gebhart/patrepeval huggingface dataset:
PEG-Like Nanoprobes: Multimodal, Pharmacokinetically and Optically Tunable Nanomaterials (2014)

"PEG-like Nanoprobes" (PN's) are pharmacokinetically and optically tunable nanomaterials whose disposition in biological systems can be determined by fluorescence or radioactivity. PN's feature a unique design where a single PEG polymer surrounds a short fluorochrome and radiometal bearing peptide, and endows the resulting nanoprobe with pharmacokinetic control (based on molecular weight of the PEG selected) and optical tunability (based on the fluorochrome selected), while the chelate provides a radiolabeling option. PN's were used to image brain capillary angiography (intravital 2-photon microscopy), tumor capillary permeability (intravital fluorescent microscopy), and the tumor enhanced permeability and retention (EPR) effect (111In-PN and SPECT). Clinical applications of PN's include use as long blood half-life fluorochromes for intraoperative angiography, for measurements of capillary permeability in breast cancer lesions, and to image EPR by SPECT, for stratifying patient candidates for long-circulating nanomedicines that may utilize the EPR mechanism.
EXPRESSION OF CYTOKINE mRNAS IN THE DRAINING LYMPH NODES FOLLOWING CONTACT SENSITIVITY IN MICE (1997)

To clarify in vivo cytokine profiles during the afferent phase of contact sensitivity, balb/C mice were sensitized by topical applications of 2.5% 1-chloro-2,4- dinitrobenzene (DNCB) and 3% 4-ethyoxymethylene-2-phenyloxazol-5-one (OXAZ), respectively. On day 6 of contact sensitization, total RNA was extracted from the draining lymph nodes. Expressions of Th1 and Th2 cellrelated cytokine mRNAs were detected by semiquantitative reverse transcription polymerase chain reaction (RT-PCR). Among the 8 cytokine mRNAs observed in naive mice, the mRNAs for IL-2, IL-4, IL-10, IL-12p35, IL-12p40, and IFNwere constitutively expressed weakly, whereas IL-5 and IL-13 mRNAs were undetectable. Contact sensitization with DNCB or OXAZ significantly up-regulated the expressions for Th1 cell-related cytokine mRNAs such as IL-2, IL12p35, IL-12p40, and IFN-, in particular IL-2 and IFN- genes. Moreover, in Th1 cytokine cases, the Th2 cytokines including IL-4, IL-5, IL-10, and IL-13 mRNAs were significantly induced or augmented in the draining lymph nodes. Among the 4 Th2 cytokine mRNAs, both contact allergens showed a much greater inducing effect on IL-4 mRNA than the other cytokines. Furthermore, OXAZ, a stronger sensitizer than DNCB, was confirmed to be much stronger than DNCB in inducing expressions of cytokine mRNAs. The study indicates that contact allergens may induce mixed expressions of both Th1 and Th2 cytokine mRNAs, not just Th1 cytokine mRNAs, in the draining lymph nodes at least at 6 days following contact sensitivity.
Performance of Lempel-Ziv compressors with deferred innovation (1989)

The noiseless data-compression algorithms introduced by Lempel and Ziv (LZ) parse an input data string into successive substrings each consisting of two parts: The citation, which is the longest prefix that has appeared earlier in the input, and the innovation, which is the symbol immediately following the citation. In extremal versions of the LZ algorithm the citation may have begun anywhere in the input; in incremental versions it must have begun at a previous parse position. Originally the citation and the innovation were encoded, either individually or jointly, into an output word to be transmitted or stored. Subsequently, it was speculated that the cost of this encoding may be excessively high because the innovation contributes roughly 1g(A) bits, where A is the size of the input alphabet, regardless of the compressibility of the source. To remedy this excess, it was suggested to store the parsed substring as usual, but encoding for output only the citation, leaving the innovation to be encoded as the first symbol of the next substring. Being thus included in the next substring, the innovation can participate in whatever compression that substring enjoys. This strategy is called deferred innovation. It is exemplified in the algorithm described by Welch and implemented in the C program compress that has widely displaced adaptive Huffman coding (compact) as a UNIX system utility. The excessive expansion is explained, an implicit warning is given against using the deferred innovation compressors on nearly incompressible data.
C1q Knock-Out Mice for the Study of Complement Deficiency in Autoimmune Disease (1998)

In humans, homozygous deficiency of the first component of the classical pathway of complement, C1q, is a powerful disease susceptibility factor for the development of systemic lupus erythematosus (SLE). This strong association indicates that a functional activity of C1q protects from the development of SLE. Studies in vitro have shown that C1q can bind apoptotic keratinocytes suggesting that it may have an important role in the clearance of apoptotic cells. C1q-deficient mice, generated by gene targeting, showed an increased mortality and 25% of the mice had histological evidence of glomerulonephritis characterised by multiple apoptotic cell bodies and immune deposits, assessed by immunofluorescence and electron microscopy. These observations are compatible with the hypothesis that C1q deficiency causes autoimmunity by an impaired clearance of apoptotic cells.
Effects of cholesterol on sodium-potassium ATPase ATP hydrolyzing activity in bovine kidney (1988)

The (Na+,K+)-ATPase ATP hydrolyzing activity from rabbit kidney medulla basolateral membrane vesicles was studied as a function of the cholesterol content of the basolateral membranes. The cholesterol content of the membranes was modified by incubation with phospholipid vesicles. When the cholesterol content was increased above that found in the native membrane, the (Na+,K+)-ATPase ATP hydrolyzing activity was inhibited. When the cholesterol content was decreased from that found in the native membranes, the (Na+,K+)-ATPase ATP hydrolyzing activity was inhibited. Analogous effects were found with the K+-activated phosphatase activity of the same membrane vesicles. Therefore, at low cholesterol contents, cholesterol was stimulatory, and at high cholesterol contents, cholesterol was inhibitory. The structural specificity of this effect was tested by introducing lanosterol and ergosterol as 50% of the membrane sterol. Ergosterol was the least effective at supporting (Na+,K+)-ATPase ATP hydrolyzing activity, while lanosterol was more effective, but still not as effective as cholesterol.
Epinephrine plasma metabolic clearance rates and physiologic thresholds for metabolic and hemodynamic actions in man. (1980)

To determine the plasma epinephrine thresholds for its metabolic and hemodynamic actions and plasma epinephrine metabolic clearance rates, 60-min intravenous epinephrine infusions at nominal rates of 0.1, 0.5, 1.0, 2.5, and 5.0 microgram/min were performed in each of six normal human subjects. These 30 infusions resulted in steady-state plasma epinephrine concentrations ranging from 24 to 1,020 pg/ml. Plasma epinephrine thresholds were 50-100 pg/ml for increments in heart rate, 75-125 pg/ml for increments in blood glycerol and systolic blood pressure, 150-200 pg/ml for increments in plasma glucose (the resultant of increments in glucose production and decrements in glucose clearance), blood lactate, blood beta-hydroxybutyrate, and diastolic blood pressure, and greater than 400 pg/ml for early decrements in plasma insulin. Changes in blood alanine, plasma glucagon, plasma growth hormone, and plasma cortisol were not detected. At steady-state plasma epinephrine concentrations of 24-74 pg/ml, values overlapping the basal normal range, the mean (+/-SE) plasma metabolic clearance rate of epinephrine was 52 +/- 4 ml x min-1 x kg-1; this value rose to 89 +/- 6 ml x min-1 x kg-1 (P less than 0.01) at steady-state epinephrine concentrations of 90-1,020 pg/ml. We conclude that in human subjects: (a) the plasma epinephrine thresholds for its hemodynamic and metabolic actions lie within the physiologic range, (b) epinephrine and norepinephrine accelerate their own metabolic clearance, and (c) epinephrine is 10 times more potent than norepinephrine.
Interaction of Ascorbate and α-Tocopherol in Resealed Human Erythrocyte Ghosts (1996)

A role for ascorbate-derived electrons in protection against oxidative damage to membrane lipids was investigated in resealed human erythrocyte ghosts. Incubation of resealed ghosts with the membrane-impermeant oxidant ferricyanide doubled the ghost membrane concentration of F2-isoprostanes, a sensitive marker of lipid peroxidation. Incorporation of ascorbate into ghosts during resealing largely prevented F2-isoprostane formation due to extravesicular ferricyanide. This protection was associated with a rapid transmembrane oxidation of intravesicular ascorbate by extravesicular ferricyanide. Transmembrane electron transfer, which was measured indirectly as ascorbate-dependent ferricyanide reduction, correlated with the content of alpha-tocopherol in the ghost membrane in several respects. First, ascorbate resealed within ghosts protected against ferricyanide-induced oxidation of endogenous alpha-tocopherol in the ghost membrane. Second, when exogenous alpha-tocopherol was incorporated into the ghost membrane during the resealing step, subsequent ferricyanide reduction was enhanced. Last, incubation of intact erythrocytes with soybean phospholipid liposomes, followed by resealed ghost preparation, caused a proportional decrease in both the membrane content of alpha-tocopherol and in ferricyanide reduction. Incorporation of exogenous alpha-tocopherol during resealing of ghosts prepared from liposome-treated cells completely restored the ferricyanide-reducing capacity of the ghosts. These results suggest that the transmembrane transfer of ascorbate-derived electrons in erythrocyte ghosts is dependent in part on alpha-tocopherol and that such transfer may help to protect the erythrocyte membrane against oxidant stress originating outside the cell.
Metabolic Engineering of a Methylmalonyl-CoA Mutase−Epimerase Pathway for Complex Polyketide Biosynthesis in Escherichia coli, (2002)

A barrier to heterologous production of complex polyketides in Escherichia coli is the lack of (2S)-methylmalonyl-CoA, a common extender substrate for the biosynthesis of complex polyketides by modular polyketide synthases. One biosynthetic route to (2S)-methylmalonyl-CoA involves the sequential actions of two enzymes, methylmalonyl-CoA mutase and methylmalonyl-CoA epimerase, which convert succinyl-CoA to (2R)- and then to (2S)-methylmalonyl-CoA. As reported [McKie, N., et al. (1990) Biochem. J. 269, 293-298; Haller, T., et al. (2000) Biochemistry 39, 4622-4629], when genes encoding coenzyme B(12)-dependent methylmalonyl-CoA mutases were expressed in E. coli, the inactive apo-enzyme was produced. However, when cells harboring the mutase genes from Propionibacterium shermanii or E. coli were treated with the B12 precursor hydroxocobalamin, active holo-enzyme was isolated, and (2R)-methylmalonyl-CoA represented approximately 10% of the intracellular CoA pool. When the E. coli BAP1 cell line [Pfeifer, B. A., et al. (2001) Science 291, 1790-1792] harboring plasmids that expressed P. shermanii methylmalonyl-CoA mutase, Streptomyces coelicolor methylmalonyl-CoA epimerase, and the polyketide synthase DEBS (6-deoxyerythronolide B synthase) was fed propionate and hydroxocobalamin, the polyketide 6-deoxyerythronolide B (6-dEB) was produced. Isotopic labeling studies using [(13)C]propionate showed that the starter unit for polyketide synthesis was derived exclusively from exogenous propionate, while the extender units stemmed from methylmalonyl-CoA via the mutase-epimerase pathway. Thus, the introduction of an engineered mutase-epimerase pathway in E. coli enabled the uncoupling of carbon sources used to produce starter and extender units of polyketides.
Real-Time Three-Dimensional Ultrasound for Guiding Surgical Tasks (2003)

Real-time 3D US can guide basic surgical tasks more efficiently and accurately than 2D US imaging. Real-time 3D US can also guide more complex surgical tasks which may prove useful for procedures where optical imaging is suboptimal, as in fetal surgery or intracardiac interventions.
The Insulin-Like Growth Factor Axis (2000)

Insulin-like growth factors I and II (IGF-I and -II) and their regulatory proteins are secreted by cells of the cardiovascular system. They are growth promoters for arterial cells and mediators of cardiovascular disease. IGFs are bound to IGF binding proteins (IGFBPs), which modulate IGF ligand-receptor interaction and consequently to IGF action. IGFBPs are in turn posttranslationally modulated by specific proteases. This dynamic balance (IGFs, IGFBPs, and IGFBP proteases) constitutes the IGF axis and ultimately determines the extent of IGF-dependent cellular effects. Dysregulated actions of this axis influence coronary atherosclerosis through effects on vascular smooth muscle cell growth, migration, and extracellular matrix synthesis in the atherosclerotic plaque. IGF-I promotes macrophage chemotaxis, excess LDL cholesterol uptake, and release of proinflammatory cytokines. Endothelial cells also receive the effects of IGFs stimulating their migration and organization forming capillary networks. Neointimal hyperplasia of restenosis after coronary artery injury is also modulated by the IGF axis. IGFs stimulate vascular smooth muscle cell proliferation and migration to form the neointima and upregulate tropoelastin synthesis after disruption of the elastic layer. Understanding IGF axis regulation establishes a scientific basis for strategies directed to limit or reverse plaque growth and vulnerability in atherosclerosis and in the neointimal hyperplasia of restenosis.
Is Arc mRNA Unique: A Search for mRNAs That Localize to the Distal Dendrites of Dentate Gyrus Granule Cells Following Neural Activity (2017)

There have been several attempts to identify which RNAs are localized to dendrites; however, no study has determined which RNAs localize to the dendrites following the induction of synaptic activity. We sought to identify all RNA transcripts that localize to the distal dendrites of dentate gyrus granule cells following unilateral high frequency stimulation of the perforant pathway (pp-HFS) using Sprague Dawley rats. We then utilized laser microdissection (LMD) to very accurately dissect out the distal 2/3rds of the molecular layer (ML), which contains these dendrites, without contamination from the granule cell layer, 2 and 4 h post pp-HFS. Next, we purified and amplified RNA from the ML and performed an unbiased screen for 27,000 RNA transcripts using Affymetrix microarrays. We determined that Activity Regulated Cytoskeletal Protein (Arc/Arg3.1) mRNA, exhibited the greatest fold increase in the ML at both timepoints (2 and 4 h). In total, we identified 31 transcripts that increased their levels within the ML following pp-HFS across the two timepoints. Of particular interest is that one of these identified transcripts was an unprocessed micro-RNA (pri-miR132). Fluorescent <i>in situ</i> hybridization and qRT-PCR were used to confirm some of these candidate transcripts. Our data indicate Arc is a unique activity dependent gene, due to the magnitude that its activity dependent transcript localizes to the dendrites. Our study determined other activity dependent transcripts likely localize to the dendrites following neural activity, but do so with lower efficiency compared to Arc.
Within‐step modulation of leg muscle activity by afferent feedback in human walking (2008)

To maintain smooth and efficient gait the motor system must adjust for changes in the ground on a step-to-step basis. In the present study we investigated the role of sensory feedback as 19 able-bodied human subjects walked over a platform that mimicked an uneven supporting surface. Triceps surae muscle activation was assessed during stance as the platform was set to different inclinations (+/-3 deg, +/-2 deg and 0 deg rotation in a parasagittal plane about the ankle). Normalized triceps surae muscle activity was significantly increased when the platform was inclined (2 deg: 0.153 +/- 0.051; 3 deg: 0.156 +/- 0.053) and significantly decreased when the platform was declined (-3 deg: 0.133 +/- 0.048; -2 deg: 0.132 +/- 0.049) compared with level walking (0.141 +/- 0.048) for the able-bodied subjects. A similar experiment was performed with a subject who lacked proprioception and touch sensation from the neck down. In contrast with healthy subjects, no muscle activation changes were observed in the deafferented subject. Our results demonstrate that the ability to compensate for small irregularities in the ground surface relies on automatic within-step sensory feedback regulation rather than conscious predictive control.
Novel microstructures and technologies applied in chemical analysis techniques (2002)

Novel glass and silicon microstructures and their application in chemical analysis are presented. The micro technologies comprise (deep) dry etching, thin layer growth and anodic bonding. With this combination it is possible to create high resolution electrically isolating silicon dioxide structures with aspect ratio's similar to those possible in silicon. Main applications are chemical separation methods such as high performance liquid chromatography (HPLC) or electrophoresis (HPCE). Beside these channel structures, a capillary connector with very low dead and mixing volume has been designed and fabricated for use in (correlation) electrophoresis, and tested by means of precision of consecutive single injections.
Comparative Subchronic Toxicity Studies of Three Disinfectants (1990)

In separate subchronic toxicity studies, male and female Sprague–Dawley rats received various dosages of chlorine, monochloramine, or chlorine dioxide in their drinking water for 90 consecutive days. None of the disinfectants caused premature death at any of the concentrations used. The highest dose of chlorine tested (250 mg/L) was concluded to be a no observable adverse effect level. At 200 mg/L (the lowest observable adverse effect level), monochloramine produced decreased body and organ weights in both sexes and a small decrease in red blood cell count and serum calcium in males. Chlorine dioxide produced dosage‐related decreases in body and organ weight at concentrations as low as 25 mg/L, but its most significant toxic effect was the induction, at all concentrations, of nasal lesions.
At-speed delay characterization for IC authentication and Trojan Horse detection (2008)

New attacker scenarios involving integrated circuits (ICs) are emerging that pose a tremendous threat to national security. Concerns about overseas fabrication facilities and the protection of deployed ICs have given rise to methods for IC authentication (ensuring that an IC being used in a system has not been altered, replaced, or spoofed) and hardware Trojan Horse (HTH) detection (ensuring that an IC fabricated in a nonsecure facility contains the desired functionality and nothing more), but significant additional work is required to quell these treats. This paper discusses how a technique for precisely measuring the combinational delay of an arbitrarily large number of register-to-register paths internal to the functional portion of the IC can be used to provide the desired authentication and design alteration (including HTH implantation) detection. This low-cost delay measurement technique does not affect the main IC functionality and can be performed at-speed at both test-time and run-time.
Soft Stethoscope for Detecting Asthma Wheeze in Young Children (2013)

Asthma is a chronic disease that is commonly suffered by children. Asthmatic children have a lower quality of life than other children. Physicians and pediatricians recommend that parents record the frequency of attacks and their symptoms to help manage their children's asthma. However, the lack of a convenient device for monitoring the asthmatic condition leads to the difficulties in managing it, especially when it is suffered by young children. This work develops a wheeze detection system for use at home. A small and soft stethoscope was used to collect the respiratory sound. The wheeze detection algorithm was the Adaptive Respiratory Spectrum Correlation Coefficient (RSACC) algorithm, which has the advantages of high sensitivity/specificity and a low computational requirement. Fifty-nine sound files from eight young children (one to seven years old) were collected in the emergency room and analyzed. The results revealed that the system provided 88% sensitivity and 94% specificity in wheeze detection. In conclusion, this small soft stethoscope can be easily used on young children. A noisy environment does not affect the effectiveness of the system in detecting wheeze. Hence, the system can be used at home by parents who wish to evaluate and manage the asthmatic condition of their children.
Aberrations of Suppressor T Cells in Human Graft-versus-Host Disease (1979)

To determine whether imbalances in immunoregulatory T-cell subsets exist in patients with graft-versus-host disease, we analyzed T cells in three patients with acute and in six patients with chronic graft-versus-host disease after bone-marrow transplantation. The normal human peripheral-blood T-cell compartment is composed of 80 per cent TH2-and 20 per cent TH2+ T cells, and defined by reactivity with subset-specific heteroantiserums. Human suppressor cells are TH2+, whereas helper cells are TH2-. Patients with acute and chronic graft-versus-host disease had abnormalities in these populations, and their T cells frequently bore la-like antigens. Patients with acute disease lacked TH2+ cells, and the reappearance of this subset preceded the cessation of disease activity. Chronic disease, in contrast, was more heterogeneous. Suppressor cells were lacking in two patients but increased in the other four. Two of these four patients had TH2+, la+ T cells, suggesting in vivo activation of suppressor cells. Studies showing that these TH2+, la+ cells actively suppressed the in vitro immune response support this hypothesis and suggest that the immunoregulatory cells may profoundly affect the overall immune response.
Energetically consistent invertible elasticity (2012)

We provide a smooth extension of arbitrary isotropic hyperelastic energy density functions to inverted configurations. This extension is designed to improve robustness for elasticity simulations with extremely large deformations and is analogous to the extension given to the first Piola-Kirchoff stress in [ITF04]. We show that our energy-based approach is significantly more robust to large deformations than the first Piola-Kirchoff fix. Furthermore, we show that the robustness and stability of a hyperelastic model can be predicted from a characteristic contour, which we call its primary contour. The extension to inverted configurations is defined via extrapolation from a convex threshold surface that lies in the uninverted portion of the principal stretches space. The extended hyperelastic energy density yields continuous stress and unambiguous stress derivatives in all inverted configurations, unlike in [TSIF05]. We show that our invertible energy-density-based approach outperforms the popular hyperelastic corotated model, and we also show how to use the primary contour methodology to improve the robustness of this model to large deformations.