gebhart/patrepeval huggingface dataset:
The inositol phosphate pathway as a mediator in the proliferative response of rat calvarial bone cells to cyclical biaxial mechanical strain (1992)

Isolated newborn rat calvarial bone cells grown in monolayer on polyurethane membranes in specially constructed culture chambers and subjected to a cyclical biaxial mechanical strain of 0.17% at a frequency of 1 Hz for 30 min demonstrated a 16% increase in DNA synthesis during the subsequent 24 h. The metabolites of the inositol phosphate pathway, shown to be an important second messenger in many cell types, were shown to be elevated using high-performance liquid chromatography to separate and quantitate the various inositol polyphosphates. Inositol 1,4,5-trisphosphate, inositol 1,4-bisphosphate, and inositol 1,3,4,5-tetrakisphosphate reached peak accumulations after 20 s of mechanical strain. Inositol 1,3,4-trisphosphate reached a peak accumulation after 2 min, and inositol 1,2,3,4,5,6 phosphate reached a peak accumulation after 60 min of mechanical strain. Neomycin, an inhibitor of phospholipase C, a membrane-bound enzyme that hydrolyzes phosphatidyl inositol 4,5-bisphosphate to start the inositol phosphate cascade, completely inhibited accumulation of the above inositol phosphates during mechanical straining of the bone cells. Neomycin also completely abolished the increase in DNA synthesis that was seen after a mechanical strain of 0.17%. It is concluded from this study that the inositol phosphate pathway is activated by mechanical strain in bone cells and that this pathway is an important and primary mediator in the transduction of mechanical strain into cellular proliferation in these cells.
Practice randomization and clinical research. The Indiana experience. (1991)

Thoughtful preparation of a research laboratory is an early step in designing a program for scientific investigation. The Division of General Internal Medicine at Indiana University has maintained a "laboratory" for outpatient clinical investigation for more than 15 years. In this report, we describe the structure and function of the General Medicine Practice in the Regenstrief Health Center on the campus of the Indiana University School of Medicine in Indianapolis. Specifically, we discuss the ongoing random allocation of subjects, the local resources for data management and tracking of patients' use of clinical services, and how combining this information system into a randomized primary care system has fostered successful ventures in clinical investigation.
Fiber scrambling for precise radial velocities at Lick and Keck Observatories (2012)

The detection of Earth analogs with radial velocity requires extreme Doppler precision and long term stability. Variations in the illumination of the slit and of the spectrograph optics occur on time scales of seconds and minutes, primarily because of guiding, seeing and focusing. These variations yield differences in the instrumental profile (IP). In order to stabilize the IP, we designed a fiber feed for the Hamilton spectrograph at Lick and for HIRES at Keck. Here, we report all results obtained with these fiber scramblers. We also present the design of a new double scrambler/pupil slicer for HIRES at Keck.
Collagen shield drug delivery: Therapeutic concentrations of tobramycin in the rabbit cornea and aqueous humor (1988)

Collagen shields made of porcine collagen were placed in a solution containing tobramycin sulfate (40 or 200 mg/ml) for five minutes, then applied to rabbit eyes. One, four, or eight hours after application, the corneas, aqueous humor samples, and shields were assayed for antibiotic. At all intervals, the concentration of antibiotic in the corneas and aqueous humor samples exceeded the mean inhibitory concentration for tobramycin, as determined for most strains of Pseudomonas. Shields immersed in 200 mg/ml tobramycin produced significantly higher concentrations of antibiotic in the cornea at one hour than subconjunctival injections of tobramycin (20 mg) (P = .0001). Shields immersed in 40 mg/ml tobramycin produced higher, although not significantly higher, concentrations of antibiotic in the cornea at one hour than subconjunctival injections of tobramycin (20 mg) (P = .318). Shields immersed in commercially available tobramycin drops or injectable tobramycin solution (40 mg/ml) caused no epithelial damage visible by slitlamp examination. Collagen shields containing antibiotics can serve as a vehicle for drug delivery and may prove superior to current methods for preoperative and postoperative antibiotic prophylaxis and the initial treatment of bacterial keratitis.
Temporal-spatial distribution of SP-B and SP-C proteins and mRNAs in developing respiratory epithelium of human lung. (1994)

We determined the temporal and spatial distribution of surfactant protein B (pro-SP-B) and C (pro-SP-C) mRNAs and proteins by immunohistochemistry and in situ hybridization in fetal, neonatal, and adult human lung. Pro-SP-B and SP-B mRNA were detected in bronchi and bronchioles by 15 weeks' gestation. After 25 weeks, pro-SP-B, active SP-B peptide, and SP-B mRNA were co-localized in bronchiolo-alveolar portal cells and in Type II epithelial cells. In adult lung, pro-SP-B and SP-B mRNA were detected primarily in non-ciliated bronchiolar epithelial cells and in Type II cells in the alveolus. Pro-SP-C and SP-C mRNA were detected in cells lining terminal airways from 15 weeks' gestation and thereafter. After 25 weeks, SP-C mRNA and precursor protein were detected in epithelial cells of the bronchiolo-alveolar portals and in Type II cells, where expression increased with advancing gestational age. Distinct cellular patterns of staining for pro-SP-B compared with SP-B active peptide support the concept that its proteolytic processing or cellular routing may be influenced by cell type and/or cell differentiation. SP-B and SP-C are expressed primarily in distal conducting and terminal airway epithelium of human fetal lung well in advance of surfactant lipid synthesis or physiologic requirements to produce pulmonary surfactant at the time of birth.
Alcohol Stabilization of Low Water Content Pyrolysis Oil during High Temperature Treatment (2017)

The addition of alcohols is a promising method to pretreat and stabilize pyrolysis oil by converting carboxylic acids and reactive carbonyl compounds into esters, ethers, and acetals. In this study a series of alcohols—methanol, ethanol, 1-propanol, 2-propanol, or 1-octanol—was added to crude pyrolysis oil, and these mixtures were stored at 200 °C for different periods from 6 to 50 h to investigate the impact of heat treatment on the oils’ physicochemical properties. All oil/alcohol mixtures were characterized by Karl Fisher titration, viscometer/rheometer, differential scanning calorimetry (DSC), gel permeation chromatography (GPC), Fourier transform infrared (FTIR) spectroscopy, and gas chromatography–mass (GC-MS) spectrometry. Phase separation is observed for all aged oil/alcohol mixtures. The time-dependent rheologies of heat treated oil/1-propanol, oil/2-propanol, and oil/1-octanol mixtures are found to be well fitted by the Herschel–Bulkley model. Isothermal DSC traces directly confirm that low molecular mass (LMM) alcohols (methanol, ethanol, 1-propanol, and 2-propanol) improve the stability of pyrolysis oil. Although 1-octanol is less efficient in slowing the aging reactions, it significantly reduces the increase rate of viscosity and molecular weight of pyrolysis oil compared with LMM alcohols. FTIR spectra suggest reactive carbonyl and aldehyde groups are captured by the added monofunctional alcohols. GC-MS results indicate esterifications contribute significantly to mitigate aging reactions. The introduction of LMM alcohols or a combination of LMM alcohols and HMM alcohols is a promising pretreatment method before the further catalytic upgrading procedure on the crude pyrolysis oil.
Tight linkage of ginA and a putative regulatory gene in<i>Rhizobium leguminosarum</i> (1987)

Rhizobium leguminosarum, biovar viceae, strain RCC1001 contains two glutamine synthetase activities, GSI and GSII. We report here the identification of glnA, the structural gene for GSI. A 2 kb fragment of DNA was shown to complement the Gln- phenotype of Klebsiella pneumoniae glnA mutant strains. DNA sequence analysis revealed an open reading frame (ORF) of 469 codons specifying a polypeptide of 52,040 daltons. Its deduced amino acid sequence was found to be highly homologous to other glutamine synthetase sequences. This ORF was expressed in Escherichia coli minicells and the corresponding polypeptide reacted with an antiserum raised against GSI. Upstream of glnA we found an ORF of 111 codons (ORF111) preceded by the consensus sequence for an ntrA-dependent promoter. Minicells experiments showed a protein band, with a molecular weight in good agreement with that (10,469) deduced from the nucleotide sequence. On the basis of homology studies we discuss the possibility that the product of ORF111 is equivalent to the PII protein of E. coli and plays a similar role in regulation of nitrogen metabolism.
Strategy of propeller design (1971)

Strategy of propeller design , Strategy of propeller design , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Oncogenic Ras Sensitizes Normal Human Cells to Tumor Necrosis Factor-α-Related Apoptosis-Inducing Ligand-Induced Apoptosis (2004)

Tumor necrosis factor-alpha-related apoptosis-inducing ligand (TRAIL) is a cytotoxic cytokine that induces apoptosis in tumor cells but rarely kills normal ones. To determine how normal human cells acquire TRAIL-sensitive phenotype during the process of malignant transformation, we used an experimental system that allows for controlled conversion of human cells from normal to cancerous by introduction of several genes. Human embryonic kidney cells and foreskin fibroblasts were first immortalized by combination of the early region of simian virus 40 and telomerase and then were transformed with oncogenic Ras. Both normal and immortalized cells were resistant to TRAIL-induced apoptosis, whereas Ras-transformed cells were susceptible. Ras transformation enhanced TRAIL-induced activation of caspase 8 by increasing its recruitment to TRAIL receptors. The proapoptotic effects of Ras could be reversed by mutations in its effector loop or by inhibitors of either farnesyl transferase or mitogen-activated protein kinase kinase. The expression of constitutively activated mitogen-activated protein kinase kinase 1 enhanced caspase 8 recruitment and sensitized immortalized human embryonic kidney cells to TRAIL-induced death. These results indicate that in normal human cells the TRAIL-induced apoptotic signal is blocked at the level of caspase 8 recruitment and that this block can be eliminated by Ras transformation, involving activation of the mitogen-activated protein kinase pathway.
Codebook-Based Lattice-Reduction-Aided Precoding for Limited-Feedback Coded MIMO Systems (2011)

Lattice-reduction-aided precoding (LRP) provides near-capacity rates with the use of low-complexity linear receivers for coded multiple-input multiple-output (MIMO) systems. However, a large amount of feedback in the feedback for an integer or binary precoding matrix has been a bottleneck in its implementation. In this paper, we propose a codebook-based LRP scheme for limited-feedback coded MIMO systems. The proposed LRP scheme follows the fundamentals of the previous LRP scheme that employed multilevel binary coset coding so that the precoding matrix is binary. In the proposed LRP scheme, the conventional precoding matrix obtained from the Lenstra-Lenstra-Lovasz algorithm is modified to specific forms that are predefined in a codebook set. The new precoding matrix is selected such that the lower bound on the capacity is maximized for a given codebook set, while the codebook set is designed offline such that the upper bound of the average capacity loss induced by the limitation on the codebook size is minimized. The simulation results show that the proposed LRP scheme nearly achieves the achievable rate of the conventional LRP scheme with a greatly reduced amount of feedback.
Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification (1997)

We describe the simultaneous localization of DNA sequences in cell and chromosome preparations by means of differently fluorochrome-labeled (AMCA, FITC, TRITC) tyramides using the catalyzed reporter deposition (CARD) procedure. For this purpose, repeated as well as single-copy DNA probes were labeled with biotin, digoxigenin, and FITC, hybridized, and visualized with three different cytochemical detection systems based on horseradish peroxidase conjugates. These were sequentially applied to interphase nuclei and metaphase chromosomes at low concentrations to prevent crossreaction and nonspecific background. In situ localized peroxidase activity was visualized by the deposition of fluorochrome-labeled tyramide molecules. To allow specific deposition of a second and a third tyramide conjugate for multiple-target fluorescence in situ hybridization (FISH), remaining peroxidase activity was always completely inactivated by a mild acid treatment before application of the next peroxidase conjugate. The CARD reactions were optimized for maximal signal-to-noise ratio and discrete localization by tuning reaction time, H2O2, and tyramide concentrations. For both repeated and single-copy DNA targets, high FISH signal intensities were obtained, providing improvement of sensitivity over conventional indirect detection systems. In addition, the fluorescence CARD detection system proved to be highly efficient and easy to implement in multiple-labeling studies, such as reported here for FISH.
Permanence for a Discrete Model with Feedback Control and Delay (2008)

The permanence of a single‐species population discrete model with feedback control is considered. We found that if we use the method of comparison theorem, then the additional condition, to some extent, is necessary. But for the system itself, this condition may not be necessary. Here, we use new methods instead of the comparison theorem to get the permanence of the system in consideration; the additional condition in Chen′s paper (2007) is deleted.
Evidence for Role of White-Tailed Deer (Artiodactyla: Cervidae) in Epizootiology of Cattle Ticks and Southern Cattle Ticks (Acari: Ixodidae) in Reinfestations Along the Texas/Mexico Border in South Texas: A Review and Update (2010)

From 1907 when the fever tick eradication campaign began until 1933, the tick eradication methods of dipping cattle in an acaricide or "pasture vacation" were enormously successful in eradicating southern cattle ticks [Rhipicephalus (Boophilus) microplus (Canestrini)], until failures began to occur in some areas of Florida. Regarding the failures in Florida, the consensus was that populations of white-tailed deer [Odocoileus virginianus (Zimmermann)] infested with southern cattle ticks were responsible. After numerous deer in several counties were killed, eradication was achieved in Florida. As in Florida, in Texas increasing numbers of failures of the pasture vacation approach to tick eradication from the 1970s to the present are known to be related to the abundance of white-tailed deer and perhaps other wild ungulate species. A sizable body of evidence confirms the hypothesis that white-tailed deer support the dispersal and maintenance of both cattle ticks [Rhipicephalus (Boophilus) annulatus (Say)] and southern cattle ticks (cattle fever ticks) within the permanent quarantine or buffer zone in South Texas along the Rio Grande, as well as in the so-called free ("cattle fever tick-free") area north and east of the buffer zone and extending to the east coast of the United States. As of August 2009, in addition to the permanent quarantine zone of approximately 2233 km2, three temporary preventative or blanket quarantines were established. Currently, only two methodologies exist to control ticks feeding on white-tailed deer: (1) a systemic treatment method involving dispersal of ivermectin-medicated corn, Zea mays L.; and (2) two topical treatment methods, '4-poster' deer treatment bait stations and '2-poster' deer treatment feeder adapters, both of which passively apply topically active acaricide to deer for the eradication of populations of cattle fever tick associated with white-tailed deer. This study presents and summarizes confirmational support for the role of white-tailed deer derived from historical accounts, circumstantial evidence from review of recent infestations, and cattle fever tick infestations on white-tailed deer that were live-captured and examined specifically for cattle fever ticks.
Cardioprotective Effects of Erythropoietin in the Reperfused Ischemic Heart (2004)

Erythropoietin has recently been shown to have effects beyond hematopoiesis such as prevention of neuronal and cardiac apoptosis secondary to ischemia. In this study, we evaluated the in vivo protective potential of erythropoietin in the reperfused rabbit heart following ventricular ischemia. We show that "preconditioning" with erythropoietin activates cell survival pathways in myocardial tissue in vivo and adult rabbit cardiac fibroblasts in vitro. These pathways, activated by erythropoietin in both whole hearts and cardiac fibroblasts, are also activated acutely by ischemia/reperfusion injury. Moreover, in vivo studies indicate that erythropoietin treatment either prior to or during ischemia significantly enhances cardiac function and recovery, including left ventricular contractility, following myocardial ischemia/reperfusion. Our data indicate that a contributing in vivo cellular mechanism of this protection is mitigation of myocardial cell apoptosis. This results in decreased infarct size as evidenced by area at risk studies following in vivo ischemia/reperfusion injury, translating into more viable myocardium and less ventricular dysfunction. Therefore, erythropoietin treatment may offer novel protection against ischemic heart disease and may act, at least in part, by direct action on cardiac fibroblasts and myocytes to alter survival and ventricular remodeling.
MPEG-4 compatible 3D facial animation based on morphable model (2005)

A novel 3D facial animation model is proposed in this paper to generate realistic facial animation sequence. The 3D facial animation model is constructed based on morphable model and compatible with MPEG-4. Uniform mesh resampling method is put forward to align prototypic 3D faces and facial animation principle defined in MPEG-4 is adopted to drive the 3D facial animation model. The animation model can automatically reconstruct realistic 3D face of specific person given a single image and be driven by FAP parameters to generate 3D facial animation sequence automatically. Experimental results show the 3D facial animation model proposed in this paper can effectively generate high realistic facial animation sequence automatically.
The Potential of Carbon Nanotube Membranes for Analytical Separations (2010)

Advances in nanotechnology have enabled the development of nanoporous membranes based on carbon nanotubes, which, by virtue of their exceptional properties, constitute excellent supports for analytical processes, including the selective separation of some molecules.
Generating program inputs for database application testing (2011)

Testing is essential for quality assurance of database applications. Achieving high code coverage of the database application is important in testing. In practice, there may exist a copy of live databases that can be used for database application testing. Using an existing database state is desirable since it tends to be representative of real-world objects' characteristics, helping detect faults that could cause failures in real-world settings. However, to cover a specific program code portion (e.g., block), appropriate program inputs also need to be generated for the given existing database state. To address this issue, in this paper, we propose a novel approach that generates program inputs for achieving high code coverage of a database application, given an existing database state. Our approach uses symbolic execution to track how program inputs are transformed before appearing in the executed SQL queries and how the constraints on query results affect the application's execution. One significant challenge in our problem context is the gap between program-input constraints derived from the program and from the given existing database state; satisfying both types of constraints is needed to cover a specific program code portion. Our approach includes novel query formulation to bridge this gap. Our approach is loosely integrated into Pex, a state-of-the-art white-box testing tool for .NET from Microsoft Research. Empirical evaluations on two real database applications show that our approach assists Pex to generate program inputs that achieve higher code coverage than the program inputs generated by Pex without our approach's assistance.
Interpreting Black Box Models via Hypothesis Testing (2020)

In science and medicine, model interpretations may be reported as discoveries of natural phenomena or used to guide patient treatments. In such high-stakes tasks, false discoveries may lead investigators astray. These applications would therefore benefit from control over the finite-sample error rate of interpretations. We reframe black box model interpretability as a multiple hypothesis testing problem. The task is to discover "important" features by testing whether the model prediction is significantly different from what would be expected if the features were replaced with uninformative counterfactuals. We propose two testing methods: one that provably controls the false discovery rate but which is not yet feasible for large-scale applications, and an approximate testing method which can be applied to real-world data sets. In simulation, both tests have high power relative to existing interpretability methods. When applied to state-of-the-art vision and language models, the framework selects features that intuitively explain model predictions. The resulting explanations have the additional advantage that they are themselves easy to interpret.
Modulating Two-Dimensional Non-Close-Packed Colloidal Crystal Arrays by Deformable Soft Lithography (2009)

We report a simple method to fabricate two-dimensional (2D) periodic non-close-packed (ncp) arrays of colloidal microspheres with controllable lattice spacing, lattice structure, and pattern arrangement. This method combines soft lithography technique with controlled deformation of polydimethylsiloxane (PDMS) elastomer to convert 2D hexagonal close-packed (hcp) silica microsphere arrays into ncp ones. Self-assembled 2D hcp microsphere arrays were transferred onto the surface of PDMS stamps using the lift-up technique, and then their lattice spacing and lattice structure could be adjusted by solvent swelling or mechanical stretching of the PDMS stamps. Followed by a modified microcontact printing (microcp) technique, the as-prepared 2D ncp microsphere arrays were transferred onto a flat substrate coated with a thin film of poly(vinyl alcohol) (PVA). After removing the PVA film by calcination, the ncp arrays that fell on the substrate without being disturbed could be lifted up, deformed, and transferred again by another PDMS stamp; therefore, the lattice feature could be changed step by step. Combining isotropic solvent swelling and anisotropic mechanical stretching, it is possible to change hcp colloidal arrays into full dimensional ncp ones in all five 2D Bravais lattices. This deformable soft lithography-based lift-up process can also generate patterned ncp arrays of colloidal crystals, including one-dimensional (1D) microsphere arrays with designed structures. This method affords opportunities and spaces for fabrication of novel and complex structures of 1D and 2D ncp colloidal crystal arrays, and these as-prepared structures can be used as molds for colloidal lithography or prototype models for optical materials.