gebhart/patrepeval huggingface dataset:
The Influence of Special Instruction on Perceptions/Opinions of Academically Talented Youth Regarding Farm Animal Welfare, Care, and Use (1992)

Pennsylvania Governor's School for the Agricultural Sciences scholars participated in a "Farm Animal Welfare, Care and Use" course in 1990 and 1991. One hundred twenty-eight scholars in this course completed a pre- and posttest based on components of animal welfare and animal rights. The study results indicate that the scholars began the course with somewhat positive perceptions/opinions and reported increased positive perceptions/opinions about animal agriculture throughout the course. This was accomplished in part because the course allowed them to expand their knowledge about practices conducted in various animal agriculture enterprises through the use of lectures/discussions, tours of Penn State beef, sheep, dairy, deer, and meats facilities, and a final debate/discussion by teams from within the class.
Towards the digital music library (1996)

Music is traditionally retrieved by title, composer or subject classification. It is possible, with current technology, to retrieve music from a database on the basis of a few notes sung or hummed into a microphone. This paper describes the implementation of such a system, and discusses several issues pertaining to music retrieval. We first describe an interface that transcribes acoustic input into standard music notation. We then analyze string matching requirements for ranked retrieval of music and present the results of an experiment which tests how accurately people sing well known melodies. The performance of several string matching criteria are analyzed using two folk song databases. Finally, we describe a prototype system which has been developed for retrieval of tunes from acoustic input.
Relationship among BER, power consumption and PAPR (2008)

The increased Peak to Average Power Ratio (PAPR) of the signal is a significant drawback for Orthogonal Frequency Division Multiplexing (OFDM) systems since it restricts the efficiency of the RF part of a wireless transmitter. An effective algorithm applied on the digital part of the transmitter to mitigate PAPR is the Partial Transmit Sequence (PTS). Exploring only the power consumption in power Amplifier (PA) the application PTS algorithm, reduces the total power consumption of the transmitter, including digital and analog part, up to 22% in comparison to OFDM systems where no PAPR reduction method is employed. Furthermore experimental results of a Digital to Analog Converter (DAC) depict that for an OFDM system with a large number of subcarriers, PTS reduces the required resolution of DAC one bit, while power consumed at the DAC is reduced by a factor of two. In this paper we study the total power consumption at the transmitter when both DAC and PA are considered. Furthermore it is shown that the reduction of power consumption comes with no penalty on Bit-Error-Performance (BER).
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (2017)

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.
Flexural rigidity in partially demineralized diaphyseal bone grafts. (1995)

Control of biomechanical properties of demineralized diaphyseal bone allografts is required for their clinical application. Therefore, the changes in flexural rigidity in human fibulae were investigated as a function of the demineralization depth using a nondestructive bending test. Starting at the facies medialis, the flexural rigidity was determined in 24 planes at 15 degrees sequential angular increments, which allowed data collection around the circumference of the bone. Test bones included 4 pairs of left and right human fibulae and 15 single fibulae. The elliptical distribution of the flexural rigidity of left and right fibulae and single fibulae before and after demineralization was compared. The stiffness index and the area ratio were defined as parameters to describe the mechanical status of the test bones. Results show that the rigidity of diaphyseal bones is strongly dependent on the reduction of their cortical thickness by demineralization. A mathematical model allowing prediction of the reduction of the rigidity of diaphyseal bone grafts as a function of the demineralization depth is presented.
Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry (2009)

Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sample of only 2 million yeast cells. By comparative lipidomics, we achieved the absolute quantification of 250 molecular lipid species covering 21 major lipid classes. This analysis provided approximately 95% coverage of the yeast lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast lipidome. This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches.
Nitric oxide effects on the function of aged cells ex vivo and in vivo. (2009)

These data underscore the complexity of using a single agent, even one with multiple mechanisms such as NO, to improve a clinical outcome such as angiogenesis or wound repair in aged animals.
Cell Delivery Using an Injectable and Adhesive Transglutaminase–Gelatin Gel (2009)

In this study, we developed an injectable gelatin-transglutaminase (TGase) gel for cell delivery. The procedure provides a minimally invasive approach to deliver cells into tissue in a manner that improves localization. The results indicate gelatin-TGase to be noncytotoxic and to have adhesive properties that help localize and prevent the scattering of the cells after delivery. The in situ crosslinking between gelatin chains and endogenous collagen can create a strong attachment between the gel and tissue extracellular matrix, preventing cells from dissipation. The gelatin-TGase was also shown to maintain the carried cells to be viable and proliferative. Finally, through the adjustment of the enzymatic crosslinker concentration, the release rate of the cells into the surrounding tissue after injection was demonstrated to be controllable.
Clay Minerals in Mixtures: Sample Preparation, Analysis, and Statistical Interpretation (1983)

Abstract A method of clay mineral sample preparation for electron microprobe analysis has been developed in which a film of clay plus 10–12 wt. % colloidal graphite is deposited on a porous ceramic disc using a specially designed suction device. Correction procedures are used to obtain quantitative elemental analyses representing the average chemical composition of the prepared sample. A statistical technique is employed to estimate the most likely proportions of clay minerals representing the known composition. Chemical compositions of clay minerals are presented in terms of five coordinates (“Si,” “Al,” “Mg,” “K,” and “Fe”). Using literature data, the chemical compositions of 13 different clay mineral groupings were defined statistically by their multivariate means and variance-covariance matrices. A correlation parameter, χ 2 , was calculated to compare the chemical composition of a sample with that of any mixture of the defined clay mineral groupings, the minimum χ 2 indicating the best-fit mixture. From chemical analyses of artificial mixtures only approximate clay mineral proportions could be determined when the various clay mineral groupings had been defined statistically from literature analyses. The best results were obtained when the actual compositions of the end-members forming the artificial mixtures replaced the statistical definitions. Tests of the estimation procedure on clay mineral mixtures for which chemical compositions and corresponding clay mineral proportions were found in the literature, indicate that the technique has appreciable merit.
Small Molecule Antagonists of the σ-1 Receptor Cause Selective Release of the Death Program in Tumor and Self-Reliant Cells and Inhibit Tumor Growth in Vitro and in Vivo (2004)

The acquisition of resistance to apoptosis, the cell's intrinsic suicide program, is essential for cancers to arise and progress and is a major reason behind treatment failures. We show in this article that small molecule antagonists of the sigma-1 receptor inhibit tumor cell survival to reveal caspase-dependent apoptosis. sigma antagonist-mediated caspase activation and cell death are substantially attenuated by the prototypic sigma-1 agonists (+)-SKF10,047 and (+)-pentazocine. Although several normal cell types such as fibroblasts, epithelial cells, and even sigma receptor-rich neurons are resistant to the apoptotic effects of sigma antagonists, cells that can promote autocrine survival such as lens epithelial and microvascular endothelial cells are as susceptible as tumor cells. Cellular susceptibility appears to correlate with differences in sigma receptor coupling rather than levels of expression. In susceptible cells only, sigma antagonists evoke a rapid rise in cytosolic calcium that is inhibited by sigma-1 agonists. In at least some tumor cells, sigma antagonists cause calcium-dependent activation of phospholipase C and concomitant calcium-independent inhibition of phosphatidylinositol 3'-kinase pathway signaling. Systemic administration of sigma antagonists significantly inhibits the growth of evolving and established hormone-sensitive and hormone-insensitive mammary carcinoma xenografts, orthotopic prostate tumors, and p53-null lung carcinoma xenografts in immunocompromised mice in the absence of side effects. Release of a sigma receptor-mediated brake on apoptosis may offer a new approach to cancer treatment.
Autologous stem cell transplantation for malignancy: a systematic review of the literature (2000)

A systematic review of the literature was undertaken to assess what published evidence is currently available to support the increasing use of autologous stem cell transplantation (ASCT), and to evaluate the published data with regard to the comparative cost of high-dose and conventional therapy. The review aimed to identify all published, randomized controlled trials (RCTs) comparing high-dose therapy (HDT) with ASCT versus conventional chemotherapy (CC) in acute lymphoblastic leukaemia, non-Hodgkin's lymphoma, Hodgkin's disease, multiple myeloma, and breast, lung, testicular and ovarian cancer. The review also aimed to identify all studies that had compared the cost of the two treatment strategies. Reports were identified by systematic searches of Cancerlit, Embase and Medline, and handsearching of several conference proceedings. Where possible, pooled odds ratios (ORs) were calculated according to the fixed-effect model. A total of 18 randomized trials were identified in acute lymphoblastic leukaemia, non-Hodgkin's lymphoma, Hodgkin's disease, multiple myeloma, and breast, lung and testicular cancer. Trials were generally small and no disease site had sufficient information to determine reliably whether high-dose therapy with autologous transplant is more effective than CC. Five studies were identified that compared the cost of the two treatments. These found the cost of HDT to be between one and four times higher than that of CC. Further randomized trials are required. Where appropriate, these should include economic assessment and assessments of long-term toxicity.
Inhibition of Gene Expression by Oligonucleotides (1989)

A glance at a map of metabolic pathways shows an enormously complex picture of interrelated reactions involving many different compounds. The structures of all these reactants, intermediates and products are only a part of the biochemical story. In the cell, reactions are generally neither spontaneous nor independent but must be co-ordinated and regulated. The agents for this are usually macromolecules, either proteins or nucleic acids. In order to understand the roles of individual components and the relationships between them in cell biology, it can be helpful to observe the effect of blocking selected processes. Here, as in drug discovery, identification of reagents capable of selectively inhibiting biochemical reactions is hindered by our poor ability to predict how macromolecules will interact with other compounds.
The cellulose-binding domain of the major cellobiohydrolase of Trichoderma reesei exhibits true reversibility and a high exchange rate on crystalline cellulose. (1996)

Cellulose-binding domains (CBDs) bind specifically to cellulose, and form distinct domains of most cellulose degrading enzymes. The CBD-mediated binding of the enzyme has a fundamental role in the hydrolysis of the solid cellulose substrate. In this work we have investigated the reversibility and kinetics of the binding of the CBD from Trichoderma reesei cellobiohydrolase I on microcrystalline cellulose. The CBD was produced in Escherichia coli, purified, and radioactively labeled by reductive alkylation with 3H. Sensitive detection of the labeled CBD allowed more detailed analysis of its behavior than has been possible before, and important novel features were resolved. Binding of the CBD was found to be temperature sensitive, with an increased affinity at lower temperatures. The interaction of the CBD with cellulose was shown to be fully reversible and the CBD could be eluted from cellulose by simple dilution. The rate of exchange measured for the CBD-cellulose interaction compares well with the hydrolysis rate of cellobiohydrolase I, which is consistent with its proposed mode of action as a processive exoglucanase.
RANK Ligand and Osteoprotegerin (2002)

In 1997, investigators isolated a secreted glycoprotein that blocked osteoclast differentiation from precursor cells, prevented osteoporosis (decreased bone mass) when administered to ovariectomized rats, and resulted in osteopetrosis (increased bone mass) when overexpressed in transgenic mice. Since then, the isolation and characterization of the protein named osteoprotegerin (OPG) has stimulated much work in the fields of endocrinology, rheumatology, and immunology. OPG functions as a soluble decoy receptor for receptor activator of nuclear factor-kappaB ligand (RANKL, or OPG ligand) and shares homologies with other members of the tumor necrosis factor receptor superfamily. OPG acts by competing with the receptor activator of nuclear factor-kappaB, which is expressed on osteoclasts and dendritic cells for specifically binding to RANKL. RANKL is crucially involved in osteoclast functions and bone remodeling as well as immune cell cross-talks, dendritic cell survival, and lymph node organogenesis. More recently, emerging evidence from in vitro studies and mouse genetics attributed OPG an important role in vascular biology. In fact, OPG could represent the long sought-after molecular link between arterial calcification and bone resorption, which underlies the clinical coincidence of vascular disease and osteoporosis, which are most prevalent in postmenopausal women and elderly people.
BAG‐1 expression in human breast cancer: interrelationship between BAG‐1 RNA, protein, HSC70 expression and clinico‐pathological data (2002)

BAG-1 (BCL-2 athanogene-1), a multifunctional protein which associates with steroid hormone receptors (including the oestrogen receptor) and the anti-apoptotic BCL-2 protein, regulates steroid hormone-dependent transcription and apoptosis. Direct interaction with 70 kD heat-shock proteins, HSC70 and HSP70, may mediate the diverse functions of BAG-1. Immunohistochemistry was used to examine the expression of BAG-1 and HSC70 in 160 cases of invasive breast cancer. BAG-1 was expressed in 92% of cases; most tumours exhibited cytoplasmic BAG-1, while a smaller proportion also had nuclear immunostaining. There was a significant inverse correlation between histological grade and nuclear BAG-1 expression, with higher-grade tumours tending to have reduced nuclear BAG-1 expression, but there was no association with cytoplasmic BAG-1. There was also no significant correlation between nuclear or cytoplasmic BAG-1 expression and oestrogen receptor positivity. Since BAG-1 may be influenced by hormonal background, the relationship between grade and oestrogen receptor was examined separately in pre-menopausal and post-menopausal women. The statistically significant correlation between nuclear BAG-1 expression and low tumour grade was strong in pre-menopausal, but not apparent in postmenopausal women. A statistically significant correlation was observed between cytoplasmic, but not nuclear, BAG-1 expression and oestrogen receptor status in pre-menopausal, but not postmenopausal, women. There was no correlation between BAG-1 protein expression and RNA, suggesting that important post-transcriptional mechanisms control BAG-1 expression in vivo. HSC70 was also detected in the majority (97%) of cases, although expression was not correlated with BAG-1 levels, oestrogen receptor status or tumour grade. Overall survival in cases with high levels of nuclear BAG-1 expression was improved, though not significantly. These results are consistent with the hypothesis that BAG-1 plays an important but variable role in breast cancers developing in pre-menopausal and post-menopausal women.
Direct Analysis of Biological Tissue by Paper Spray Mass Spectrometry (2011)

Paper spray mass spectrometry (PS-MS) is explored as a fast and convenient way for direct analysis of molecules in tissues with minimum sample pretreatment. This technique allows direct detection of different types of compounds such as hormones, lipids, and therapeutic drugs in short total analysis times (less than 1 min) using a small volume of tissue sample (typically 1 mm(3) or less). The tissue sample could be obtained by needle aspiration biopsy, by punch biopsy, or by rubbing a thin tissue section across the paper. There exists potential for the application of paper spray mass spectrometry together with tissue biopsy for clinical diagnostics.
Recent Advances in Flame Retardant Polymer Nanocomposites (2020)

Mica-type clays nano-dispersed In commodity polymers. These “nanocomposites” exhibit the unusual combination of reduced flammability, in the form of lower peak heat release rates, and However, the details of the fire retardant mechanism are not well understood. In October of 1998 a NIST-industrial consortium was formed to study the flammability of these unique materials. The focus of research within this consortium was to development a fundamental understanding of the fire retardant (FR) mechanism of polymer clay nanocomposites. We report here on some of the results of the first year of this study; we focus our discussions on the results for polystyrene (PS) a polymer system commonly used in flame retarded applications such as information technology (IT) equipment. The most important aspect of the nanocomposite approach is the combined improvement in both clay dispersion. We also report on our recent efforts to address these issues; specifically, our efforts to develop thermally stable immidazolium treated clays, and using solid state NMR to evaluate clay dispersion and alkyl ammonium stability.
Adiabatic thermo-optic Mach–Zehnder switch (2013)

In this Letter, we propose and demonstrate a high-speed and power-efficient thermo-optic switch using an adiabatic bend with a directly integrated silicon heater to minimize the heat capacity and therein maximize the performance of the thermo-optic switch. A rapid, τ=2.4 μs thermal time constant and a low electrical power consumption of P(π)=12.7 mW/π-phase shift were demonstrated representing a P(π)τ product of only 30.5 mW·μs in a compact device with a phase shifter of only ~10 μm long.
Evaluation of the SPf66 vaccine for malaria control when delivered through the EPI scheme in Tanzania (1999)

This has been the first trial of a malaria vaccine among very young infants. It provides information on the safety of peptide vaccines administered at this early age as well as their capacity to induce immune responses without negatively interacting with EPI vaccines. Given the modest protection previously documented in older age groups and the lack of efficacy in younger infants, this vaccine in its current alum-based formulation does not appear to have a role in malaria control in sub-Saharan Africa. The lack of efficacy found in this trial also raises concerns about potential difficulties of inducing protective immune responses against malaria through immunization in infants.
Implementing jalapeño in Java (1999)

Jalapeno is a virtual machine for Java™ servers written in Java.A running Java program involves four layers of functionality: the user code, the virtual-machine, the operating system, and the hardware. By drawing the Java / non-Java boundary below the virtual machine rather than above it, Jalapeno reduces the boundary-crossing overhead and opens up more opportunities for optimization.To get Jalapeno started, a boot image of a working Jalapeno virtual machine is concocted and written to a file. Later, this file can be loaded into memory and executed. Because the boot image consists entirely of Java objects, it can be concocted by a Java program that runs in any JVM. This program uses reflection to convert the boot image into Jalapeno's object format.A special MAGIC class allows unsafe casts and direct access to the hardware. Methods of this class are recognized by Jalapeno's three compilers, which ignore their bytecodes and emit special-purpose machine code. User code will not be allowed to call MAGIC methods so Java's integrity is preserved.A small non-Java program is used to start up a boot image and as an interface to the operating system.Java's programming features — object orientation, type safety, automatic memory management — greatly facilitated development of Jalapeno. However, we also discovered some of the language's limitations.