gebhart/patrepeval huggingface dataset:
Inference of Resource Management Specifications (2023)

A resource leak occurs when a program fails to free some finite resource after it is no longer needed. Such leaks are a significant cause of real-world crashes and performance problems. Recent work proposed an approach to prevent resource leaks based on checking resource management specifications. A resource management specification expresses how the program allocates resources, passes them around, and releases them; it also tracks the ownership relationship between objects and resources, and aliasing relationships between objects. While this specify-and-verify approach has several advantages compared to prior techniques, the need to manually write annotations presents a significant barrier to its practical adoption. This paper presents a novel technique to automatically infer a resource management specification for a program, broadening the applicability of specify-and-check verification for resource leaks. Inference in this domain is challenging because resource management specifications differ significantly in nature from the types that most inference techniques target. Further, for practical effectiveness, we desire a technique that can infer the resource management specification intended by the developer, even in cases when the code does not fully adhere to that specification. We address these challenges through a set of inference rules carefully designed to capture real-world coding patterns, yielding an effective fixed-point-based inference algorithm. We have implemented our inference algorithm in two different systems, targeting programs written in Java and C#. In an experimental evaluation, our technique inferred 85.5% of the annotations that programmers had written manually for the benchmarks. Further, the verifier issued nearly the same rate of false alarms with the manually-written and automatically-inferred annotations.
Computational Chemistry Predictions of Kinetics and Major Reaction Pathways for Germane Gas‐Phase Reactions (1996)

Gas‐phase reaction pathways for decomposition are proposed and the relevant reaction rates are evaluated by transition‐state theory with molecular structures and thermochemical data predicted by ab initio molecular orbital calculations, specifically Hartree‐Fock with second‐order Møller‐Plesset perturbation theory. Pressure and temperature effects are included in computed unimolecular reaction rates through the application of Rice‐Ramsperger‐Kassel‐Marcus theory. Quantum‐Rice‐Ramsperger‐Kassel theory is used to estimate the relative rates of stabilization and chemical activation pathways for the insertion of into to form and , respectively. The predicted and measured reaction rates agree well with reactions for which experimental kinetic data have been reported. The developed decomposition mechanism is subsequently used in a finite‐element reactor simulation of germanium deposition to demonstrate the utility of quantum chemistry for developing kinetic rates required in realistic macroscopic models of deposition processes. Contribution of gas‐phase reactions to the germanium growth rate is predicted to be important at pressures higher than 1 Torr and temperatures greater than 1000 K.
Fluorene-functionalized aliphatic polycarbonates: design, synthesis and aqueous self-assembly of amphiphilic block copolymers (2013)

In this study, a fluorene-functionalized aliphatic cyclic carbonate monomer, spiro[fluorene-9,5′-[1,3]-dioxan]-2′-one (F-TMC) was synthesized, and organo-catalytic ring opening polymerization of F-TMC was explored with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). By using mPEG-OH with a variety of different molecular weights (1.6–10.0 kDa) as macro-initiators, well-defined amphiphilic diblock copolymers mPEGn-b-P(F-TMC)m, were readily synthesized with relatively low polydispersity indices, encompassing hydrophilic PEG weight fractions (f) from 0.24 to 0.67. Depending upon the specific amphiphilic balance, under aqueous conditions, these block copolymers self-assembled to form unique nanostructures such as tapes, elongated micelles and spherical micelles. The electro-active nature of the fluorene moieties combined with the biodegradable polycarbonate platform could render these nanostructures useful as novel materials for the encapsulation and release of active ingredients through π–π and hydrophobic interactions.
Mucosal B Cell Deficiency in IgA−/− Mice Abrogates the Development of Allergic Lung Inflammation (2005)

We have investigated the consequence of lack of IgA on host immunity using a murine model of allergic lung inflammation. Mice with a targeted disruption of the alpha-switch region and 5' H chain gene (IgA(-/-) mice), which lack total IgA, developed significantly reduced pulmonary inflammation with fewer inflammatory cells in lung tissue and bronchoalveolar lavage fluids, as well as reduced levels of total and IgG1 OVA-specific Abs and decreased IL-4 and IL-5 in bronchoalveolar lavage fluids compared with IgA(+/+) controls, following allergen sensitization and challenge. This defect was attributable to fewer B cells in the lungs of IgA(-/-) mice. Polymeric IgR-deficient (pIgR(-/-)) mice, which lack the receptor that transports polymeric IgA across the mucosal epithelium where it is cleaved to form secretory IgA, were used to assess the contribution of secretory IgA vs total IgA in the induction of allergic lung inflammation. pIgR(-/-) and pIgR(+/+) mice had comparable levels of inflammation, demonstrating that IgA bound to secretory component is not necessary for the development of allergic lung inflammation, although this does not necessarily rule out a role for transudated IgA in lung secretions because of "mucosal leakiness" in these mice. The results indicate that Ag-specific B cells are required at mucosal surfaces for induction of inflammation and likely function as major APCs in the lung for soluble protein Ags.
Interaction of AsymmetricABCC9-Encoded Nucleotide Binding Domains Determines KATPChannel SUR2A Catalytic Activity (2008)

Nucleotide binding domains (NBDs) secure ATP-binding cassette (ABC) transporter function. Distinct from traditional ABC transporters, ABCC9-encoded sulfonylurea receptors (SUR2A) form, with Kir6.2 potassium channels, ATP-sensitive K+ (K ATP) channel complexes. SUR2A contains ATPase activity harbored within NBD2 and, to a lesser degree, NBD1, with catalytically driven conformations exerting determinate linkage on the Kir6.2 channel pore. While homodomain interactions typify NBDs of conventional ABC transporters, heterodomain NBD interactions and their functional consequence have not been resolved for the atypical SUR2A protein. Here, nanoscale protein topography mapped assembly of monodisperse purified recombinant SUR2A NBD1/NBD2 domains, precharacterized by dynamic light scattering. Heterodomain interaction produced conformational rearrangements inferred by secondary structural change in circular dichroism, and validated by atomic force and transmission electron microscopy. Physical engagement of NBD1 with NBD2 translated into enhanced intrinsic ATPase activity. Molecular modeling delineated a complemental asymmetry of NBD1/NBD2 ATP-binding sites. Mutation in the predicted catalytic base residue, D834E of NBD1, altered NBD1 ATPase activity disrupting potentiation of catalytic behavior in the NBD1/NBD2 interactome. Thus, NBD1/NBD2 assembly, resolved by a panel of proteomic approaches, provides a molecular substrate that determines the optimal catalytic activity in SUR2A, establishing a paradigm for the structure-function relationship within the K ATP channel complex.
prism-DGTD with GDM to analyze pixelized metasurfaces (2020)

This simulation package is the prism-based Discontinuous Galerkin Time Domain method with General Dispersion Model for analysis of gold pixelized metasurfaces.
Uncooled focal plane array for thermal observation of the Earth (1998)

A medium scale infrared sensor dedicated to applications in agriculture, hydrology, forest fires and environment has been studied within the framework of a European Commission contract. An innovative push broom concept using linear arrays of uncooled microbolometers has been preferred to a traditional scanner concept using cryogenically cooled photoconductor detectors, for its performances and because it does not require any cooling, and is free of micro-vibrations. The instrument offers a resolution of 250 m for a swath width of about 1400 km, and the radiometric resolution is better than 0.5 K in two spectral channels around 11 and 12 micrometer. Focal plane topology and radiometric modeling will be presented in this paper, demonstrating the suitability of microbolometers focal planes for medium resolution radiometric missions on board Low Earth Orbit satellites.
Differential effects of hydrocortisone and TNFα on tight junction proteins in an in vitro model of the human blood–brain barrier (2008)

Homeostasis of the central nervous system (CNS) microenvironment is maintained by the blood-brain barrier (BBB) which regulates the transport of molecules from blood into brain and back. Many disorders change the functionality and integrity of the BBB. Glucocorticoids are being used sucessfully in the treatment of some disorders while their effects on others are questionable. In addition, conflicting results between clinical and experimental experience using animal models has arisen, so that the results of molecular studies in animal models need to be revisited in an appropriate in vitro model of the human BBB for more effective treatment strategies. Using the human brain microvascular endothelial cell line hCMEC/D3, the influence of glucocorticoids on the expression of barrier constituting adherens junction and tight junction transmembrane proteins (VE-cadherin, occludin, claudins) was investigated and compared to other established BBB models. In hCMEC/D3 cells the administration of glucocorticoids induced expression of the targets occludin 2.75 +/- 0.04-fold and claudin-5 up to 2.32 +/- 0.11-fold, which is likely to contribute to the more than threefold enhancement of transendothelial electrical resistance reflecting barrier tightness. Our analyses further provide direct evidence that the GC hydrocortisone prevents endothelial barrier breakdown in response to pro-inflammatory stimuli (TNFalpha administration), which could be demonstrated to be partly based on maintenance of occludin levels. Our studies strongly suggest stabilization of BBB function as a mode of GC action on a molecular level in the human brain vasculature.
Engineering the Emergence of Stem Cell Therapeutics (2013)

The long-awaited translation of stem cell–based therapies to the clinic requires engineering approaches.
The stochastic CRB for array processing in unknown noise fields (2002)

The stochastic Cramer-Rao bound (CRB) plays an important role in array processing because several high-resolution direction-of-arrival (DOA) estimation methods are known to achieve! this bound asymptotically In this paper, we study the stochastic CRB on DOA estimation accuracy in the general case of arbitrary unknown noise field parametrized by a vector of unknowns. We derive explicit closed-form expressions for the CRB and examine its properties theoretically and by representative numerical examples.
A subset of solitary fibrous tumors express nuclear PAX8 and PAX2: a potential diagnostic pitfall. (2016)

Solitary fibrous tumor (SFT), a mesenchymal neoplasm with widespread anatomic distribution, can be diagnostically challenging in limited samples. We recently encountered an aspirate of a pancreatic mass, incorrectly interpreted as metastatic renal cell carcinoma based on strong PAX8 expression by immunohistochemistry (IHC). After resection, morphologic features with additional IHC (CD34 positivity) correctly identified this lesion as a SFT. PAX8 and PAX2 are commonly used as renal tumor markers; however, no series has investigated PAX8 or PAX2 expression in SFT. IHC for PAX8 and PAX2 was performed on 41 SFTs (biopsy and resections) from varying sites. Eight were histologically malignant and eight were recurrences of previous resections. PAX8 staining was observed at least focally in 26.8% (11 of 41) SFT cases; additionally, PAX2 was positive in 12.2% (5 of 41 cases) of SFTs. For PAX8 and PAX2 positive cases 45.6% and 40%, respectively, showed diffuse expression. No correlation was found between PAX8/PAX2 positivity and age, tumor size, site, malignancy, or recurrence. In conclusion, a substantial minority of SFTs express PAX8 and PAX2 via IHC. This presents a diagnostic pitfall when evaluating possible metastases from the kidney, particularly when primary tumors show sarcomatoid or spindle cell morphologies.
Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age‐associated increase of the diversity (2009)

The methanogenic diversity of the human intestinal microbiota has long been viewed as composed of two Methanobacteriales: Methanobrevibacter smithii and Methanosphaera stadtmanae. Recently, Mx-01, a new phylotype hypothesized to belong to a putative sixth methanogenic order, was recovered from human faeces. Here we examined the diversity and the distribution of methanogens among healthy people of three age groups by analysing mcrA and 16S rDNA clones. The mcrA analysis of ∼1200 clones revealed that the usual Methanobacteriales were present without any significant difference among adults and elderly (respectively 60% and 80% of carriers, n = 40, P = 0.3). In addition, four new phylotypes that grouped with Mx-01 in the same monophyletic clade were recovered. These phylotypes were significantly more frequently detected in elderly people (40%, n = 20) than in adults (10%, n = 20, P = 0.065). In parallel, new 16S rDNA phylotypes affiliated near or within Thermoplasmatales were recovered. Altogether, these results indicate an age-related apparition of Mx-phylotypes, putatively methanogenic, which are formed of several species carrying a mcrA gene and that are not related to any of the five methanogenic orders. These species may be related to Thermoplasmatales or may cohabit with archaeal species related to Thermoplasmatales.
Maternal vitamin B12 in mice positively regulates bone, but not muscle mass and strength in post-weaning and mature offspring (2021)

Vitamin B<sub>12</sub> deficiency has been shown to affect bone mass in rodents and negatively impact bone formation in humans. In this study using mouse models, we define the effect of B<sub>12</sub> supplementation in the wild-type mother and B<sub>12</sub> deficiency in a mouse genetic model (<i>Gif</i><sup>-/-</sup> mice) during gestation on bone and muscle architecture and mechanical properties in the offspring. Analysis of bones from 4-wk-old offspring of the wild-type mother following vehicle or B<sub>12</sub> supplementation during gestation (from <i>embryonic day 0.5</i> to <i>20.5</i>) showed an increase in bone mass caused by an isolated increase in bone formation in the B<sub>12</sub>-supplemented group compared with vehicle controls. Analysis of the effect of B<sub>12</sub> deficiency in the mother in a mouse genetic model (<i>Gif</i><sup>-/-</sup> mice) on the long bone architecture of the offspring showed a compromised cortical and trabecular bone mass, which was completely prevented by a single injection of B<sub>12</sub> in the B<sub>12</sub>-deficient <i>Gif</i><sup>-/-</sup> mothers. Biomechanical analysis of long bones of the offspring born from B<sub>12</sub>-supplemented wild-type mothers showed an increase in bone strength, and conversely, offspring born from B<sub>12</sub>-deficient <i>Gif</i><sup>-/-</sup> mothers revealed a compromised bone strength, which could be rescued by a single injection of B<sub>12</sub> in the B<sub>12</sub>-deficient <i>Gif</i><sup>-/-</sup> mother. Muscle structure and function analysis however revealed no significant effect on muscle mass, structure, and grip strength of B<sub>12</sub> deficiency or supplementation in <i>Gif</i><sup>-/-</sup> mice compared with littermate controls. Together, these results demonstrate the beneficial effect of maternally derived B<sub>12</sub> in the regulation of bone structure and function in the offspring.
Interruption of progerin–lamin A/C binding ameliorates Hutchinson-Gilford progeria syndrome phenotype (2016)

Hutchinson-Gilford progeria syndrome (HGPS) is a rare autosomal dominant genetic disease that is caused by a silent mutation of the LMNA gene encoding lamins A and C (lamin A/C). The G608G mutation generates a more accessible splicing donor site than does WT and produces an alternatively spliced product of LMNA called progerin, which is also expressed in normal aged cells. In this study, we determined that progerin binds directly to lamin A/C and induces profound nuclear aberrations. Given this observation, we performed a random screening of a chemical library and identified 3 compounds (JH1, JH4, and JH13) that efficiently block progerin-lamin A/C binding. These 3 chemicals, particularly JH4, alleviated nuclear deformation and reversed senescence markers characteristic of HGPS cells, including growth arrest and senescence-associated β-gal (SA-β-gal) activity. We then used microarray-based analysis to demonstrate that JH4 is able to rescue defects of cell-cycle progression in both HGPS and aged cells. Furthermore, administration of JH4 to LmnaG609G/G609G-mutant mice, which phenocopy human HGPS, resulted in a marked improvement of several progeria phenotypes and an extended lifespan. Together, these findings indicate that specific inhibitors with the ability to block pathological progerin-lamin A/C binding may represent a promising strategy for improving lifespan and health in both HGPS and normal aging.
Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing (2019)

This study categorizes the range, frequency, coexisting driver mutations and clinical characteristics of the three classes of BRAF mutations in a large cohort of melanomas in a clinical diagnostic setting. Further prospective studies are warranted to elucidate the clinical outcomes and benefits of newly developed targeted therapy in melanoma patients carrying each class of BRAF mutation.
Colorimetric Disposable Paper Coated with ZnO@ZnS Core–Shell Nanoparticles for Detection of Copper Ions in Aqueous Solutions (2014)

In this study, we have proposed a new nanoparticle-containing test paper sensor that could be used as an inexpensive, easy-to-use, portable, and highly selective sensor to detect Cu(2+) ions in aqueous solutions. This disposable paper sensor is based on ZnO@ZnS core-shell nanoparticles. The core-shell nanoparticles were synthesized using a chemical method and then they were used for coating the paper. The synthesis of the ZnO@ZnS core-shell nanoparticles was performed at a temperature as low as 60 °C, and so far this is the lowest temperature for the synthesis of such core-shell nanoparticles. The sensitivity of the paper sensor was investigated for different Cu(2+) ion concentrations in aqueous solutions and the results show a direct linear relation between the Cu(2+) ions concentration and the color intensity of the paper sensor with a visual detection limit as low as 15 μM (∼0.96 ppm). Testing the present paper sensor on real river turbulent water shows a maximum 5% relative error for determining the Cu(2+) ions concentration, which confirms that the presented paper sensor can successfully be used efficiently for detection in complex solutions with high selectivity. Photographs of the paper sensor taken using a regular digital camera were transferred to a computer and analyzed by ImageJ Photoshop software. This finding demonstrates the potential of the present disposable paper sensor for the development of a portable, accurate, and selective heavy metal detection technology.
Effect of MWCNT size, carboxylation, and purification on in vitro and in vivo toxicity, inflammation and lung pathology (2013)

Taken together, the results indicated that in vitro and in vivo bioactivity of MWCNT increased with diameter and length. Purification had no significant modifying effect from the original MWCNT. Functionalization by carboxylation completely eliminated the bioactive potential of the MWCNT regardless of size in in vitro testing.
Localization of the EPM1 gene for progressive myoclonus epilepsy on chromosome 21: linkage disequilibrium allows high resolution mapping (1993)

The gene for Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) has previously been mapped by linkage to markers on chromosome 21q22.3. By analyzing crossover events in multiplex disease families with newly detected markers from the region we were able to narrow the localization of EPM1 to an interval of approximately 7 cM, between loci D21S212 and CD18. To further refine the localization of the EPM1 gene we applied linkage disequilibrium mapping in 38 Finnish families, consisting of 12 with multiple affected children and 26 with a single affected child. Based on existing knowledge about the structure and history of the isolated Finnish population, we estimated genetic distances based on strong linkage disequilibrium to several marker loci and found that EPM1 resides within 0.3 cM or less of loci PFKL, D21S25 and D21S154. As this genetic distance translates into a likely physical distance of 300 kb or less, these data provide a basis for highly focused attempts to clone EPM1.
Modélisation de l'élasticité d'une pâte de ciment au jeune âge (2007)

ABSTRACT Concrete is a complex multi-scale composite involving multi-physics processes. As it is the only evolving component, the cement paste has a major influence on the mechanical properties of concrete at early age. The homogenization theory for disordered media is used in order to model the development of the elastic properties of a cement paste during its hydration. The morphological model refers to two types of C-S-H distinguished by many authors: high density C-S-H or inner products build up layers surrounding the anhydrous particles, while low density C-S-H or outer products play the role of a porous matrix. The effective Young's modulus evolution with respect to the degree of hydration proves to be in excellent agreement with the experimental results available in the literature.
Growth factor independence underpins a paroxysmal, aggressive Wnt5aHigh/EphA2Low phenotype in glioblastoma stem cells, conducive to experimental combinatorial therapy (2022)

We show how the preservation of a mitogen-independent phenotype in GSCs plays a central role in determining the exacerbated tumorigenic and high mobility features distinctive of GBM. The exploitation of the I-GSCs' peculiar features shown here offers new ways to identify novel, GSCs-specific effectors, whose modulation can be used in order to identify novel, potential molecular therapeutic targets. Furthermore, we show how the combined use of PepA, the anti-Wnt5a drug, and of ephrinA1-Fc to can hinder GSCs' lethality in a clinically relevant xenogeneic in vivo model thus being conducive to perspective, novel combinatorial clinical application.
Dynamics of an ultracold cascade three-level atom interacting with a two-mode cavity field (2002)

The interaction between an ultracold cascade three-level atom and a two-mode cavity field has been studied. The effects of the centre-of-mass motion, the cavity length, the coupling constants, the initial field states and the initial field intensity on the atomic dynamics have been examined. We have found that the population probabilities show dependence on the interaction time in the fast-atom region while they show dependence on the interaction length in the slow-atom region. The variations of the probabilities versus the cavity length show resonant peaks, and the peaks become sharper as the atom moves more slowly. The coupling constants, the initial field states and the initial field intensity also influence the atomic dynamics significantly. The two transitions are competitive for the atomic probability in the middle state, while they are cooperative for that in the lower state.