gebhart/patrepeval huggingface dataset:
Mint (2010)

Multi-stage programming (MSP) provides a disciplined approach to run-time code generation. In the purely functional setting, it has been shown how MSP can be used to reduce the overhead of abstractions, allowing clean, maintainable code without paying performance penalties. Unfortunately, MSP is difficult to combine with imperative features, which are prevalent in mainstream languages. The central difficulty is scope extrusion, wherein free variables can inadvertently be moved outside the scopes of their binders. This paper proposes a new approach to combining MSP with imperative features that occupies a "sweet spot" in the design space in terms of how well useful MSP applications can be expressed and how easy it is for programmers to understand. The key insight is that escapes (or "anti-quotes") must be weakly separable from the rest of the code, i.e. the computational effects occurring inside an escape that are visible outside the escape are guaranteed to not contain code. To demonstrate the feasibility of this approach, we formalize a type system based on Lightweight Java which we prove sound, and we also provide an implementation, called Mint, to validate both the expressivity of the type system and the effect of staging on the performance of Java programs.
Intratumoral 5-fluorouracil produced by cytosine deaminase/5-fluorocytosine gene therapy is effective for experimental human glioblastomas. (2002)

5-Fluorouracil (5-FU) is a potent antimetabolite used for chemotherapy of gastrointestinal (GI), breast, and head and neck malignancies. Although clinical trials have been conducted, the poor therapeutic index of 5-FU has precluded its clinical use for a number of other tumor types. It is unclear whether this lack of utility is due to problems with drug delivery or inherent insensitivity. Adenovirus (Ad) vector-mediated cytosine deaminase (CD)/5-fluorocytosine (5-FC) gene therapy has the potential to overcome pharmacokinetic issues associated with systemic 5-FU and is particularly well suited to use with tumors in which local control is paramount, such as recurrent, localized prostate cancer and malignant gliomas. In this study, the in vitro response by a panel of human tumor cell lines derived from both GI (colon, pancreas) and non-GI (prostate, glioma) tumors to 5-FU and to AdCMVCD (an Ad encoding Escherichia coli CD)/5-FC was examined. Whereas the sensitivity (IC(50)) of individual cell lines to these agents varied, no significant difference in median IC(50) for either 5-FU or AdCMVCD/5-FC was evident for the four tumor types tested (P > 0.1). The relevant contributions of Ad gene transfer efficiency and inherent 5-FU sensitivity in determining response to AdCMVCD/5-FC were then assessed. Multiple linear regression analysis revealed that whereas both factors significantly contribute to the response, inherent 5-FU sensitivity was substantially more important (beta= 0.78 versus 0.48; P < 0.001). Finally, the therapeutic efficacy of a single intratumoral injection of AdCMVCD followed by systemic 5-FC was assessed in three intracranial C.B17 severe combined immunodeficient mouse models of human glioma. AdCMVCD/5-FC efficacy was specific, virus dose-dependent, and closely paralleled in vitro 5-FU and CD/5-FC sensitivity in two of three models tested. These results reveal that glioma cells are as sensitive as GI tumor cells to the antineoplastic effects of 5-FU, identify inherent 5-FU sensitivity as an important factor in determining CD/5-FC efficacy, and confirm previous findings in rat models that demonstrate the potential clinical utility of AdCMVCD/5-FC gene therapy for gliomas.
Influence of the Cr Content on the Electrochemical Behavior of the LiCr[sub y]Mn[sub 2−y]O[sub 4] (0≤y≤1) Compounds: III. Galvanostatic Study of Bulk and Superficial Processes (2001)

Changing y in the materials enables the monitoring of the average discharge voltage between 4 and 4.5 V. The Cr substitution is beneficial to the specific energy (and to the specific capacity) that increases by 16% compared to for The cycling behavior is all the more poor as y is high in the composition range The best cyclability is observed for Its loss of the relative capacity after 280 cycles is about twice as small as that observed for The irreversible capacity, due to electrolyte oxidation, decreases rapidly with the cycle number and reaches a limit of about 2 to 6% of the cyclable capacity, depending on the experimental conditions. This limit is lowered when the end-of-charge voltage is decreased and/or when the charge rate is increased. The capacity decrease is negligible for discharge rates slower than D/2 in the 5.4-3.4 V range, and remains smaller than 50% for discharge rates slower than 8D. The power behavior of materials with 0.25, and 0.5 has proved to be excellent, with very high powers of ∼6000 mW g−1 for energies of 100 mWh g−1. © 2001 The Electrochemical Society. All rights reserved.
Studies of intestinal stem cells using normal, chimeric, and transgenic mice <sup>1</sup> (1992)

The mouse intestinal epithelium represents a continuous developmental system. Its four principal differentiated cell types--enterocytes, goblet, enteroendocrine, and Paneth cells--are derived from a common multipotent stem cell located near the base of monoclonal crypts. Members of these four lineages undergo rapid and perpetual renewal along an anatomically well-defined pathway. The gut epithelium provides a unique mammalian model for studying the biological features of stem cells (e.g., their ability to undergo asymmetric division, their enormous proliferative potential, their capacity for functional anchorage in a niche), examining how stem cell hierarchies are established and maintained in renewing cell populations, analyzing the relationships between passage through the cell cycle and lineage allocation (commitment), and defining the mechanisms that give stem cells a "positional address" along the cephalocaudal axis, allowing them to generate regional differences in the differentiation programs of their derived lineages (axial pattern formation).
Hyperpolarized water as an authentic magnetic resonance imaging contrast agent (2007)

Pure water in a highly (1)H spin-polarized state is proposed as a contrast-agent-free contrast agent to visualize its macroscopic evolution in aqueous media by MRI. Remotely enhanced liquids for image contrast (RELIC) utilizes a (1)H signal of water that is enhanced outside the sample in continuous-flow mode and immediately delivered to the sample to obtain maximum contrast between entering and bulk fluids. Hyperpolarization suggests an ideal contrast mechanism to highlight the ubiquitous and specific function of water in physiology, biology, and materials because the physiological, chemical, and macroscopic function of water is not altered by the degree of magnetization. We present an approach that is capable of instantaneously enhancing the (1)H MRI signal by up to 2 orders of magnitude through the Overhauser effect under ambient conditions at 0.35 tesla by using highly spin-polarized unpaired electrons that are covalently immobilized onto a porous, water-saturated gel matrix. The continuous polarization of radical-free flowing water allowed us to distinctively visualize vortices in model reactors and dispersion patterns through porous media. A (1)H signal enhancement of water by a factor of -10 and -100 provides for an observation time of >4 and 7 s, respectively, upon its injection into fluids with a T(1) relaxation time of >1.5 s. The implications for chemical engineering or biomedical applications of using hyperpolarized solvents or physiological fluids to visualize mass transport and perfusion with high and authentic MRI contrast originating from water itself, and not from foreign contrast agents, are immediate.
Multicenter Study to Assess Safety and Efficacy of INH-A21, a Donor-Selected Human Staphylococcal Immunoglobulin, for Prevention of Nosocomial Infections in Very Low Birth Weight Infants (2005)

INH-A21 750 mg/kg demonstrated potential to reduce sepsis caused by S. aureus, candidemia and mortality in VLBW infants. Although statistical significance was not reached, based on the magnitude of the estimated differences, the efficacy and safety of INH-A21 750 mg/kg should be evaluated in an adequately powered, well-controlled study.
Tumor angiogenesis and molecular targets for therapy (2009)

Tumors produce multiple angiogenic factors to induce neovascularization by angiogenesis, vasculogenesis and vascular remodeling. Although tumors utilize similar mechanisms as normal growing tissues, tumor blood vessels usually appear as malformed vasculatures that have several distinctive features including a high degree of disorganization, lack of clear separation between arterioles and venules, lack of appropriate coating with mural cells, high permeability, and composition of mosaic cell types, which might express specific markers. These unusual features of tumor blood vessels offer a great opportunity for therapeutic intervention and might paradoxically restrict cytotoxic drug delivery. Following an initial clinical success of bevacizumab in combination with chemotherapy for the treatment of human colorectal cancer, several other anti-angiogenesis agents are now available in the clinic. Understanding basic mechanisms of tumor angiogenesis, defining novel and accurate molecular targets, designing optimal clinical trials, and minimizing side effects are crucial issues for a further successful development of anti-angiogenic compounds for the treatment of various human cancers.
Maspin and tumor metastasis (2006)

For most cancer cell types, the acquisition of metastatic activity leads to clinically incurable disease. Improvements in surgery and radiotherapy, and the development of new chemotherapeutic agents or their use in new combinations, have, so far, only incrementally improved patient survival. Despite the obvious importance of metastasis, the process remains incompletely characterized at the molecular and biochemical levels. Tumor metastasis is a complex process and requires multiple cellular functions over time. From cellular invasion, extravasation from the primary tumor, intravasation to the secondary organs, to successful colonization, tumor cells utilize many cellular or biochemical mechanisms to complete the metastatic spread. During the process of metastasis, there are consistent changes in gene expression. Studies of genes that are reduced or silenced have yielded surprising insights into in vivo mechanisms of regulating tumor metastasis. This review describes a tumor suppressor gene, Maspin, which is often silenced in cancer cells and exhibits suppressing activity against tumor growth and metastasis. Maspin has been shown to be involved in processes that are important to both tumor growth and metastasis such as cell invasion, angiogenesis, and more recently apoptosis. Hence, many efforts have been devoted to deciphering the molecular mechanism of maspin. While some insights have come from the protease inhibitory effect of maspin, more perceptive results on how maspin may function in suppressing tumor metastasis have come from studies of gene manipulation, protein interactions and global protein profiling.
Centronuclear (myotubular) myopathy (2008)

Centronuclear myopathy (CNM) is an inherited neuromuscular disorder characterised by clinical features of a congenital myopathy and centrally placed nuclei on muscle biopsy. The incidence of X-linked myotubular myopathy is estimated at 2/100000 male births but epidemiological data for other forms are not currently available. The clinical picture is highly variable. The X-linked form usually gives rise to a severe phenotype in males presenting at birth with marked weakness and hypotonia, external ophthalmoplegia and respiratory failure. Signs of antenatal onset comprise reduced foetal movements, polyhydramnios and thinning of the ribs on chest radiographs; birth asphyxia may be the present. Affected infants are often macrosomic, with length above the 90th centile and large head circumference. Testes are frequently undescended. Both autosomal-recessive (AR) and autosomal-dominant (AD) forms differ from the X-linked form regarding age at onset, severity, clinical characteristics and prognosis. In general, AD forms have a later onset and milder course than the X-linked form, and the AR form is intermediate in both respects. Mutations in the myotubularin (MTM1) gene on chromosome Xq28 have been identified in the majority of patients with the X-linked recessive form, whilst AD and AR forms have been associated with mutations in the dynamin 2 (DNM2) gene on chromosome 19p13.2 and the amphiphysin 2 (BIN1) gene on chromosome 2q14, respectively. Single cases with features of CNM have been associated with mutations in the skeletal muscle ryanodine receptor (RYR1) and the hJUMPY (MTMR14) genes. Diagnosis is based on typical histopathological findings on muscle biopsy in combination with suggestive clinical features; muscle magnetic resonance imaging may complement clinical assessment and inform genetic testing in cases with equivocal features. Genetic counselling should be offered to all patients and families in whom a diagnosis of CNM has been made. The main differential diagnoses include congenital myotonic dystrophy and other conditions with severe neonatal hypotonia. Management of CNM is mainly supportive, based on a multidisciplinary approach. Whereas the X-linked form due to MTM1 mutations is often fatal in infancy, dominant forms due to DNM2 mutations and some cases of the recessive BIN1-related form appear to be associated with an overall more favourable prognosis.
MicroRNA Expression and Identification of Putative miRNA Targets in Ovarian Cancer (2008)

Our results identify several differentially expressed miRNAs in ovarian cancer and identify potential target transcripts that may be regulated by these miRNAs. These miRNAs and their targets may have important roles in the initiation and development of ovarian cancer.
Substrate specificities of rat liver peroxisomal acyl-CoA oxidases: palmitoyl-CoA oxidase (inducible acyl-CoA oxidase), pristanoyl-CoA oxidase (non-inducible acyl-CoA oxidase), and trihydroxycoprostanoyl-CoA oxidase. (1992)

Rat liver peroxisomes contain three acyl-CoA oxidases:palmitoyl-CoA oxidase, pristanoyl-CoA oxidase, and trihydroxycoprostanoyl-CoA oxidase. The three oxidases were separated by anion-exchange chromatography of a partially purified oxidase preparation, and the column eluate was analyzed for oxidase activity with different acyl-CoAs. Short chain mono (hexanoyl-) and dicarboxylyl (glutaryl-)-CoAs and prostaglandin E2-CoA were oxidized exclusively by palmitoyl-CoA oxidase. Long chain mono (palmitoyl-) and dicarboxylyl (hexadecanedioyl-)-CoAs were oxidized by palmitoyl-CoA oxidase and pristanoyl-CoA oxidase, the former enzyme catalyzing approximately 70% of the total eluate activity. The very long chain lignoceroyl-CoA was also oxidized by palmitoyl-CoA oxidase and pristanoyl-CoA oxidase, the latter enzyme catalyzing approximately 65% of the total eluate activity. Long chain 2-methyl branched acyl-CoAs (2-methylpalmitoyl-CoA and pristanoyl-CoA) were oxidized for approximately 90% by pristanoyl-CoA oxidase, the remaining activity being catalyzed by trihydroxycoprostanoyl-CoA oxidase. The short chain 2-methylhexanoyl-CoA was oxidized by trihydroxycoprostanoyl-CoA oxidase and pristanoyl-CoA oxidase (approximately 60 and 40%, respectively, of the total eluate activity). Trihydroxycoprostanoyl-CoA was oxidized exclusively by trihydroxycoprostanoyl-CoA oxidase. No oxidase activity was found with isovaleryl-CoA and isobutyryl-CoA. Substrate dependences of palmitoyl-CoA oxidase and pristanoyl-CoA oxidase were very similar when assayed with the same (common) substrate. Since the two oxidases were purified to a similar extent and with a similar yield, the contribution of each enzyme to substrate oxidation in the column eluate probably reflects its contribution in the intact liver.
Effective Schottky barrier lowering in silicon-on-insulator Schottky-barrier metal-oxide-semiconductor field-effect transistors using dopant segregation (2005)

We present an investigation of the use of dopant segregation in Schottky-barrier metal-oxide-semiconductor field-effect transistors on silicon-on-insulator. Experimental results on devices with fully nickel silicided source and drain contacts show that arsenic segregation during silicidation leads to strongly improved device characteristics due to a strong conduction/valence band bending at the contact interface induced by a very thin, highly doped silicon layer formed during the silicidation. With simulations, we study the effect of varying silicon-on-insulator and gate oxide thicknesses on the performance of Schottky-barrier devices with dopant segregation. It is shown that due to the improved electrostatic gate control, a combination of both ultrathin silicon bodies and gate oxides with dopant segregation yields even further improved device characteristics greatly relaxing the need for low Schottky barrier materials in order to realize high-performance Schottky-barrier transistors.
Assembly of a chondrocyte-like pericellular matrix on non-chondrogenic cells Role of the cell surface hyaluronan receptors in the assembly of a pericellular matrix (1991)

In this study, we have examined the capacity of various cell types, which express cell surface hyaluronan receptors, to organize a chondrocyte-like pericellular matrix when given chondrocyte-derived extracellular matrix macromolecules exogenously. The assembly of a pericellular matrix was visualized by a particle exclusion assay. Without the addition of exogenous macromolecular components, none of the cell types studied exhibited significant pericellular matrices extending from their plasma membranes. However, upon the addition of high molecular weight hyaluronan in combination with aggregating cartilage proteoglycan monomers, large pericellular matrices were formed within two hours of incubation. No pericellular matrices were formed if these macromolecular components were added separately at equivalent concentrations or if the components were added in the presence of hyaluronan hexasaccharide, a competitive inhibitor of hyaluronan interaction with cell surface hyaluronan receptors. Fully assembled pericellular matrices could also be displaced by the subsequent addition of hyaluronan hexasaccharides. Nonliving, glutaraldehyde-fixed cells, which retained functional hyaluronan receptors, maintained the capacity to assembly pericellular matrices with exogenous components, in serum-containing or serum-free medium. Cells that were incubated with exogenous matrix macromolecules for 24 h, followed by a chase incubation in medium minus the exogenous macromolecules, continued to maintain the matrix for up to 6 h on live cells and more than 24 h on glutaraldehyde-fixed cells. Cell types that did not express hyaluronan receptors were not capable of organizing such pericellular matrices when incubated with these exogenous components. These findings suggest that cells expressing hyaluronan receptors have a significant capacity to organize their immediate extracellular environment via hyaluronan-hyaluronan receptor interactions. Possible physiological functions for this type of matrix organizing capacity are discussed.
Auditory Prostheses Research with Multiple Channel Intracochlear Stimulation in Man (1978)

Although single-channel electrode arrays implanted in the scala tympani of deaf patients are useful as an aid to lip reading and for distinguishing some environmental sounds, they do not transmit intelligible speech. However, multichannel electrode arrays, which take advantage of the cochlea's tonotopic organization, may be capable of generating the complex patterns of neural activity necessary for speech discrimination. In this study, multichannel electrodes were implanted in the cochleas of four volunteers, with access to the connecting wires made through the skin via a percutaneous connector. The major portion of the data presented is from two of these subjects: one has been bilaterally deaf since birth and the other has been unilaterally deaf for 15 years. Preliminary results of experiments with two more recently implanted subjects are described as well as experiments with a fifth volunteer who was implanted with five electrodes by House in 1969. Data on pitch and loudness discrimination as well as the effects of stimulation parameters on threshold, impedance, and electrode interaction are presented. Place pitch and periodicity pitch were observed in all five volunteers. The results of pitch-matching experiments with the unilaterally deaf volunteer were consistent with tonotopic maps of the cochlea, and experiments indicated that a pitch continuum may be achieved by combining place and periodicity pitch modulation. Preliminary experiments in tune recognition with one subject demonstrate his ability to recognize simple melodies based on periodicity pitch cues. These results, coupled with the finding that subjective sensations remain stable over the long-term, support the feasibility of providing artificial hearing with a multichannel cochlear stimulation system.
Dynamic coupling measurement for object-oriented software (2004)

The relationships between coupling and external quality factors of object-oriented software have been studied extensively for the past few years. For example, several studies have identified clear empirical relationships between class-level coupling and class fault-proneness. A common way to define and measure coupling is through structural properties and static code analysis. However, because of polymorphism, dynamic binding, and the common presence of unused ("dead") code in commercial software, the resulting coupling measures are imprecise as they do not perfectly reflect the actual coupling taking place among classes at runtime. For example, when using static analysis to measure coupling, it is difficult and sometimes impossible to determine what actual methods can be invoked from a client class if those methods are overridden in the subclasses of the server classes. Coupling measurement has traditionally been performed using static code analysis, because most of the existing work was done on nonobject oriented code and because dynamic code analysis is more expensive and complex to perform. For modern software systems, however, this focus on static analysis can be problematic because although dynamic binding existed before the advent of object-orientation, its usage has increased significantly in the last decade. We describe how coupling can be defined and precisely measured based on dynamic analysis of systems. We refer to this type of coupling as dynamic coupling. An empirical evaluation of the proposed dynamic coupling measures is reported in which we study the relationship of these measures with the change proneness of classes. Data from maintenance releases of a large Java system are used for this purpose. Preliminary results suggest that some dynamic coupling measures are significant indicators of change proneness and that they complement existing coupling measures based on static analysis.