gebhart/patrepeval huggingface dataset:
Identification of Heregulin, a Specific Activator of p185 erbB2 (1992)

The proto-oncogene designated erbB2 or HER2 encodes a 185-kilodalton transmembrane tyrosine kinase (p185erbB2), whose overexpression has been correlated with a poor prognosis in several human malignancies. A 45-kilodalton protein heregulin-alpha (HRG-alpha) that specifically induced phosphorylation of p185erbB2 was purified from the conditioned medium of a human breast tumor cell line. Several complementary DNA clones encoding related HRGs were identified, all of which are similar to proteins in the epidermal growth factor family. Scatchard analysis of the binding of recombinant HRG to a breast tumor cell line expressing p185erbB2 showed a single high affinity binding site [dissociation constant (Kd) = 105 +/- 15 picomolar]. Heregulin transcripts were identified in several normal tissues and cancer cell lines. The HRGs may represent the natural ligands for p185erbB2.
Expression of vascular endothelial growth factor and its receptors in human renal ontogenesis and in adult kidney (1995)

Vascular endothelial growth factor (VEGF) may modulate vascular permeability, chemotaxis for monocytes, and protease activity. In addition, VEGF may play a role in embryonic and tumor angiogenesis. In fetal mouse kidney, VEGF mRNA and protein expression have been demonstrated. This finding led to the hypothesis that VEGF might be involved in renal growth and development. To further elucidate the role of VEGF in human kidney, expression of VEGF and its receptors, the specific tyrosine kinase receptors, fit-1 and KDR, were studied. In fetal (6-24 gestational wk; mesonephros and metanephros) and adult kidney, VEGF mRNA and protein could be colocalized in glomerular epithelia and collecting duct cells by in situ hybridization and immunohistology. By reverse transcription-polymerase chain reaction, mRNA of three VEGF isoforms, VEGF121, VEGF165, and VEGF189, were found in fetal kidney and cortex, isolated glomeruli, and medulla of adult human kidney. KDR and flt-1 mRNA were coexpressed in endothelia of glomeruli and in peritubular capillaries in fetal and adult kidney. These data support the assumption that VEGF and its receptors may influence renal ontogenesis. We speculate that the constitutive expression of VEGF in adult kidney may be required for the function of VEGF receptor positive-fenestrated endothelia in glomeruli and postglomerular vessels. The expression of VEGF in collecting duct and of its receptors in medullary capillaries may in addition be relevant for maintaining medullary osmolality.
Mechanically Durable and Highly Stretchable Transistors Employing Carbon Nanotube Semiconductor and Electrodes (2015)

Mechanically durable stretchable trans-istors are fabricated using carbon nanotube electrical components and tough thermoplastic elastomers. After an initial conditioning step, the electrical characteristics remain constant with strain. The strain-dependent characteristics are similar in orthogonal stretching directions. Devices can be impacted with a hammer and punctured with a needle while remaining functional and stretchable.
Optimization of Multilayer Optical Films with a Memetic Algorithm and Mixed Integer Programming (2017)

Multilayer optical films have been extensively used in optical technology, but the design of multilayer structures for broadband applications is often challenging due to the need to incorporate material dispersion. Here, we present an implementation of a memetic algorithm based on mixed integer programming, which is especially suited for practical broadband optimization of layered thin-film materials. In our implementation, the optimization variables consist of a list of discrete variables that represents different dielectric materials, along with a list of continuous variables that represents the thicknesses of each material. As a set of concrete demonstrations, we optimize the spectra of a radiative cooling device and an incandescent light bulb filter. The resulting structures from the optimization can, by using more materials, achieve better performance than their counterparts in the literature while using fewer numbers of material layers.
The Principles of Nonlinear Optics (1984)

Introduction. Nonlinear Optical Susceptibilities. General Description of Wave Propagation in Nonlinear Media. Electrooptical and Magnetooptical Effects. Optical Rectification and Optical Field-Induced Magnetization. Sum-Frequency Generation. Harmonic Generation. Difference Frequency Generation. Parametric Amplification and Oscillation. Stimulated Raman Scattering. Stimulated Light Scattering. Two-Photon Absorption. High-Resolution Nonlinear Optical Spectroscopy. Four-Wave Mixing. Four-Wave Mixing Spectroscopy. Optical-Field-Induced Birefringence. Self-Focusing. Multiphoton Spectroscopy. Detection of Rare Atoms and Molecules. Laser Manipulation of Particles. Transient Coherent Optical Effects. Strong Interaction of Light with Atoms. Infrared Multiphoton Excitation and Dissociation of Molecules. Laser Isotope Separation. Surface Nonlinear Optics. Nonlinear Optics in Optical Waveguides. Optical Breakdown. Nonlinear Optical Effects in Plasmas. Index.
Job Level Risk Assessment Using Task Level ACGIH Hand Activity Level TLV Scores: A Pilot Study (2005)

Existing upper extremity musculoskeletal disorder analytical tools are primarily intended for single or mono-task jobs. However, many jobs contain more than 1 task and some include job rotation. This case/control study investigates methods of modifying an existing tool, the American Conference of Governmental Industrial Hygienists (ACGIH) Hand Activity Level (HAL) Threshold Limit Value (TLV), to assess the upper extremity risk of multi-task jobs. Various methods of combining the task differences and ratios into a job level assessment were explored. Two methods returned significant odds ratios, (p < .05) of 18.0 (95% CI 1.8-172) and 12.0 (95% CI 1.2-120). These results indicate that a modified ACGIH HAL TLV may provide insight into the work-related risk of multi-task jobs. Further research is needed to optimize this process.
Turbo codes with non-uniform constellations (2002)

This paper presents parallel concatenated turbo codes that employ a non-uniform constellation to achieve shaping gain. The output signal approximates the Gaussian distribution by using equally likely signals with unequal spacing (a non-uniform constellation). The small distance of points near the center of the constellation may lead to a small overall free distance and thus a high error floor for turbo codes. We avoid this situation by a two-step design procedure, that first creates an interleaver, and then identifies the constituent encoders that maximize the turbo code free distance. Simulation results for 4 bits/sec/Hz show that this use of shaping can offer an improvement of approximately 0.2 dB for turbo codes.
CD1 stimulation of human T cell lines induces a rapid increase in the intracellular free Ca2+ concentration and the production of IL-2. (1990)

The effect of a battery of CD1 mAb on intracellular free Ca2+ concentration and IL-2 production has been examined on different T cell lines in this study. Both 0249F and NU-T2 two CD1b specific mAb tested, induced a rapid increase in the intracellular Ca2+ concentration on HPBALL T cells whereas only one (L161) among three different CD1c mAb (L161, 10C3, and M241) produced a similar effect. In contrast the addition of four different CD1a mAb directed against two different epitopic groups of this molecule were uneffective in modifying the intracellular Ca2+. Both L161 and 0249F also induced a comparable increase in the intracellular Ca2+ concentration on MOLT 4 and JURKAT, two other T cell lines of similar phenotype. The effect of L161 mAb on the IL-2 production of the IL-2 producing T cell line JURKAT was also examined. The association of the latter with PMA strongly induced the production of IL-2 on this cell model while either L161 or PMA alone had no effect. Although the natural ligand and the function of CD1 molecules are still unknown, the accumulation of these data strongly suggest that CD1b and CD1c might represent two activatory pathways for immature T cells operating before the classical CD2 and CD3 activation pathways.
Oxidative Stress Induced by Pure and Iron-Doped Amorphous Silica Nanoparticles in Subtoxic Conditions (2012)

Amorphous silica nanoparticles (SiO₂-NPs) have found broad applications in industry and are currently intensively studied for potential uses in medical and biomedical fields. Several studies have reported cytotoxic and inflammatory responses induced by SiO₂-NPs in different cell types. The present study was designed to examine the association of oxidative stress markers with SiO₂-NP induced cytotoxicity in human endothelial cells. We used pure monodisperse amorphous silica nanoparticles of two sizes (16 and 60 nm; S16 and S60) and a positive control, iron-doped nanosilica (16 nm; SFe), to study the generation of hydroxyl radicals (HO·) in cellular-free conditions and oxidative stress in cellular systems. We investigated whether SiO₂-NPs could influence intracellular reduced glutathione (GSH) and oxidized glutathione (GSSG) levels, increase lipid peroxidation (malondialdehyde (MDA) and 4-hydroxyalkenal (HAE) concentrations), and up-regulate heme oxygenase-1 (HO-1) mRNA expression in the studied cells. None of the particles, except SFe, produced ROS in cell-free systems. We found significant modifications for all parameters in cells treated with SFe nanoparticles. At cytotoxic doses of S16 (40-50 μg/mL), we detected weak alterations of intracellular glutathione (4 h) and a marked induction of HO-1 mRNA (6 h). Cytotoxic doses of S60 elicited similar responses. Preincubation of cells being exposed to SiO₂-NPs with an antioxidant (5 mM N-acetylcysteine, NAC) significantly reduced the cytotoxic activity of S16 and SFe (when exposed up to 25 and 50 μg/mL, respectively) but did not protect cells treated with S60. Preincubation with NAC significantly reduced HO-1 mRNA expression in cells treated with SFe but did not have any effect on HO-1 mRNA level in cell exposed to S16 and S60. Our study demonstrates that the chemical composition of the silica nanoparticles is a dominant factor in inducing oxidative stress.
Iron overload in Beta thalassaemia major and intermedia patients. (2013)

There is an urgent need to rationalize the chelation therapy and to create awareness about the consequences of iron overload in the patients. The study showed high levels of serum ferritin beta thalassaemia major patients which give an overall bleak view.
Novel Bacillus thuringiensis Binary Insecticidal Crystal Proteins Active on Western Corn Rootworm, Diabrotica virgifera virgifera LeConte (2002)

A new family of insecticidal crystal proteins was discovered by screening sporulated Bacillus thuringiensis cultures for oral activity against western corn rootworm (WCR) larvae. B. thuringiensis isolates PS80JJ1, PS149B1, and PS167H2 have WCR insecticidal activity attributable to parasporal inclusion bodies containing proteins with molecular masses of ca. 14 and 44 kDa. The genes encoding these polypeptides reside in apparent operons, and the 14-kDa protein open reading frame (ORF) precedes the 44-kDa protein ORF. Mutagenesis of either gene in the apparent operons dramatically reduced insecticidal activity of the corresponding recombinant B. thuringiensis strain. Bioassays performed with separately expressed, biochemically purified 14- and 44-kDa polypeptides also demonstrated that both proteins are required for WCR mortality. Sequence comparisons with other known B. thuringiensis insecticidal proteins failed to reveal homology with previously described Cry, Cyt, or Vip proteins. However, there is evidence that the 44-kDa polypeptide and the 41.9- and 51.4-kDa binary dipteran insecticidal proteins from Bacillus sphaericus are evolutionarily related. The 14- and 44-kDa polypeptides from isolates PS80JJ1, PS149B1, and PS167H2 have been designated Cry34Aa1, Cry34Ab1, and Cry34Ac1, respectively, and the 44-kDa polypeptides from these isolates have been designated Cry35Aa1, Cry35Ab1, and Cry35Ac1, respectively.
Johannes von Kries and the History of Water Hammer (2006)

Water hammer in pipe systems encompasses a range of phenomena familiar to engineers, including 1 the propagation of disturbances created by valve operations, turbomachinery regulation, and accidents, through waves traveling at the speed of sound because of the compressibility of the liquid and the elasticity of the pipe walls; 2 the reflection of these waves off pipe-end boundaries and internal features, such as changes in cross section or branches, leading to characteristic frequencies or periods of oscillation; 3 large pressure changes arising from fluid velocity changes, especially in liquids, because of their high density and low compressibility; and 4 associated unsteady flow phenomena, such as column separation and gas release at low pressures or inertial mass oscillations associated with free surfaces. The propagation and reflection of pressure waves are of interest in many other fields, such as in acoustics, hemodynamics, and solid mechanics, but the need to calculate the high pressure rises and pipe-wall stresses characteristic of relatively rigid pipes carrying liquids is the focus of water hammer in hydraulic engineering. Only in hemodynamics is there a similar interest in pressures and tube wall stresses, even though they tend to be lower in flexible systems. Historically, therefore, the development of what is now widely called the Joukowsky equation defines the origins of a water-hammer theory that is appropriate for engineering practice. This paper reviews the history of the Joukowsky equation and the forgotten contributions by Johannes von Kries. The waterhammer community is ignorant of the work of Kries: for example, the extensive reviews by Wood 1970 , Thorley 1976 , and Ghidaoui et al. 2005 do not mention them; and the reviews by Boulanger 1913 , Lambossy 1950 , and Stecki and Davis 1986 briefly refer to Kries’s 1892 book only. In the hemodynamics community, Kries found some recognition Frank 1927; Evans 1962; Bernstein and Evans 1962; Kenner 1972; Sperling et al. 1975 . Researchers of water hammer highlighted in historical papers include the following: Joukowsky, portrayed by Golubev 1947 , Strizhevsky 1957 , and Stepanov 1997 ; Gariel and waterhammer research before 1914 , reviewed by Remenieras 1961 ; Menabrea, translated by Anderson 1976 ; Michaud, commemorated by Almeida 1979 ; and Allievi, commemorated by Franke 1992 and Ceccarelli 1999 . Skalak 1999 wrote an “in memoriam” on his father, Hager 2001 celebrated Schnyder and Jaeger, and Wiggert and Wylie 2003 paid a tribute to Streeter. This paper on Johannes von Kries is a further contribution to archiving
Electrically Programmable Surfaces for Configurable Patterning of Cells (2008)

A microfluidic device surface coated with block copolymer and extracellular matrix (ECM) protein layers (see Figure) shows electrical programmability for cell immobilization. The surface has demonstrated the ability to pattern C2C12 murine myoblasts cells with their morphology and surface density adjustable by varying the applied electrode bias.
Decreased expression of the gut‐enriched Krüppel‐like factor gene in intestinal adenomas of multiple intestinal neoplasia mice and in colonic adenomas of familial adenomatous polyposis patients (2000)

Gut-enriched Krüppel-like factor (GKLF) is a zinc finger-containing transcription factor, the expression of which is associated with growth arrest. We compared Gklf expression in intestinal and colonic adenomas to normal mucosa in multiple intestinal neoplasia (Min) mice and familial adenomatous polyposis (FAP) patients, respectively, using semi-quantitative RT-PCR. In Min mice, the level of Gklf transcript is highest in normal-appearing intestinal tissues and decreases as the size of the adenoma increases. In FAP patients, the level of GKLF transcript is lower in adenomas compared to paired normal-appearing mucosa from the same patient or normal colonic mucosa from control individuals without FAP. The possibility of DNA methylation as a cause for the decreased expression of Gklf in adenomas of Min mice was investigated by methylation-specific PCR. Results indicate that the Gklf gene is not methylated in either normal or tumorous tissues. The findings of our study are therefore consistent with the potential role of GKLF as a negative growth regulator of gut epithelial cells.
Pyridine nucleotide metabolites stimulate calcium release from sea urchin egg microsomes desensitized to inositol trisphosphate. (1987)

Inositol trisphosphate (IP3) was previously shown to release Ca2+ from a nonmitochondrial store in sea urchin eggs. In this study, egg homogenates and purified microsomes were monitored with either fura 2 or Ca2+-sensitive minielectrodes to determine whether other stimuli would induce Ca2+ release. Pyridine nucleotides (whose concentrations are known to change at fertilization) were found to release nearly as much Ca2+ as did IP3. Average releases/ml of homogenate were: 0.6 microM IP3, 10.9 nmol of Ca2+; 50 microM NADP, 7.3 nmol of Ca2+; and 100 microM NAD, 6.5 nmol of Ca2+ (n = 6). Specificity was demonstrated by screening a series of other phosphorylated metabolites, and none was found to reproducibly release Ca2+. Calcium release induced by IP3 or NADP was immediate, whereas a lag of 1-4 min occurred with NAD. This lag before NAD-induced Ca2+ release led to the discovery that a soluble egg factor (Mr greater than 100,000) converts NAD into a highly active metabolite that releases Ca2+ without a lag. The NAD metabolite (E-NAD) was purified to homogeneity by high pressure liquid chromatography and produced half-maximal Ca2+ release at about 40 nM. Injection of E-NAD into intact eggs produced both an increase in intracellular Ca2+ (as assayed with indo-1) and a cortical reaction. Following Ca2+ release by each of the active agents (IP3, NAD, and NADP), the homogenates resequestered the released Ca2+ but were desensitized to further addition of the same agent. A series of desensitization experiments showed that homogenates desensitized to any two of these agents still responded to the third, indicating the presence of three independent Ca2+ release mechanisms. This is further supported by experiments using Percoll density gradient centrifugation in which NADP-sensitive microsomes were partially separated from those sensitive to IP3 and NAD.
Correlation between in vitro and in vivo activity of antimicrobial agents against gram-negative bacilli in a murine infection model (1991)

We studied the relationship between in vitro susceptibility tests (MICs, MBCs) and in vivo activity of tobramycin, pefloxacin, ceftazidime, and imipenem against 15 gram-negative bacilli from five different species in a murine thigh infection model. Complete dose-response curves were determined for each antimicrobial agent against each strain, and three parameters of in vivo activity were defined: maximal attainable antimicrobial effect (i.e., reduction in log10 CFU per thigh compared with untreated controls) at 24 h (Emax), total dose required to reach 50% of maximal effect (P50), and total dose required to achieve a bacteriostatic effect (static dose). Pefloxacin demonstrated the greatest Emax (P less than 0.05). Tobramycin was the most potent antimicrobial agent, as indicated by its having the lowest static dose/MIC ratio (P less than 0.002). Log10 P50s and static doses correlated significantly with log10 MICs or MBCs for the 15 strains of each antibiotic (P less than 0.01) except imipenem (P greater than 0.50). The greater potency of imipenem against the three Pseudomonas aeruginosa strains than against strains of the family Enterobacteriaceae (P less than 0.01) explained this lack of correlation. A longer duration of postantibiotic effect for imipenem against P. aeruginosa (P = 0.02) contributed to its increased potency against these strains. We conclude that in vitro susceptibility tests correlated well with in vivo activity in this animal model and that variations in potency among the four antimicrobial agents could be explained by differences in pharmacokinetics or pharmacodynamic activity.
Global code motion/global value numbering (1995)

We believe that optimizing compilers should treat the machine-independent optimizations (e.g., conditional constant propagation, global value numbering) and code motion issues separately.’ Removing the code motion requirements from the machine-independent optimization allows stronger optimizations using simpler algorithms. Preserving a legal schedule is one of the prime sources of complexity in algorithms like PRE [18, 13] or global congruence finding [2, 20].
A Psycholinguistic Look at the Informal Reading Inventory Part II: Inappropriate Inferences from an Informal Reading Inventory (1979)

In this article we propose to discuss in more detail the kinds of inferences that may be inappropriately drawn from an informal reading inventory. This discussion should strengthen the rationale for our approach to analyzing a reader's miscues (errors) and determining what kinds of instructional approaches might be appropriate for that reader (see the preceding issue of Reading Horizons).
Synergistic effects of metformin, resveratrol, and hydroxymethylbutyrate on insulin sensitivity (2013)

Resveratrol-HMB combined with metformin may act synergistically on AMP-activated protein kinase-dependent pathways, leading to increased insulin sensitivity, which may reduce the therapeutic doses of metformin necessary in the treatment of diabetes.
The Early Region 4 orf4 Protein of Human Adenovirus Type 5 Induces p53-Independent Cell Death by Apoptosis (1998)

Previous studies by our group showed that infection of human and rodent cells by human adenovirus type 5 (Ad5) results in the induction of p53-independent apoptosis and cell death that are dependent upon transactivation of early region 4 (E4). To identify which E4 products are involved, studies were conducted with p53-deficient human SAOS-2 cells infected with various Ad5 E4 mutants. An E4orf6-deficient mutant was defective in cell killing, whereas another that expressed only E4orf6 and E4orf4 killed like wild-type virus, suggesting that E4orf6 may be responsible for cytotoxicity; however, a mutant expressing only E4orf4 induced high levels of cell death, indicating that this E4 product may also be able to induce cytotoxicity. To define the E4 cell death-inducing functions more precisely, cDNAs encoding individual E4 products were introduced into cells by DNA transfection in the absence of other Ad5 proteins. In cotransfections with a cDNA encoding firefly luciferase, enzymatic activity was high in all cases except with E4orf4, where luciferase levels were less than 20% of those in controls. In addition, drug selection of several cell types following transfection with retroviral vector DNA encoding individual E4 products as well as puromycin resistance yielded a large number of cell colonies except when E4orf4 was expressed. These data demonstrated that E4orf4 is the only E4 product capable of independent cell killing. Cell death induced by E4orf4 was due to apoptosis, as evidenced by 4',6-diamidino-2-phenylindole (DAPI) staining of cell nuclei in E4orf4-expressing cells. Thus, although E4orf6 may play some role, these results suggested that E4orf4 may be the major E4 product responsible for induction of p53-independent apoptosis.