gebhart/patrepeval huggingface dataset:
Demand-driven type inference with subgoal pruning (2005)

Highly dynamic languages like Smalltalk do not have much static type\ninformation immediately available before the program runs. Static\ntypes can still be inferred by analysis tools, but historically, such\nanalysis is only effective on smaller programs of at most a few tens\nof thousands of lines of code.\n\nThis dissertation presents a new type inference algorithm, DDP,\nthat is effective on larger programs with hundreds of thousands\nof lines of code. The approach of the algorithm borrows from the\nfield of knowledge-based systems: it is a demand-driven algorithm that\nsometimes prunes subgoals. The algorithm is formally described,\nproven correct, and implemented. Experimental results show that the\ninferred types are usefully precise. A complete program understanding\napplication, Chuck, has been developed that uses DDP type\ninferences.\n\nThis work contributes the DDP algorithm itself, the most thorough\nsemantics of Smalltalk to date, a new general approach for analysis\nalgorithms, and experimental analysis of DDP including\ndetermination of useful parameter settings. It also contributes\nan implementation of DDP, a general analysis framework for\nSmalltalk, and a complete end-user application that uses DDP.
Epithelial apoptosis in mechanistically distinct methods of injury in the murine small intestine. (2007)

Gut epithelial apoptosis is involved in the pathophysiology of multiple diseases. This study characterized intestinal apoptosis in three mechanistically distinct injuries with different kinetics of cell death. FVB/N mice were subjected to gamma radiation, Pseudomonas aeruginosa pneumonia or injection of monoclonal anti-CD3 antibody and sacrificed 4, 12, or 24 hours post-injury (n=10/time point). Apoptosis was quantified in the jejunum by hematoxylin and eosin (H&E), active caspase-3, terminal deoxynucleotidyl transferase dUTP-mediated nick end labeling (TUNEL), in situ oligoligation reaction (ISOL,) cytokeratin 18, and annexin V staining. Reproducible results were obtained only for H&E, active caspase-3, TUNEL and ISOL, which were quantified and compared against each other for each injury at each time point. Kinetics of injury were different with early apoptosis highest following radiation, late apoptosis highest following anti CD3, and more consistent levels following pneumonia. ISOL was the most consistent stain and was always statistically indistinguishable from at least 2 stains. In contrast, active caspase-3 demonstrated lower levels of apoptosis, while the TUNEL assay had higher levels of apoptosis in the most severely injured intestine regardless of mechanism of injury. H&E was a statistical outlier more commonly than any other stain. This suggests that regardless of mechanism or kinetics of injury, ISOL correlates to other quantification methods of detecting gut epithelial apoptosis more than any other method studied and compares favorably to other commonly accepted techniques of quantifying apoptosis in a large intestinal cross sectional by balancing sensitivity and specificity across a range of times and levels of death.
IMMUNIZATION WITH LIVE TYPE 4 ADENOVIRUS: DETERMINATION OF INFECTIOUS VIRUS DOSE AND PROTECTIVE EFFECT OF ENTERIC INFECTION1 (1967)

Journal Article IMMUNIZATION WITH LIVE TYPE 4 ADENOVIRUS: DETERMINATION OF INFECTIOUS VIRUS DOSE AND PROTECTIVE EFFECT OF ENTERIC INFECTION Get access R. R. GUTEKUNST, R. R. GUTEKUNST Search for other works by this author on: Oxford Academic PubMed Google Scholar R. J. WHITE, R. J. WHITE Search for other works by this author on: Oxford Academic PubMed Google Scholar W. P. EDMONDSON, W. P. EDMONDSON Search for other works by this author on: Oxford Academic PubMed Google Scholar R. M. CHANOCK R. M. CHANOCK 2Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesda, Maryland 20014. Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 86, Issue 2, September 1967, Pages 341–349, https://doi.org/10.1093/oxfordjournals.aje.a120744 Published: 01 September 1967 Article history Revision received: 07 November 1966 Published: 01 September 1967
Understanding the natural biology of kidney cancer: implications for targeted cancer therapy. (2007)

During the past several decades, there has been a significant increase in the understanding of the biology, clinical behavior, and prognostic factors of renal cell carcinoma (RCC). Such progress has led to greater sophistication in the diagnosis and classification of RCC. Here, we review recent advances in our knowledge of the biologic characteristics of RCC that have resulted in notable achievements in staging, prognosis, patient selection, and treatment.
Data Supplement from Redirected T-Cell Killing of Solid Cancers Targeted with an Anti-CD3/Trop-2–Bispecific Antibody Is Enhanced in Combination with Interferon-α (2023)

&lt;p&gt;Methods for DNL conjugation of (E1)-3s and its biochemical characterization. These include SE-HPLC, LC-MS and Biacore methods.&lt;/p&gt;
Perianal Crohnʼs disease findings other than fistulas in a population-based cohort (2011)

Perianal lesions other than fistulas occurred frequently during the clinical course of CD. Female gender and extraintestinal manifestations were associated with increased risks for perianal lesions other than fistulas, while older age at diagnosis was associated with a slightly decreased risk.
Setipiprant, a selective CRTH2 antagonist, reduces allergen‐induced airway responses in allergic asthmatics (2014)

Setipiprant at multiple oral doses was well tolerated and reduced both the allergen-induced LAR and the associated AHR in allergic asthmatics. Our findings confirm that CRTH2 may be a promising target for the treatment of allergic disorders.
EBOV Protection Is Supported by T Cell-Dependent Humoral Responses But Is Not Requisite for Survival (2016)

Abstract : Despite agreement across Ebola virus (EBOV) vaccine platforms of a requisite role for antibody-dependent protection and extensive efforts in development of antibody therapy against lethal EBOV infection, the establishment of protective EBOV B cell responses has yet to be fully described. Previously, we demonstrated that vaccination of mice, guinea pigs, or nonhuman primates with virus-like particles (eVLP) expressing EBOV glycoprotein (GP) elicited full protection. More recently, we illustrated that inclusion of the Toll-like receptor 3 agonist and clinical grade adjuvant, Hiltonol, enhanced GP-specific antibody titers and durable EBOV protection. Here in, we outline that the cellular events mediating EBOV humoral responses are exclusively generated from T-cell dependent mechanisms. We show that Hiltonol both augmented and sustained eVLP-mediated GC B cell formation and increased antigen-specific B cell frequencies. In addition, we define the in-vivo requirement of T-cell follicular help and CD40-CD40L signaling in establishing EBOV GP antibody responses. Finally and unexpectedly, we demonstrate that while EBOV antibody responses can enhance protection, survival in the complete absence of antibodies can be achieved; however, B cells are obligate.
Supplementary Figures 1-7, Tables 1-2 from miR-221 Silencing Blocks Hepatocellular Carcinoma and Promotes Survival (2023)

&lt;p&gt;PDF file - 106K&lt;/p&gt;
Acquired von Willebrand disease caused by an autoantibody selectively inhibiting the binding of von Willebrand factor to collagen (1994)

An 82-year-old man with a low-grade malignant non-Hodgkin lymphoma and an IgG3 lambda monoclonal gammopathy presented a recently acquired bleeding tendency, characterized by recurrent epistaxis, easy bruising, and episodes of melena, requiring packed red blood cell transfusions. Coagulation studies showed a von Willebrand factor (vWF) defect (Ivy bleeding time, &gt; 15 minutes; vWF antigen [vWF:Ag], 0.08 U/mL; ristocetin cofactor activity [vWF:RCoF], &lt; 0.05 U/mL; collagen binding activity [vWF:CBA], 0.01 U/mL; absence of the high molecular weight multimers of vWF on multimeric analysis). Mixing experiments suggested the presence of an inhibitor directed against the vWF:CBA activity of vWF without significantly inhibiting the FVIII:C, vWF:Ag, and vWF:RCoF activities. The inhibitor was identified as an antibody of the IgM class by immunoabsorption of vWF and inhibitor-vWF complexes from the plasma of the patient. Subsequent immunoprecipitation experiments using recombinant fragments of vWF showed that the inhibitor reacted with both the glycoprotein Ib binding domain (amino acids [aa] 422–826) and the A3 (aa 909–1112) domain of vWF, but not with the A2 (aa 716–908) or D4 (aa 1183–1535) domains. We conclude that the IgM autoantibody inhibits the vWF:CBA activity by reacting with an epitope present on both the glycoprotein Ib and A3 domains of vWF.
Parameter estimation of random modulated chirp signals (2002)

Source or target tracking is an important problem in radar and sonar. If the target is moving with significant velocity, the received signal is nonstationary because of the time-varying delay. Usually the transmitted signal s(t) is narrowband with carrier frequency w, so that the delay does not distort the amplitude but affects only the carrier term. The signal received at the observation sensor is: x(t)=m(t)s(t-/spl phi/(t))+n(t)/spl ap/m(t)s(t)e(jw/sub 0spl phi/(t))+n(t) (1) where, n(t) is the zero-mean, stationary additive noise which models the sensor noise and other ocean interference. The transmitted signal s(t) undergoes random multiplicative transformations m(t) due to platform motion and vibration, ocean effects, and target scintillation. If the target or source is moving with constant acceleration, the time-varying delay is a second-order polynomial /spl phi/(t)=d/sub e/+d/sub l/t+d/sub 2/t/sup 2/, (2) with the coefficients related to its range, velocity, and acceleration. Hence, tracking the target is equivalent to estimating the coefficients of the phase polynomial /spl phi/(t). Such signals also arise in continuous phase modulation and passive array processing with moving sources. The process in (1) is nonstationary and has time-varying second and higher-order moments and cumulants. However, specific higher-order cumulants of it are (almost) periodic with the period being related to the polynomial coefficients. The Fourier Series coefficient of the time-varying correlation called the cyclic cumulant conveys information about the time-variation and can be exploited to estimate the time-varying delay via the coefficients.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Erratum: Bharti D., et al. In Vitro Generation of Oocyte Like Cells and Their In Vivo Efficacy: How Far We have been Succeeded. Cells 2020, 9, 557 (2020)

The wrong grant number was erroneously entered in the original manuscript and needs to be changed from NRF-2017R1D1A1B03035677 to NRF-2019R1I1A3A01060073 in [...].
Dendritic Cell Immunotherapy for HIV-1 Infection Using Autologous HIV-1 RNA (2016)

Despite the induction of HIV-specific effector/memory CD8 T-cell responses, no antiviral effect was seen after the administration of AGS-004 when compared with placebo.
Multimodal 4-arylchromene derivatives with microtubule-destabilizing, anti-angiogenic, and MYB-inhibitory activities (2023)

<b>Aim:</b> Efficient and readily available anticancer drugs are sought as treatment options. For this reason, chromene derivatives were prepared using the one-pot reaction and tested for their anticancer and anti-angiogenic properties. <b>Methods:</b> 2-Amino-3-cyano-4-(aryl)-7-methoxy-4H-chromene compounds (2A-R) were repurposed or newly synthesized via a three-component reaction of 3-methoxyphenol, various aryl aldehydes, and malononitrile. We performed assays to study the inhibition of tumor cell growth [3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromid (MTT) assay], effects on microtubules (immunofluorescence), cell cycle (flow-activated cell sorting analysis), angiogenesis (zebrafish model), and MYB activity (luciferase reporter assay). Fluorescence microscopy was applied for localization studies via copper-catalyzed azide-alkyne click reaction of an alkyne-tagged drug derivative. <b>Results:</b> Compounds 2A-C and 2F exhibited robust antiproliferative activities against several human cancer cell lines (50% inhibitory concentrations in the low nanomolar range) and showed potent MYB inhibition. The alkyne derivative 3 was localized in the cytoplasm after only 10 min of incubation. Substantial microtubule disruption and G2/M cell-cycle arrest were observed, where compound 2F stood out as a promising microtubule-disrupting agent. The study of anti-angiogenic properties showed that 2A was the only candidate with a high potential to inhibit blood vessel formation <i>in vivo</i>. <b>Conclusion:</b> The close interplay of various mechanisms, including cell-cycle arrest, MYB inhibition, and anti-angiogenic activity, led to identifying promising multimodal anticancer drug candidates.
Discovery of Small Peptide Antagonists of PED/PEA15–D4α Interaction from Simplified Combinatorial Libraries (2011)

Most biological processes involve permanent and temporary interactions between different proteins: protein complexes often play key roles in human diseases and, as a consequence, molecules that prevent protein-protein interactions can be potential new therapeutic agents to treat diseases. Here, we describe a simplified approach by which small synthetic peptide libraries were screened to identify the inhibitors of the complex between phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes15 (PED/PEA15) and D4α, a functional domain of the phospholipase D1, that is involved in the molecular mechanisms of insulin resistance occurring in type 2 diabetes. By using an enzyme-linked immunosorbent assay (ELISA)-based screening, performed on a fully automated platform, we analyzed two simplified peptide libraries in a positional scanning format. This screening led to the identification of small peptides able to inhibit PED/PEA15-D4α interaction. The selection of inhibitors was carried out employing combined competitive and direct experiments, through ELISA and surface plasmon resonance techniques, providing peptides with IC(50) values in the micromolar range. Our results showed that the protein complex PED/PEA15-D4α is susceptible to peptides having H-donor groups and aromatic rings on specific positions. These small sequences can be considered as promising scaffolds that could be converted into higher-affinity inhibitor compounds.
Application of flowing thermal lens to flow sensors for microchemical chips (2005)

A flowing thermal lens microflow velocimeter, in which a photothermally produced local refractive index change (a thermal lens) was used as a tracer, was developed for microchemical chips made of glass. A laser pulse was focused with a microlens on a liquid flow inside a microchannel, and a thermal lens was produced. The thermal lens drifted downstream and was detected using another beam. The velocity was calculated from the time required for the thermal lens to travel between the two points. The microflow velocimeters enabled non-contact measurement with only slight disturbance to the microfluid possible and were suitable for microchemical systems.
CD40 Ligand Stimulation of Multiple Myeloma Cells Results in Upregulation of Surface Expressed Heat Shock Proteins and Increased Antigenicity. (2004)

Abstract Effective immune-based therapies against the plasma cell malignancy, multiple myeloma (MM), are currently lacking. Identification of novel antigens (Ag) on the surface of MM cells to use as cellular targets for the destruction of cancer cells by the body’s immune system has been of great interest. We and others have demonstrated that CD40 stimulation of MM cells results in marked upregulation of membrane bound proteins such as Ku86. Using CD40 triggered MM cells as immunogens and hybridoma technology; we generated a monoclonal antibody (mAb), 6D11, that recognizes a CD40 induced cell membrane Ag on MM cells. This Ag is detectable on the surface of MM cells using indirect immunofluorescence flow cytometric analysis. Moreover, in Western immunoblotting assays, 6D11 mAb reacts with a 94 kDa protein, which is strongly associated with a 78 kDa protein. Using high performance liquid chromatography and protein microsequencing, we confirm that these proteins are the heat shock proteins (HSP), glucose-regulated peptide 94 (GRP94) and GRP78, respectively. These data were confirmed using co-immunprecipitation experiments. Furthermore, we demonstrate through indirect immunofluorescence flow cytometric analysis and quantitative real time reverse transcription polymerase chain reaction (RQ-PCR) that CD40 ligand (CD40L) stimulation of MM cells results in rapid upregulation of both GRP94 and GRP78. Since HSPs have been shown to play a role in both Ag presentation, as well as the intracellular transport of cellular Ags, it is tempting to speculate that cell membrane expression of tumor-specific peptides could also be induced via CD40 triggering. Accordingly, CD40 induced cell membrane HSP expression resulted in increased antigenicity as determined by increased co-stimulatory molecule expression on Ag presenting cells (APC) and by increased immunoreactivity in mixed lymphocyte reactions (MLR). This suggests that CD40 induced HSP expression may indeed result in increased recognition of MM cancer by the immune system. Our study therefore supports the development of CD40-based targeted cell therapies against MM.
Capacitive Interfaces for MEMS (2004)

This chapter contains sections titled: Introduction Capacitive Sensing and Actuation Capacitance-to-Voltage Converters Electrostatic Force-feedback Electromechanical Sigma-Delta Interfaces Conclusions References
Space Solar Cell Research and Development Projects at Emcore Photovoltaics (2007)

The GaInP2/InGaAs/Ge triple junction device lattice matched to germanium has achieved the highest power conversion efficiency and the most commercial success for space applications [1]. What are the practical performance limits of this technology? In this paper we will describe what we consider to be the practical performance limits of the lattice matched GaInP2/InGaAs/Ge triple junction cell. In addition, we discuss the options for next generation space cell performance.
Multiple Selection Approximation for improved spatio-temporal prediction in video coding (2010)

In this contribution, a novel spatio-temporal prediction algorithm for video coding is introduced. This algorithm exploits temporal as well as spatial redundancies for effectively predicting the signal to be encoded. To achieve this, the algorithm operates in two stages. Initially, motion compensated prediction is applied on the block being encoded. Afterwards this preliminary temporal prediction is refined by forming a joint model of the initial predictor and the spatially adjacent already transmitted blocks. The novel algorithm is able to outperform earlier refinement algorithms in speed and prediction quality. Compared to pure motion compensated prediction, the mean data rate can be reduced by up to 15% and up to 1.16 dB gain in PSNR can be achieved for the considered sequences.
Cerium Oxide Nanoparticles Decorated SAM Modified Gold Electrode for ROS Biosensing (2014)

Informatics is a new and flourishing sector in biomedical engineering with biosensors playing a crucial, central role. Self-Assembled monolayer (SAM) based biosensors constitute a large portion of these due to their simplistic design and broad application. Herein we present a cerium oxide nanoparticle (CNPs) functionalized SAM biosensor for amperometric reactive oxygen species (ROS) detection. SAM-based biosensors often times employ enzymes to detect analytes. These sensors are limited to particular pH, salt concentration, and temperature conditions specific to normal conditions for the enzyme. Operation outside these conditions can cause irreversible protein denature and loss of sensation. It is well established that CNPs has unique oxidase like activity.[1, 2] Therefore, by using inorganic CNPs, this sensor is able to operate at adverse conditions without loss of sensitivity. The inorganic material also prevents phase interactions which could result in bio-fouling. The presented sensor is able to detect extremely low concentrations for H2O2 and with high selectivity. Bare gold electrode was used as a substrate and coated with an SAM of mercaptododecanoic acid (MDDA), a well-established SAM polymer. The carboxylic terminus of MDDA was used for CNPs conjugation. Cyclic voltammetry and chronoamperometric testing was performed in phosphate-buffered saline and potassium hexacyanoferrate, a well-known redox couple. Hydrogen peroxide was infused in micromolar concentrations for sensing. Comparison to bare gold electrodes shows orders of magnitude greater sensitivity to [H2O2] and significantly more defined analyte selectivity. References: 1. Hirst, S.M., et al., Anti inflammatory Properties of Cerium Oxide Nanoparticles. Small, 2009. 5(24): p. 2848-2856. 2. Gaynor, J.D., et al., Enzyme-free Detection of Hydrogen Peroxide from Cerium Oxide Nanoparticles Immobilized on Poly (4-vinylpyridine) Self–Assembled Monolayers. J. Mater. Chem. B, 2013.
Chemical Synthesis of Proteins (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
59‐5: Simultaneous Transfer and Bonding (SITRAB) Process for Mini‐LED Display (2021)

We developed a simultaneous transfer and bonding (SITRAB) process based on laser‐assisted bonding with compression (LABC) and our proprietary SITRAB adhesive technology. As its name implies, the SITRAB process performs transfer and bonding simultaneously, unlike the conventional sequential process, in which transfer is followed by the bonding process. SITRAB's process time is less than 6 s. The SITRAB adhesive was developed in the form of a paste and a film, and an appropriate type of adhesive can be applied depending on the applications. The adhesive was proved to be applied as SnAg and In solders during the SITRAB process. Two 35 × 35 arrays of 80 µm × 130 µm sized mini LEDs with a 288 µm pitch with SnAg or In interconnects have been successfully processed. The repair process based on SITRAB technology was proposed and confirmed experimentally.
Evolution of cooperation in populations with heterogeneous multiplicative resource dynamics (2019)

In the pooling and sharing mechanism of multiplicatively grown individual resources, the evolution of cooperation is uniquely determined by the physical traits of the population. If the entities in the population exhibit homogeneous traits, cooperation is always favored. However, if there is heterogeneity within the population, the evolution of cooperation is dependent on both the interaction structure and the decision making rules implemented by the entities. Here, we perform a detailed analysis on the role of the interaction structures in the evolutionary stability of cooperation in heterogeneous multiplicative environments. We utilize this analysis to examine the applicability of a simple state-based decision making rule in a variety of settings. We thereby show that the introduced rule leads to steady state cooperative behavior that is always greater than or equal to the one predicted by evolutionary stability analysis and discuss relevant implications to natural and artificial systems.
Hybrid transmissive optical star couplers with gain using fiber amplifiers (1993)

A hybrid transmissive star coupler incorporating fiber amplifiers for wavelength-division multiplexed/frequency-division multiplexed (WDM/FDM) networks is proposed. It is found that the total fiber length and conduit length required for this hybrid star coupler/network can be reduced tremendously compared with either the centralized or the distributed cases. Furthermore, this coupler is easier to construct and more cost-effective.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>