gebhart/patrepeval huggingface dataset:
Revisiting Android reuse studies in the context of code obfuscation and library usages (2014)

In the recent years, studies of design and programming practices in mobile development are gaining more attention from researchers. Several such empirical studies used Android applications (paid, free, and open source) to analyze factors such as size, quality, dependencies, reuse, and cloning. Most of the studies use executable files of the apps (APK files), instead of source code because of availability issues (most of free apps available at the Android official market are not open-source, but still can be downloaded and analyzed in APK format). However, using only APK files in empirical studies comes with some threats to the validity of the results. In this paper, we analyze some of these pertinent threats. In particular, we analyzed the impact of third-party libraries and code obfuscation practices on estimating the amount of reuse by class cloning in Android apps. When including and excluding third-party libraries from the analysis, we found statistically significant differences in the amount of class cloning 24,379 free Android apps. Also, we found some evidence that obfuscation is responsible for increasing a number of false positives when detecting class clones. Finally, based on our findings, we provide a list of actionable guidelines for mining and analyzing large repositories of Android applications and minimizing these threats to validity
In vivo multiphoton microscopy of deep tissue with gradient index lenses (2004)

Gradient index lenses enable multiphoton microscopy of deep tissues in the intact animal. In order to assess their applicability to clinical research, we present in vivo multiphoton microscopy with gradient index lenses in brain regions associated with Alzheimer's disease and Parkinson's disease in both transgenic and wild-type mice. We also demonstrate microscopy of ovary in wild type mouse using only intrinsic fluorescence and second harmonic generation, signal sources which may prove useful for both the study and diagnosis of cancer.
An outer product neural network for extracting principal components from a time series (2002)

An outer product neural network architecture has been developed based on subspace concepts. The network is trained by auto-encoding the input exemplars, and will represent the input signal by k-principal components, k being the number of neurons or processing elements in the network. The network is essentially a single linear layer. The weight matrix columns orthonormalize during training. The output signal converges to the projection of the input onto a k-principal component subspace, while the residual signal represents the novelty of the input. An application to extracting sinusoids from a noisy time series is given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Role of guanylate cyclase-activating proteins (GCAPs) in setting the flash sensitivity of rod photoreceptors (2001)

The retina's photoreceptor cells adjust their sensitivity to allow photons to be transduced over a wide range of light intensities. One mechanism thought to participate in sensitivity adjustments is Ca(2+) regulation of guanylate cyclase (GC) by guanylate cyclase-activating proteins (GCAPs). We evaluated the contribution of GCAPs to sensitivity regulation in rods by disrupting their expression in transgenic mice. The GC activity from GCAPs-/- retinas showed no Ca(2+) dependence, indicating that Ca(2+) regulation of GCs had indeed been abolished. Flash responses from dark-adapted GCAPs-/- rods were larger and slower than responses from wild-type rods. In addition, the incremental flash sensitivity of GCAPs-/- rods failed to be maintained at wild-type levels in bright steady light. GCAP2 expressed in GCAPs-/- rods restored maximal light-induced GC activity but did not restore normal flash response kinetics. We conclude that GCAPs strongly regulate GC activity in mouse rods, decreasing the flash sensitivity in darkness and increasing the incremental flash sensitivity in bright steady light, thereby extending the rod's operating range.
An empirical study on pertinent aspects of sketch maps for navigation (2012)

Navigation systems which employ sequence-based directions have been found not effective in facilitating the spatial awareness of an environment. Traditional maps are found easily conveying the configuration of spatial objects but having difficulty to facilitate the correspondence to spatial objects in the real world. Sketch maps as schematic map-like representations, have been suggested being a possible way of achieving goals of facilitating both navigation and spatial awareness. Moreover, sketch maps as externalizations of cognitive maps have been proved as reliable representations for human spatial thinking. In this study, we investigate the characteristics of directions given in two different forms: sketch maps and turn-by-turn instructions (verbal descriptions). The investigation addresses three aspects of spatial relations which are orientation, street topology and sequential order and their representations using qualitative reasoning calculi. The results of this study demonstrate sketch maps as a better direction-giving method and provide insights of applying sketch-map-like components for navigation.
N-Heterocyclic Carbene-Catalyzed Redox Amidations of α-Functionalized Aldehydes with Amines (2007)

A catalytic method for the direct synthesis of carboxylic acid amides from amines and α-functionalized aldehydes is possible through the synergistic role of a N-heterocyclic carbene catalyst and imidazole, affording amides via activated carboxylates catalytically generated via an internal redox reaction of the aldehyde substrates. The use of imidazole or other N-heterocycles as an additive is essential to overcoming imine formation and serves as a uniquely reactive substrate for the generation of an acyl imidazolium intermediate that is converted to the final amide product.
Efficient implementation of wideband multibeam forming network using SOPOT coefficients and multiplier block (2003)

This paper proposes an efficient implementation structure for the wideband multi-beamforming network in a beamspace adaptive array for wideband signals. The filter coefficients of the beamforming network are represented as sum-of-powers-to-two coefficients (SOPOT) and are implemented using the multiplier block technique. The SOPOT representation allows the coefficients to be implemented as limited number of adders and shifters without any multiplications. The redundancy in the SOPOT coefficients is further removed by the multiplier block technique to yield minimum adder realization. Design results show that significant reduction in hardware complexity can be obtained by the proposed structure as compared with the conventional direct form implementation.
Radiotherapeutic for Glucagon-Like Peptide-1Receptor ^ Targeted Therapy for Insulinoma (2007)

Purpose: Although metabolic changes make diagnosis of insulinoma relatively easy, surgical removal is hampered by difficulties in locating it, and there is no efficient treatment for malignant insulinoma.We have previously shown that the high density of glucagon-like peptide-1receptors (GLP-1R) in human insulinoma cells provides an attractive target for molecular imaging and internal radiotherapy. In this study, we investigated the therapeutic potential of (Lys 40 (Ahx-DTPA- 111 In)NH2)-Exendin-4, an 111 In-labeled agonist of GLP-1, in a transgenic mouse model of human insulinoma. Experimental Design: (Lys 40 (Ahx-DTPA- 111 In)NH2)-Exendin-4 was assessed in the Rip1Tag2 mouse model of pancreatic h-cell carcinogenesis, which exhibits a GLP-1R expression compara- ble with human insulinoma. Mice were injected with 1.1, 5.6, or 28 MBq of the radiopeptide and sacrificed 7 days after injection. Tumor uptake and response, the mechanism of action of the radiopeptide, and therapy toxicity were investigated. Results: Tumor uptake was >200 % injected activity per gram, with a dose deposition of 3G y/MBq at 40 pmol (Lys 40 (Ahx-DTPA- 111 In)NH2)-Exendin-4. Other GLP-1R ^ positive organs showed z30 times lower dose deposition. A single injection of (Lys 40 (Ahx-DTPA- 111 In)NH2)- Exendin-4 resulted in a reduction of the tumor volume by up to 94% in a dose-dependent manner without significant acute organ toxicity. The therapeutic effect was due to increased tumor cell apoptosis and necrosis and decreased proliferation. Conclusions: The results suggest that (Lys 40 (Ahx-DTPA- 111 In)NH 2)-Exendin-4 is a promising radiopeptide capable of selectively targeting insulinoma. Furthermore, Auger-emitting radiophar- maceuticals such as 111 In are able to produce a marked therapeutic effect if a high tumor uptake is achieved.
The limited intestinal absorption via paracellular pathway is responsible for the low oral bioavailability of doxorubicin (2012)

1. Doxorubicin exhibited dose-independent pharmacokinetics after intravenous (5-20 mg/kg) and oral (20-100 mg/kg) administration to rats. Nearly all (82.1-99.7%) of the orally administered doxorubicin remained unabsorbed, and the hepatic first-pass extraction ratio and oral bioavailability of doxorubicin were approximately 0.5% and 1%, respectively. Based on these results, it is likely that the primary factor responsible for the low oral bioavailability of doxorubicin is the limited intestinal absorption, rather than the CYP3A4-mediated first-pass metabolism. 2. Moreover, the in vitro transport and cellular uptake studies using Caco-2 cell monolayers have revealed that doxorubicin crosses the intestinal epithelium primarily via the paracellular pathway (accounting for 85.6% of the overall absorptive transport) probably due to its physicochemical properties (hydrophilic cation; pKa = 9.67, log P = -0.5). These results suggest that P-glycoprotein (P-gp)-mediated efflux activity does not play a significant role in limiting the intestinal absorption of doxorubicin, attenuating the absorptive transport by only 5.56-13.2%. 3. Taken together, the present study demonstrated that the limited and paracellular intestinal absorption of doxorubicin was a major factor responsible for its low oral bioavailability, restricting the role of CYP3A4-mediated first-pass metabolism and P-gp-mediated efflux.
Epstein-Barr virus-associated gastric adenocarcinoma. (1992)

The Epstein-Barr virus (EBV) has been detected in certain types of lymphoma and some epithelial neoplasms including nasopharyngeal lymphoepithelioma, and rare lymphoepithelioma-like carcinomas occurring in a variety of organs including, most recently, the stomach. The authors investigated the possibility that EBV may be present not only in the rare gastric cancers that resemble nasopharyngeal lymphoepithelioma, but also in typical gastric adenocarcinoma. EBV sequences were detected in 22 of 138 (16%) cases of typical gastric adenocarcinoma by polymerase chain reaction and in situ hybridization (ISH) techniques. The EBV genomes were specifically present within the gastric carcinoma cells in an even distribution. The EBV genomes were also present in adjacent dysplastic epithelium but were absent in surrounding lymphocytes, other normal stromal cells, intestinal metaplasia, and normal gastric mucosa. The EBV genomes in the infected gastric carcinoma cells are expressed as EBV RNA was detected by ISH. EBV was most often detected in gastric tumors from men (21%) compared with women (3%). Thus some cases of gastric adenocarcinoma are EBV-associated.
Intramolecular Hetero-Diels-Alder Reaction of 3-Benzylidene-1,2-dicarbonyl Compounds (1987)

The intramolecular hetero-Diels-Alder reaction of benzylidene 2-oxocarboxylic acid esters 7 is described, and the diastereoselectivity of the reaction determined. Condensation of the aldehyde 1 with 2-oxocarboxylic acids 5a, b followed by esterification gives 7a, b which cyclize in refluxing xylene to 8a, b and 9a, b in better than 95% yield.
Richard Smith Ankle Arthroplasty (1985)

The indications for ankle joint replacement and the advantages of a 'ball-and-socket' type of prosthesis are examined. The results of 24 Richard Smith ankle replacements of which 18 were followed for an average of 7 years are analysed and the case for abandoning this prosthesis is discussed.
Role of Complex Carbohydrates in Human Immunodeficiency Virus Type 1 Infection and Resistance to Antibody Neutralization (2010)

Complex N-glycans flank the receptor binding sites of the outer domain of HIV-1 gp120, ostensibly forming a protective "fence" against antibodies. Here, we investigated the effects of rebuilding this fence with smaller glycoforms by expressing HIV-1 pseudovirions from a primary isolate in a human cell line lacking N-acetylglucosamine transferase I (GnTI), the enzyme that initiates the conversion of oligomannose N-glycans into complex N-glycans. Thus, complex glycans, including those that surround the receptor binding sites, are replaced by fully trimmed oligomannose stumps. Conversely, the untrimmed oligomannoses of the silent domain of gp120 are likely to remain unchanged. For comparison, we produced a mutant virus lacking a complex N-glycan of the V3 loop (N301Q). Both variants exhibited increased sensitivities to V3 loop-specific monoclonal antibodies (MAbs) and soluble CD4. The N301Q virus was also sensitive to "nonneutralizing" MAbs targeting the primary and secondary receptor binding sites. Endoglycosidase H treatment resulted in the removal of outer domain glycans from the GnTI- but not the parent Env trimers, and this was associated with a rapid and complete loss in infectivity. Nevertheless, the glycan-depleted trimers could still bind to soluble receptor and coreceptor analogs, suggesting a block in post-receptor binding conformational changes necessary for fusion. Collectively, our data show that the antennae of complex N-glycans serve to protect the V3 loop and CD4 binding site, while N-glycan stems regulate native trimer conformation, such that their removal can lead to global changes in neutralization sensitivity and, in extreme cases, an inability to complete the conformational rearrangements necessary for infection.
IL-9 and its receptor are predominantly involved in the pathogenesis of UC (2014)

Our results provide evidence that IL-9 is predominantly involved in the pathogenesis of UC suggesting that targeting IL-9 might become a therapeutic option for patients with UC.
Time-resolved observation of electron-phonon relaxation in copper (1987)

Amplified 150--300-fs laser pulses are applied to monitor the thermal modulation of the transmissivity of thin copper films. Non- equilibrium electron-lattice temperatures are observed. The process of electron-phonon energy transfer was time resolved and was observed to be 1--4 ps increasing with the laser fluence.
T Cell Receptor Repertoire in Rheumatoid Arthritis (1998)

CD4+ T cells are a major component of the inflammatory infiltrate in rheumatoid synovitis. Within synovial lesions, clonal CD4+ T cell populations are detectable, supporting the notion of an antigen specific recognition even in the joint. In general, the clonal size of individual T cell clones is small and does not lead to a marked distortion of the synovial T cell receptor (TCR) repertoire. Comparison of TCR sequences derived from different patients has not provided evidence for common sequences. Either multiple antigens are recognized or the TCR repertoire is sufficiently plastic with a multitude of different TCR structures responding to the same antigen(s). However, within one individual, the repertoire of clonal T cell populations is restricted. Identical T cell clones can be identified in different joints and at different timepoints of the disease, emphasizing that the spectrum of antigens recognized is conserved over time and that the T cell response pattern is not subject to evolution. Characterization of antigens involved in the latter stages of the disease may thus provide critical information on disease-initiating events. Recent data have led to the new concept that the role of T cells in rheumatoid arthritis (RA) is not limited to synovial inflammation. Evidence has been provided that the premorbid TCR repertoires of RA patients and normal controls can be distinguished. The T cell repertoire in RA patients is prone to recognize certain microbial products and autoantigens. The selection of this response pattern can only partially be attributed to the disease associated HLA-DRB1 alleles. Additional factors common in RA patients but not in HLA-DR matched control individuals seem to be important in shaping the TCR repertoire. Furthermore, the repertoire of mature T cells in RA patients is characterized by oligoclonality which involves T cells in the peripheral blood compartment. Possibly, these clonal T cell populations react to widespread autoantigens, raising the possibility that RA patients have a defect in controlling peripheral tolerance and an anomaly of lymphoproliferation. In contrast to joint residing CD4+ T cells, expanded clonotypes isolated from the blood of different patients have been described to share TCR beta chain structures. How these characteristic features of the global TCR repertoire in RA patients translate into mechanisms of disease remains to be elucidated.
A 2 kbit array of symmetric self-electrooptic effect devices (1990)

A 64*32 array of symmetric self-electrooptic effect devices, each of which can be operated as a memory element or logic gate, is discussed. The required optical switching energies of the devices were approximately 800 fJ and approximately 2.5 pJ at 6 and 15 V bias, respectively, and the fastest switching time measured was approximately 1 ns. Either state of the devices could be held with continuous or pulsed incident optical signals with an average optical incident power per input beam of approximately 200 nW or less than 1 mW for the entire array. Photocurrent and reflectivity were measured for all 2048 devices. Only one device failed to have the negative resistance required for bistability, and only nine of the devices fell outside a band of +or-20% of the mean. Additionally, over 200 devices in the array were operated in parallel using low-power semiconductor laser diodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer (2020)

The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
Artificially soft and hard surfaces in electromagnetics (1990)

A transversely corrugated surface as used in corrugated horn antennas represents a soft boundary. A hard boundary is made by using longitudinal corrugations filled with dielectric material. The concept of soft and hard surfaces is treated in detail, considering different geometries. It is shown that both the hard and soft boundaries have the advantage of a polarization-independent reflection coefficient for geometrical optics ray fields, so that a circularly polarized wave is circularly polarized in the same sense after reflection. The hard boundary can be used to obtain strong radiation fields along a surface for any polarization, whereas the soft boundary makes the fields radiated along the surface zero.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of deformable registration uncertainty on lung SBRT dose accumulation (2015)

Reductions in average uncertainty in DIR algorithms by 1.6 mm may have a clinically significant impact on the decision-making metrics used in dose planning and dose accumulation assessment.
ChemInform Abstract: STRUCTURE AND CONFORMATION OF HETEROCYCLES. X. ON 1,4,5,8‐TETRAAZADECALINS (1979)

Abstract Die Strukturen und Konformationen der Tetraazadecaline (I)‐(II) (zugänglich in 54‐78proz. Ausb. aus den entsprechenden Ethylendiaminen und Glyoxal) bzw. (III) bis (IV) (zugänglich in 44/50 bzw. 19proz. Ausb. durch säurekatalysierte Kondensation von 2,3‐Dimethoxy‐1,4‐dimethyl‐piperazin mit den entsprechenden Ethylendiaminen)" werden ausführlich untersucht.
Low-power Capacitor Arrays for Charge Redistribution SAR A-D Converter in 65nm CMOS (2009)

Through the research on charge redistribution SAR A/D converter, three energy-efficient capacitor arrays are discussed in this paper. The switching energy of the traditional architecture, charge sharing architecture, capacitor splitting architecture and two-step architecture capacitor arrays is derived and analyzed. Based on SMIC 65 nm CMOS process, 10-bit SAR A/D converters of all these architectures are designed to validate these concepts. The energy dissipation from Hspice simulation is discussed. At the smallest output code, charge sharing architecture and capacitor splitting architecture consume respectively 65.5% and 44.8% of the energy conventional architecture dissipates. At the smallest and largest output codes, two-step architecture just consumes respectively 10.4% and 23.1% of the traditional architecturepsilas dissipation.
S1P <sub>3</sub> ‐mediated Akt activation and crosstalk with platelet‐derived growth factor receptor (PDGFR) (2003)

Akt plays a pivotal role in cell survival and tumorigenesis. We investigated the potential interaction between sphingosine-1-phosphate (S1P) and platelet-derived growth factor (PDGF) in the Akt signaling pathway. Using mouse embryonic fibroblasts (MEFs) from S1P receptor knockout mice, we show here that S1P3 was required for S473 phosphorylation of Akt by S1P. In addition, S1P-stimulated activation of Akt, but not ERK, was blocked by a PDGF receptor (PDGFR)-specific inhibitor, AG1296, suggesting a S1P3-mediated specific crosstalk between the Akt signaling pathways of S1P and PDGFR in MEFs. We investigated this crosstalk under different conditions and found that both Akt and ERK activation induced by S1P, but not lysophosphatidic acid (LPA), in HEY ovarian cancer cells required PDGFR but not epidermal growth factor receptor (EGFR) or insulin-like growth factor-I receptor (IGFR). Importantly, S1P induced a Gi-dependent tyrosine phosphorylation of PDGFR in HEY cells. This dependence on PDGFR in S1P-induced Akt activation was also observed in A2780, T47D, and HMEC-1 cells (which express S1P3), but not in PC-3 or GI-101A cells (which do not express S1P3), further supporting that S1P3 mediates the crosstalk between S1P and PDGFR. This is the first report demonstrating a unique interaction between S1P3 and PDGFR, in addition to demonstrating a specific role for S1P3 in S1P-induced Akt activation.