetry illustrate the ability to quantitatively capture time-dynamic sweat chemistry in scenarios compatible with field use.
Effects of Growth Hormone on Abnormal Visceral Adipose Tissue Accumulation and Dyslipidemia in HIV-Infected Patients (2004)

These results suggest that r-hGH dosed at 4 mg daily for 12 weeks decreases VAT and cholesterol concentrations in HIV-infected patients with excess VAT. The optimal regimen to sustain these effects awaits determination.
All plasma products are not created equal (2015)

The differences in cellular, microparticle, and functional hemostatic parameters measured between plasma products have the potential to affect efficacy and safety. Further study is needed to elucidate the potential immune effects of the cellular and microparticle differences noted as well as the clinical implications of altered thrombin generation kinetics in SD products.
An approximate string matching algorithm for content-based music data retrieval (2003)

An approach for content based music data retrieval is proposed. In this approach, thematic feature strings, such as melody strings, rhythm strings, and chord strings are extracted from the original music objects and treated as the meta data to represent their contents. The problem of content based music data retrieval is then transformed into the string matching problem. A new approximate string matching algorithm is also proposed which provides fault tolerance ability according to the music characteristics. To show the efficiency of the algorithm, a set of experiments are performed to compare with the agrep and the fgrep utility on both synthetic and real music data.
Oxygenation of human tumors: the Mainz experience. (1998)

Tumor oxygenation is dependent on the cellular O2 consumption rate and on the O2 supply to the respiring cells. The latter is mainly determined by the convective transport via the blood and by the diffusional flux from the microvessels to the O2 consuming sites. Peculiarities of tumor tissue oxygenation can therefore mainly be attributed to characteristic structural and functional abnormalities of the tumor microcirculation (perfusion-limited O2 delivery), to a deterioration of the diffusion geometry (diffusion-limited O2 delivery), and--in some cases--to a reduced O2-carrying capacity of the blood due to tumor-associated anemia. As a result of a compromised and anisotropic microcirculation, the O2 availability to the cancer cells shows great variability, and many human malignancies reveal hypoxic tissue areas which are heterogeneously distributed within the tumor mass and which may be located next to well-perfused tumor areas (intra-tumor heterogeneity). As a rule, in most solid malignancies the tissue O2 status is poorer than in normal tissue at the site of tumor growth. Hypoxia in human tumors per se has been shown to contribute to resistance to standard radiotherapy, chemotherapy and photodynamic therapy with photosensitizing hematoporphyrins. In addition to conferring a direct resistance, hypoxia-induced inhibition of proliferation may also contribute to resistance since both modalities are primarily effective against rapidly dividing cells. Hypoxia in solid tumors, however, has further implications in the clinical setting: Recent data provide strong evidence suggesting that O2 deprived tumor cells are predisposed to a more malignant phenotype, i.e., tumor cells are more likely to be more metastatic and/or invasive. In addition, clonal heterogeneity is more pronounced in hypoxic tumors.
The fate of autogenous grafts to the spinal dura (1978)

✓ An experimental study was designed to compare the efficacy of autogenous fat and Gelfoam in minimizing scar tissue attachment to the dura and nerve roots. A multiple level lumbar laminectomy was performed in 20 dogs, and Gelfoam and autogenous fat were placed in the epidural space at two laminectomy sites, over the dura, interposed between the overlying paraspinal muscles and the dura. A third lumbar laminectomy site in each dog served as a control. The animals were sacrificed after different time periods (3, 6, 12, 18, and 24 weeks), and the specimens were examined histologically and histochemically. The colloidal iron-periodic acid Schiff-Bismarck brown-picric acid (CI-PAS-BB-PA) and high iron diamine-Alcian blue 8Gx (HID-AB) techniques were used to demonstrate connective tissues and glycosaminoglycans. The scar at the laminectomy sites where Gelfoam was placed and at the control sites was composed of dense irregular connective tissue. Examination of the laminectomy sites where autogenous fat was used revealed less scar tissue. In addition, there was a layer of fat with a slight increase in intercellular connective tissue fibers interposed between the overlying erector spinae musculature and the dura. Our results indicate that autogenous fat interposed between the dura and the overlying paraspinal musculature serves as a barrier limiting the growth of connective tissue into the spinal canal. We could find no evidence that Gelfoam prevented the ingrowth of scar tissue into the operated area.
Effects of Hydrophobicity on the Antifungal Activity of α‐Helical Antimicrobial Peptides (2008)

We utilized a series of analogs of D-V13K (a 26-residue amphipathic alpha-helical antimicrobial peptide, denoted D1) to compare and contrast the role of hydrophobicity on antifungal and antibacterial activity to the results obtained previously with Pseudomonas aeruginosa strains. Antifungal activity for zygomycota fungi decreased with increasing hydrophobicity (D-V13K/A12L/A20L/A23L, denoted D4, the most hydrophobic analog was sixfold less active than D1, the least hydrophobic analog). In contrast, antifungal activity for ascomycota fungi increased with increasing hydrophobicity (D4, the most hydrophobic analog was fivefold more active than D1). Hemolytic activity is dramatically affected by increasing hydrophobicity with peptide D4 being 286-fold more hemolytic than peptide D1. The therapeutic index for peptide D1 is 1569-fold and 62-fold better for zygomycota fungi and ascomycota fungi, respectively, compared with peptide D4. To reduce the hemolytic activity of peptide D4 and improve/maintain the antifungal activity of D4, we substituted another lysine residue in the center of the non-polar face (V16K) to generate D5 (D-V13K/V16K/A12L/A20L/A23L). This analog D5 decreased hemolytic activity by 13-fold, enhanced antifungal activity to zygomycota fungi by 16-fold and improved the therapeutic index by 201-fold compared with D4 and represents a unique approach to control specificity while maintaining high hydrophobicity in the two hydrophobic segments on the non-polar face of D5.
Prolonged Allograft Survival in Cynomolgus Monkeys Treated with a Monoclonal Antibody to the Human Type I Interferon Receptor and Low Doses of Cyclosporine (1998)

A monoclonal antibody (mAb) directed against the extracellular domain of the IFNAR1 chain of the human interferon-alpha (IFN-alpha) receptor (IFN-alphaR), which inhibits activation of the Jak-Stat signal transduction pathway, administered together with a subeffective dose of cyclosporine induced prolonged survival of skin allografts in major histocompatibility complex (MHC) divergent cynomolgus monkeys. Skin biopsies from animals treated with anti-IFN-alphaR mAb and cyclosporine revealed very low levels of MHC class I and class II antigen expression and the absence of histologic signs of rejection. Monkey antibodies (IgG) to the mouse antihuman IFN-alphaR mAb were not detected in the serum of any of the animals treated with the anti-IFN-alphaR mAb either alone or together with cyclosporine. The anti-IFN-alphaR mAb abrogated activation of the Jak-Stat signal transduction pathway in IFN-treated cells. These results, which show that selective and long-lasting immunosuppression can be obtained by short-term administration of an IFN-alpha antagonist together with a subeffective dose of cyclosporine, may have important implications for the therapy of human allograft rejection.
Near-infrared spectroscopy use in patients with head injury (1995)

A multimodality recording system was used in 14 ventilated patients with closed head injury to assess the potential use of near-infrared spectroscopy (NIRS) in the neurointensive care unit. Signals of intracranial pressure, cerebral perfusion pressure, peripheral oxygen saturation, jugular venous saturation, and NIRS-derived changes in the chromophores of oxy- and deoxyhemoglobin were digitized and recorded. After a review of 886 hours of continuous monitoring, 376 hours were considered free from artifact and were entered for final analysis. In nine of the patients 38 events were recorded that demonstrated clear changes in cerebral perfusion pressure accompanied by hemodynamic changes in middle cerebral artery flow velocity (transcranial Doppler) and cortical perfusion (laser Doppler flowmetry). Near-infrared spectroscopy showed correlated changes in 37 events (97%) whereas jugular venous saturation monitoring registered only 20 (53%). There was associated peripheral oxygen desaturation in eight cases (21%), intracranial hypertension in 10 (26%), and cerebral hyperemia in eight (21%). The remaining 12 events (32%) appeared to be complex changes of uncertain origin. Iatrogenic factors were identified as causative in 14 cases (37%). The potential application of NIRS in adults and the importance of using multiple parameter recording systems in the interpretation of cerebral events are discussed.
MR fingerprinting for rapid quantification of myocardial T1, T2, and proton spin density (2016)

MRF can provide quantitative single slice T<sub>1</sub> , T<sub>2</sub> , and M<sub>0</sub> maps in the heart within a single breath-hold. Magn Reson Med 77:1446-1458, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Condensation of Ordered Nanocrystal Thin Films (1998)

45 \AA{} diameter dodecanethiol capped gold nanocrystals self-organize during solvent evaporation on a carbon substrate, with the final thickness of the nanocrystal film depending on solvent polarity. A quantitative model for the film thickness is presented, showing the film structure (thickness) to depend on the balance of van der Waals attraction between the particles themselves and between the particles and the substrate. This attraction influences the film thickness while permitting nanocrystal self-organization into hexagonal close-packed structures. Model predictions and measured film thicknesses agree well.
Arsenic Exposure Perturbs the Gut Microbiome and Its Metabolic Profile in Mice: An Integrated Metagenomics and Metabolomics Analysis (2014)

Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.
Cellular Internalization of Poly(ethylene oxide)-b-poly(ε-caprolactone) Diblock Copolymer Micelles (2002)

Poly(ethylene oxide)-b-poly(epsilon-caprolactone) (PEO-b-PCL) block copolymers self-assemble into micelles in aqueous solution. We have examined whether these micelles can internalize into P19 cells in vitro. Fluorescently labeled PEO(45)-b-PCL(23) block copolymer was prepared by conjugating a tetramethylrhodamine molecule to the end of the hydrophobic PCL block. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) studies yielded 24 +/- 2 and 25 +/- 2 nm, respectively, for the diameters of the micelles. The studies also showed that chemical labeling did not effect the morphology or size. When the rhodamine-labeled PEO(45)-b-PCL(23) block copolymer micelles were tested in vitro, time-, concentration-, and pH-dependence of the internalization process suggested that internalization proceeded by endocytosis. The results from these studies provide the first direct evidence for the internalization of PEO(45)-b-PCL(23) micelles. Future studies will utilize multiple labeling of these micelles, allowing questions to be addressed related to the fate of internalized micelles as drug carriers, the destination of the incorporated drugs or fluorescent probes released from micelles, and the identification of the subcellular localization of the whole drug-carrier system within cells, both in vitro and in vivo.