gebhart/patrepeval huggingface dataset:
PED: Proof-Guided Error Diagnosis by Triangulation of Program Error Causes (2008)

Error diagnosis, which is the process of identifying the root causes of bugs in software, is a time-consuming process. In general, it is hard to automate error diagnosis due to the unavailability of a full ldquogoldenrdquo specification of the system behavior in realistic software development. We propose a repair-based proof-guided error diagnosis (PED) framework, that provides a first-line attack to find the root causes of the errors in programs by pin-pointing the possible error-sites (buggy statements), and suggesting possible repair fixes. Our framework does not need a complete system specification. Instead, it automatically ldquominesrdquo partial specifications of the intended program behavior from the proofs obtained by static program analysis for standard safety checkers. It uses these partial specifications along with the multiple error traces provided by a model checker to narrow down the possible error sites. It also exploits inherent correlations among the program statements. To capture common programming mistakes, it directs the search to those statements that could be buggy due to simple copy-paste operations or syntactic mistakes such as using les instead of <. To further improve debugging, it prioritizes the repair solutions. We implemented and integrated the PED tool as a plug-in module to a software verification framework. We show the efficacy of such a framework on public benchmarks.
A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection (2021)

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) uses full-length angiotensin converting enzyme 2 (ACE2), which is membrane bound, as its initial cell contact receptor preceding viral entry. Here we report a human soluble ACE2 variant fused with a 5kD albumin binding domain (ABD) and bridged via a dimerization motif hinge-like 4-cysteine dodecapeptide, which we term ACE2 1-618-DDC-ABD. This protein is enzymatically active, has increased duration of action in vivo conferred by the ABD-tag, and displays 20-30-fold higher binding affinity to the SARS-CoV-2 receptor binding domain than its des-DDC monomeric form (ACE2 1-618-ABD) due to DDC-linked dimerization. ACE2 1-618-DDC-ABD was administered for 3 consecutive days to transgenic k18-hACE2 mice, a model that develops lethal SARS-CoV-2 infection, to evaluate the preclinical preventative/ therapeutic value for COVID-19. Mice treated with ACE2 1-618-DDC-ABD developed a mild to moderate disease for the first few days assessed by a clinical score and modest weight loss. The untreated control animals, by contrast, became severely ill and had to be sacrificed by day 6/7 and lung histology revealed extensive pulmonary alveolar hemorrhage and mononuclear infiltrates. At 6 days, mortality was totally prevented in the treated group, lung histopathology was improved and viral titers markedly reduced. This demonstrates for the first time in vivo the preventative/ therapeutic potential of a novel soluble ACE2 protein in a preclinical animal model.
A core-extended naphthalene diimide as a p-channel semiconductor (2011)

A novel naphthalene diimide with a fully conjugated, extended π-core was synthesized in a one-pot, two-step reaction. This organic semiconductor exhibits ambipolar transport properties with a large hole mobility of 0.56 cm(2) V(-1) s(-1) and a current on/off ratio of 10(6) in bottom-gate, top-contact thin-film transistors prepared by vacuum deposition.
Fluorescence Versus White-Light Bronchoscopy for Detection of Preneoplastic Lesions: a Randomized Study (2001)

LIFE was more sensitive than WLB in detecting preneoplastic bronchial changes in high-risk subjects. The prognostic implication of this finding is not yet clear.
Supplementary Methods and References from Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1 (2023)

&lt;p&gt;Description of additional methods and procedures used in the study. Also includes Supplementary References.&lt;/p&gt;
Solution‐Phase Metal Atom Preparation of Catalytically Active Zeolite‐Encapsulated Metal Clusters; Characterization and Application to the Selective Reduction of CO to Butene (1983)

Abstract The complete manuscript of this communication appears in: Angew. Chem. Suppl. 1983 , 898. DOI: 10.1002/anie.198308980
Composite materials on the basis of phenylenecarboxylate framework MOF-5 and calix[4]arenes with various structures (2011)

A comparative study of the texture and adsorption characteristics of newly synthesized composite materials based on 1,4-benzenedicarboxylate metal-organic framework MOF-5 and calix[4]arenes with various structures was performed.
The Further Improvement of the Ionic Thermoelectric Generator (2014)

The power conversion efficiency of the proton-conductive thermoelectric cell is improved by the unidirectional orientation of ionic conductivity in the electrospun Nafion cell. The thermoelectric performance of nanofibers is experimentally demonstrated.
Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A (2002)

We have identified widerborst (wdb), a B' regulatory subunit of PP2A, as a conserved component of planar cell polarization mechanisms in both Drosophila and in zebrafish. In Drosophila, wdb acts at two steps during planar polarization of wing epithelial cells. It is required to organize tissue polarity proteins into proximal and distal cortical domains, thus determining wing hair orientation. It is also needed to generate the polarized membrane outgrowth that becomes the wing hair. Widerborst activates the catalytic subunit of PP2A and localizes to the distal side of a planar microtubule web that lies at the level of apical cell junctions. This suggests that polarized PP2A activation along the planar microtubule web is important for planar polarization. In zebrafish, two wdb homologs are required for convergent extension during gastrulation, supporting the conjecture that Drosophila planar cell polarization and vertebrate gastrulation movements are regulated by similar mechanisms.
Time-resolved pump-probe experiments with subwavelength lateral resolution (1996)

We demonstrate picosecond time-resolved pump-probe experiments with subwavelength resolution using a reflection near-field scanning optical microscope (NSOM). The sample was a laterally patterned gold nanostructure. Strain-induced reflectivity changes as low as ΔR/R≊10−4 were detected in the near-field.
Polyurethane/Polylactide-Based Electrospun Nonwovens as Carriers for Human Adipose-Derived Stromal Stem Cells and Chondrogenic Progenitor Cells (2016)

Articular cartilage dysfunctions are major cause of pain and disability and lead to serious health complications. Cell-based therapies are proposed as treatment methods for cartilage regeneration. In this study, we proposed polyurethane/poly(L-lactide-co-D, L-lactide)-based electrospun nonwovens as carriers for the delivery of human adipose-derived stromal stem cells. We found that 6:4 and 8:2 polyurethane/poly(L-lactide-co-D, L-lactide) initially enhance proliferative rate of human adipose-derived stromal stem cells, shorten their population doubling time, promote creation of functional chondrogenic nodules during chondrogenic differentiation, improve the collagen-2-to-collagen-1 protein ratio, and upregulate the expression of collagen-2 and aggrecan genes.
IGBTs working in the NDR region of their I-V characteristics (2015)

This paper demonstrates the detailed work on high voltage IGBTs using simulations and experiments. The current-voltage characteristics were measured up to the break through point in forward bias operating region at two different temperatures for a 50 A/4.5 kV rated IGBT chip. The experimentally measured data were in good agreement with the simulation results. It was also shown that the IGBTs are able to clamp high collector-emitter voltages although a low gate turn-off resistor in combination with a high parasitic inductance was applied. Uniform 4-cell and 8-cell IGBT models were created into the TCAD device simulator to conduct an investigation. An engendered filamentation behaviour during short-circuit turn-off was briefly reviewed using isothermal as well as thermal simulations and semiconductor approaches for development of filaments. The current filament inside the active cells of the IGBT is considered as one of the possible destruction mechanism for the device failure.
Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex (2016)

HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn<sup>2+</sup>-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.
Measurements of four-lepton production in pp collisions at s=8 TeV with the ATLAS detector (2015)

The four-lepton (4 , = e, ) production cross section is measured in the mass range from 80 to 1000 GeV using 20.3 fb -1 of data in pp collisions at s = 8 TeV collected with the ATLAS detector at the LHC. The 4 events are produced in the decays of resonant Z and Higgs bosons and the nonresonant Z Z continuum originating from q q, gg, and qg initial states. A total of 476 signal candidate events are observed with a background expectation of 26.2 3.6 events, enabling the measurement of the integrated cross section and the differential cross section as a function of the invariant mass and transverse momentum of the four-lepton system.
Subgroup Analyses of Kte-X19, an Anti-CD19 Chimeric Antigen Receptor (CAR) T-Cell Therapy, in Adult Patients (Pts) with Relapsed/Refractory B-Cell Acute Lymphoblastic Leukemia (R/R B-ALL) in Zuma-3 (2023)

Patients with hematologic malignancies have both an increased risk for SARS-CoV2 infections and higher morbidity/mortality. They have lower seroconversion rates post-vaccination, potentially leading to inferior COVID-19 outcomes, despite vaccination. We consequently evaluated the clinical outcomes of COVID-19 infections in 243 vaccinated and 175 unvaccinated patients with hematologic malignancies. Hospitalization rates were lower in the vaccinated group when compared to the unvaccinated group (31.3% vs 52.6%, p≤0.001). However, the rates of COVID-associated death were similar at 7.0% and 8.6% in vaccinated and unvaccinated patients, respectively (p=0.61). By univariate logistic regression, females (odds ratio (OR) 2.77, p=0.01), older patients (OR 1.03, p=0.02), and individuals with higher modified Charlson Co-morbidity Index scores (OR 1.32, p=0.003) were at a higher risk of death from COVID-19 infections. To account for the non-randomized nature of COVID-19 vaccination status, a propensity score weighting approach was utilized. In the final propensity weighted model, vaccination status was not significantly associated with the risk of death from COVID-19 infections (OR 0.70, p=0.36) but associated with the risk of hospitalizations (OR 0.38, p<0.001). The predicted benefit of vaccination was an absolute decrease in the probability of death and hospitalization from COVID-19 infections by 2.3% and 22.9%, respectively. In conclusion, COVID-19 vaccination status in patients with hematologic malignancies was associated with a decreased risk of hospitalization but not associated with a decreased risk of death from COVID-19 infections in the pre-Omicron era. Protective strategies, in addition to immunization, are warranted in this vulnerable patient population.
49.3 Tb/s Transmission Over 9100 km Using C+L EDFA and 54 Tb/s Transmission Over 9150 km Using Hybrid-Raman EDFA (2015)

We review recent high capacity ultralong haul demonstrations using amplification schemes with extended C+L optical bandwidth and optimized nonlinear performance. These demonstrations achieve 49.3 Tb/s capacity over 9100 km with the use of C+L EDFAs and 54 Tb/s capacity over 9150 km using hybridRaman EDFAs. Using the same hybrid-Raman EDFAs, a capacity of 52.2 Tb/s over 10 230 km (534 Pb/s*km) was also demonstrated. Different combinations of three 16QAM-based coded modulation schemes with spectral efficiencies SE = 4.86, 5.4/5.45, 6.14 bit/s/Hz were used in order to maximize capacity for each amplification scheme and transmission distance. We also compare the merits of optimized transmission performance of hybrid Raman-EDFA and C+L EDFA amplification schemes based on our loop experiments. At the nonlinear limit, the use of hybrid Raman-EDFA provides a modest 9.5% increase in capacity at a cost of ~2× higher electrical power.
Biosynthesis of an unusual copolyester (10 mol % 3-hydroxybutyrate and 90 mol % 3-hydroxyvalerate units) in Alcaligenes eutrophus from pentanoic acid (1987)

Bacterial poly(3-hydroxybutyrate-co-3-hydroxyvalerate) esters with a wide range of compositions (0–90 mol % 3-hydroxyvalerate units) have been isolated from Alcaligenes eutrophus grown in nitrogen-free culture media containing pentanoic acid and glucose.
Publisher Correction: Primary functional brain connections associated with melancholic major depressive disorder and modulation by antidepressants (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Electrostatic Stabilization of Colloids in Carbon Dioxide:  Electrophoresis and Dielectrophoresis (2005)

Over the past decade, steric stabilization has been achieved for a variety of inorganic and organic colloids in supercritical fluid carbon dioxide (scCO2). Herein we demonstrate that colloids may also be stabilized in CO2 by electrostatic forces, despite the ultralow dielectric constant of 1.5. Zeta potentials of micrometer-sized water droplets, measured in a microelectrophoresis cell, reached -70 mV corresponding to a few elementary charges per square micrometer of droplet surface. This degree of charge was sufficient to stabilize water/CO2 emulsions for an hour, even with water volume fractions of 5%. Hydrogen ions partition preferentially, relative to bicarbonate ions, from the emulsion droplets to the cores of surfactant micelles in the diffuse double layer surrounding the droplets. The micelles, formed with a low molecular weight branched hydrocarbon surfactant, prevent ion pairing of the hydrogen counterions to the negatively charged emulsion droplets. Dielectrophoresis of the water droplets at a frequency of 60 Hz leads to chains containing a dozen droplets with lengths of 50 mum. The ability to form electrostatically stabilized colloids in carbon dioxide is particularly useful in practical applications, because steric stabilization in CO2 is often limited by the poor solvation of the stabilizers.
Disruption of primary auditory cortex by synchronous auditory inputs during a critical period (2002)

In the primary auditory cortex (AI), the development of tone frequency selectivity and tonotopic organization is influenced by patterns of neural activity. Introduction of synchronous inputs into the auditory pathway achieved by exposing rat pups to pulsed white noise at a moderate intensity during P9-P28 resulted in a disrupted tonotopicity and degraded frequency-response selectivity for neurons in the adult AI. The latter was manifested by broader-than-normal tuning curves, multipeaks, and discontinuous, tone-evoked responses within AI-receptive fields. These effects correlated with the severe impairment of normal, developmental sharpening, and refinement of receptive fields and tonotopicity. In addition, paradoxically weaker than normal temporal correlations between the discharges of nearby AI neurons were recorded in exposed rats. In contrast, noise exposure of rats older than P30 did not cause significant change of auditory cortical maps. Thus, patterned auditory inputs appear to play a crucial role in shaping neuronal processing/decoding circuits in the primary auditory cortex during a critical period.
Vaccine Potentiation by Combination Adjuvants (2014)

Adjuvants are crucial components of vaccines. They significantly improve vaccine efficacy by modulating, enhancing, or extending the immune response and at the same time reducing the amount of antigen needed. In contrast to previously licensed adjuvants, current successful adjuvant formulations often consist of several molecules, that when combined, act synergistically by activating a variety of immune mechanisms. These "combination adjuvants" are already registered with several vaccines, both in humans and animals, and novel combination adjuvants are in the pipeline. With improved knowledge of the type of immune responses needed to successfully induce disease protection by vaccination, combination adjuvants are particularly suited to not only enhance, but also direct the immune responses desired to be either Th1-, Th2- or Th17-biased. Indeed, in view of the variety of disease and population targets for vaccine development, a panel of adjuvants will be needed to address different disease targets and populations. Here, we will review well-known and new combination adjuvants already licensed or currently in development-including ISCOMs, liposomes, Adjuvant Systems Montanides, and triple adjuvant combinations-and summarize their performance in preclinical and clinical trials. Several of these combination adjuvants are promising having promoted improved and balanced immune responses.
Engineering cross-presentation in vivo (2003)

Apoptotic bodies deliver antigens (Ags) to the cross-presentation pathways of dendritic cells (DCs), where their presentation has been associated with both the maintenance of tolerance as well as the induction of protective immunity. The manner in which apoptotic bodies are generated, their abundance in relation to local DCs, and the milieu in which they are generated appear to be the major factors determining whether apoptotic bodies will induce CD8(+) T cell activation or anergy. These observations have been extended to the field of vaccination, where the engineered apoptosis of Ag-bearing/loaded cells in vivo has been used to prime strong CD8(+) T cell immunity. This review will examine Ag capture and cross-presentation by DCs, with particular emphasis on the manipulation of apoptotic bodies in vivo for the purpose of vaccination.
Treatment of premenstrual syndrome with gonadotropin‐releasing hormone agonist in a low dose regimen (1999)

GnRH treatment significantly reduced premenstrual depression and irritability. However, low dose GnRH therapy is prone to induce anovulation, particularly with increasing age.
Characterization of the Non-uniform Reaction in Chemically Amplified Calix[4]resorcinarene Molecular Resist Thin Films1 (2011)

The ccc stereoisomer-purified tert-butoxycarbonyloxy-protected calix[4]resorcinarene molecular resists blended with photoacid generator exhibit a non-uniform photoacid-catalyzed reaction in thin films. The surface displays a reduced reaction extent, compared with the bulk, with average surface-layer thickness 7.0 ± 1.8 nm determined by neutron reflectivity with deuterium-labelled tert-butoxycarbonyloxy groups. Ambient impurities (amines and organic bases) are known to quench surface reactions and contribute, but grazing-incidence X-ray diffraction shows an additional effect that the protected molecular resists are preferentially oriented at the surface, whereas the bulk of the film displays diffuse scattering representative of amorphous packing. The surface deprotection reaction and presence of photoacid were quantified by near-edge X-ray absorption fine-structure measurements.
High-throughput label-free molecular fingerprinting flow cytometry (2019)

Flow cytometry is an indispensable tool in biology for counting and analyzing single cells in large heterogeneous populations. However, it predominantly relies on fluorescent labeling to differentiate cells and, hence, comes with several fundamental drawbacks. Here, we present a high-throughput Raman flow cytometer on a microfluidic chip that chemically probes single live cells in a label-free manner. It is based on a rapid-scan Fourier-transform coherent anti-Stokes Raman scattering spectrometer as an optical interrogator, enabling us to obtain the broadband molecular vibrational spectrum of every single cell in the fingerprint region (400 to 1600 cm<sup>-1</sup>) with a record-high throughput of ~2000 events/s. As a practical application of the method not feasible with conventional flow cytometry, we demonstrate high-throughput label-free single-cell analysis of the astaxanthin productivity and photosynthetic dynamics of <i>Haematococcus lacustris</i>.
High-Mobility Thin-Film Transistors with Polycrystalline In–Ga–O Channel Fabricated by DC Magnetron Sputtering (2012)

Oxide thin-film transistors (TFTs) were fabricated using a polycrystalline In–Ga–O (IGO) thin film as the n-channel active layer by direct current magnetron sputtering. The 50-nm-thick IGO TFT showed a field-effect mobility of 39.1 cm2 V-1 s-1, a threshold voltage of 1.4 V, and a subthreshold gate voltage swing of 0.12 V/decade. The polycrystalline IGO thin film showed the cubic bixbyite structure of In2O3 without an obvious preferred orientation. The average grain size of polycrystalline IGO was approximately 10 µm. The high mobility of IGO TFT is related to the In2O3 crystalline phase and large grain size of the IGO film.
Anticounterfeiting Measures Using Portable Raman Spectroscopy (2010)

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Ferret and Pig Models of Cystic Fibrosis: Prospects and Promise for Gene Therapy (2014)

Large animal models of genetic diseases are rapidly becoming integral to biomedical research as technologies to manipulate the mammalian genome improve.The creation of cystic fibrosis (CF) ferrets and pigs is an example of such progress in animal modeling, with the disease phenotypes in the ferret and pig models more reflective of human CF disease than mouse models.The ferret and pig CF models also provide unique opportunities to develop and assess the effectiveness of gene and cell therapies to treat affected organs.In this review, we examine the organ disease phenotypes in these new CF models and the opportunities to test gene therapies at various stages of disease progression in affected organs.We then discuss the progress in developing recombinant replication-defective adenoviral, adeno-associated viral, and lentiviral vectors to target genes to the lung and pancreas in ferrets and pigs, the two most affected organs in CF.Through this review, we hope to convey the potential of these new animal models for developing CF gene and cell therapies.