gebhart/patrepeval huggingface dataset:
Optical properties and material studies of InGaN/GaN multi-quantum well light emitting diode wafers with different structures (2009)

Three blue emission multi-quantum well (MQW) light emitting diode (LED) samples with different indium composition and different amount of quantum wells were studied. From x-ray diffraction and transmission electron microscopy experimental measurements, the period thickness and indium composition of the sample have been obtained. The temperature dependent photoluminescence (PL) shows that the signal from InGaN/GaN samples was influenced by two kinds of factors. One is the band to band transition of InGaN; another is the localization effect caused by the non-uniformity of the In composition in In-rich samples. While the temperature increases, full width half maximum becomes larger, and the signal tends to shift to the red side. Through theoretical fitting on the temperature dependent PL data, the activation energies (Ea) of the InGaN multi-quantum well samples were obtained. Time-resolved photoluminescence (TRPL) results show that as the indium composition increases and the QW number increases, a longer decay time will get. From the results of photoluminescence excitation (PLE) experiment, a large Stokes shift (SS) was observed. The large Stokes shift can be attributed to the variation of indium composition or the quantum confined Stark effect (QCSE). Also, the Photoluminescence spectra exhibit weak blue peaks and the optical intensity is improved by increasing the number of wells.
Flash DSC crystallization study of blown film grade bimodal high density polyethylene (HDPE) resins. Part 2. Non‐isothermal kinetics (2017)

ABSTRACT Non‐isothermal ultra‐fast cooling crystallization tests were conducted on three blown film grade bimodal high density polyethylene (HDPE) resins using a fast differential scanning calorimeter, the Flash DSC. Non‐isothermal tests were performed at cooling rates between 50 and 4000°K/s, and the data were analyzed using the modified Avrami model by Jeziorny ( Polymer , 1978 , 19 , 1142). Non‐isothermal data were used to propose a new method named crystallization–time–temperature–superposition, and the two activation energies were obtained for each of the resins. This is very useful for obtaining theoretical crystallization kinetics data at different cooling rates, allowing its use in ultra‐fast cooling polymer processes such as blown film. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1822–1827
Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? (2012)

Field cancerization effects as well as isolated tumor cell foci extending well beyond the invasive tumor margin have been described previously to account for local recurrence rates following breast conserving surgery despite adequate surgical margins and breast radiotherapy. To look for evidence of possible tumor cell contamination or field cancerization by genetic effects, a pilot study (Study 1: 12 sample pairs) followed by a verification study (Study 2: 20 sample pairs) were performed on DNA extracted from HER2-positive breast tumors and matching normal adjacent mammary tissue samples excised 1-3 cm beyond the invasive tumor margin. High-resolution molecular inversion probe (MIP) arrays were used to compare genomic copy number variations, including increased HER2 gene copies, between the paired samples; as well, a detailed histologic and immunohistochemical (IHC) re-evaluation of all Study 2 samples was performed blinded to the genomic results to characterize the adjacent normal tissue composition bracketing the DNA-extracted samples. Overall, 14/32 (44 %) sample pairs from both studies produced genome-wide evidence of genetic aberrations including HER2 copy number gains within the adjacent normal tissue samples. The observed single-parental origin of monoallelic HER2 amplicon haplotypes shared by informative tumor-normal pairs, as well as commonly gained loci elsewhere on 17q, suggested the presence of contaminating tumor cells in the genomically aberrant normal samples. Histologic and IHC analyses identified occult 25-200 μm tumor cell clusters overexpressing HER2 scattered in more than half, but not all, of the genomically aberrant normal samples re-evaluated, but in none of the genomically normal samples. These genomic and microscopic findings support the conclusion that tumor cell contamination rather than genetic field cancerization represents the likeliest cause of local clinical recurrence rates following breast conserving surgery, and mandate caution in assuming the genomic normalcy of histologically benign appearing peritumor breast tissue.
RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection (2018)

RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3'-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.
LiJAR (2017)

Online professional social networks such as LinkedIn serve as a marketplace, wherein job seekers can find right career opportunities and job providers can reach out to potential candidates. LinkedIn's job recommendations product is a key vehicle for efficient matching between potential candidates and job postings. However, we have observed in practice that a subset of job postings receive too many applications (due to several reasons such as the popularity of the company, nature of the job, etc.), while some other job postings receive too few applications. Both cases can result in job poster dissatisfaction and may lead to discontinuation of the associated job posting contracts. At the same time, if too many job seekers compete for the same job posting, each job seeker's chance of getting this job will be reduced. In the long term, this reduces the chance of users finding jobs that they really like on the site. Therefore, it becomes beneficial for the job recommendation system to consider values provided to both job seekers as well as job posters in the marketplace.
Total Synthesis of Meayamycin and O-Acyl Analogues (2020)

A short, scalable total synthesis of meayamycin is described by an approach that entails a longest linear sequence of 12 steps (22 steps overall) from commercially available chiral pool materials (ethyl l-lactate, BocNH-Thr-OH, and d-ribose) and introduces the most straightforward preparation of the right-hand subunit detailed to date. The use of the approach in the divergent synthesis of a representative series of <i>O</i>-acyl analogues is exemplified.
Coating Solution for High-Voltage Cathode: AlF3 Atomic Layer Deposition for Freestanding LiCoO2 Electrodes with High Energy Density and Excellent Flexibility (2017)

Freestanding LiCoO<sub>2</sub>/multiwall carbon nanotube/nanocellulose fibril (LCO-MWCNT-NCF) electrodes are fabricated by a vacuum filtration technique. The electrode has a high LCO loading of 20 mg/cm<sup>2</sup> with excellent flexibility, uniform material distribution, and low surface resistivity. When coated with 2 ALD cycles of AlF<sub>3</sub>, LCO-MWCNT-NCF has a high specific capacity of 216 mAh/g at 4.7 V. The freestanding AlF<sub>3</sub>-coated electrode preserves 75.7% of its initial capacity after 100 cycles and 70% after 160 cycles of charge discharge. In contrast, electrodes coated with 2 ALD cycles of Al<sub>2</sub>O<sub>3</sub> cannot be cycled above 4.5 V. By elimination of the unnecessary weight of current collector, and increasing in the working voltage simultaneously, this freestanding LCO-MWCNT-NCF electrode can significantly improve the gravimetric and volumetric energy density of lithium ion batteries.
Pump-induced frequency shifting of switched pulses in an interferometric all-optical switch (1993)

The induced frequency chirping of switched pulses in an interferometric all-optical switch that uses pump-induced nonlinear phase shifts is investigated. Using a nonlinear fiber Sagnac interferometer switch, it is shown that switched pulses suffer from frequency shift and broadening and can be compressed by using an anomalous group-velocity-dispersion fiber. It is also demonstrated that picosecond probe pulses can be switched while retaining their temporal and spectral profiles if pump-probe walk-off is employed.
Supplementary Table S3 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across <i>FGFR2</i> Alterations and Resistance Mutations (2023)

&lt;p&gt;Antiproliferative effect of RLY-4008 and pan-FGFRi in human tumor cell lines&lt;/p&gt;
Reflections on Slide with a Twist Attacks. (2014)

Abstract. Slide attacks use pairs of encryption operations which are slid against each other. Slide with a twist attacks are more sophisticated variants of slide attacks which slide an encryption operation against a decryption operation, and were used in 2000 to attack several cryp-tosystems, including DESX, the Even-Mansour construction, and Feistel structures with four-round self-similarity. They were further extended in 2012 to the mirror slidex framework, which was used to attack 20-round GOST and several additional variants of the Even-Mansour construction. In this paper, we revisit all the previously published applications of these techniques and show that in almost all cases, the same or better results can be achieved by a simpler attack which is based on the seemingly unrelated idea of exploiting their internal fixed points. The observation that such fixed points can be useful in cryptanalysis had already been pointed out in 2007 by Kara, but all the examples he gave for his re-flection attack were based on particular constructions such as Feistel structures or GOST key schedules in which it was easy to explicitly list and count their fixed points. In this paper, we generalize Kara’s reflec-tion attack by using the combinatorial result that random involutions on 2n values are expected to have a surprisingly large number of O(2n/2) fixed points (whereas random permutations are expected to have only O(1) fixed points). This makes it possible to reduce the complexity of the best known attack on additional cryptographic schemes in which it is difficult to explicitly characterize and count their internal fixed points.
Unrepeated transmission over 253.4 km ultra low loss fiber achieving 6.95 b/s/Hz SE using EDFA-only pre-amplification (2014)

A 560 Gb/s (7×80 Gb/s Nyquist spaced PDM-16QAM) superchannel achieving 6.95 b/s/Hz spectral efficiency is transmitted over 253.4 km SMF-28® ULL fiber using only EDFA pre-amplification and full-field nonlinear back-propagation, corresponding to a record SE-distance product of 1761.1 b/s/Hz·km.
Audio-tactile proximity feedback for enhancing 3D manipulation (2018)

In presence of conflicting or ambiguous visual cues in complex scenes, performing 3D selection and manipulation tasks can be challenging. To improve motor planning and coordination, we explore audio-tactile cues to inform the user about the presence of objects in hand proximity, e.g., to avoid unwanted object penetrations. We do so through a novel glove-based tactile interface, enhanced by audio cues. Through two user studies, we illustrate that proximity guidance cues improve spatial awareness, hand motions, and collision avoidance behaviors, and show how proximity cues in combination with collision and friction cues can significantly improve performance.
Multimodal Abnormalities of Brain Structure and Function in Major Depressive Disorder: A Meta-Analysis of Neuroimaging Studies (2020)

Coordinate-based meta-analysis identified spatially convergent structural (VBM) and functional (VBP) abnormalities in major depression. The findings suggest replicable neuroimaging features associated with major depression, beyond the transdiagnostic effects reported in previous meta-analyses, and support a continued research focus on the subgenual cingulate and other selected regions' role in depression.
Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi (2013)

The filamentous fungus Aspergillus niger is an industrially exploited protein expression platform, well known for its capacity to secrete high levels of proteins. To study the process of protein secretion in A. niger, we established a GFP-v-SNARE reporter strain in which the trafficking and dynamics of secretory vesicles can be followed in vivo. The biological role of putative A. niger orthologues of seven secretion-specific genes, known to function in key aspects of the protein secretion machinery in Saccharomyces cerevisiae, was analysed by constructing respective gene deletion mutants in the GFP-v-SNARE reporter strain. Comparison of the deletion phenotype of conserved proteins functioning in the secretory pathway revealed common features but also interesting differences between S. cerevisiae and A. niger. Deletion of the S. cerevisiae Sec2p orthologue in A. niger (SecB), encoding a guanine exchange factor for the GTPase Sec4p (SrgA in A. niger), did not have an obvious phenotype, while SEC2 deletion in S. cerevisiae is lethal. Similarly, deletion of the A. niger orthologue of the S. cerevisiae exocyst subunit Sec3p (SecC) did not result in a lethal phenotype as in S. cerevisiae, although severe growth reduction of A. niger was observed. Deletion of secA, secH and ssoA (encoding SecA, SecH and SsoA the A. niger orthologues of S. cerevisiae Sec1p, Sec8p and Sso1/2p, respectively) showed that these genes are essential for A. niger, similar to the situation in S. cerevisiae. These data demonstrate that the orchestration of exocyst-mediated vesicle transport is only partially conserved in S. cerevisiae and A. niger.
Attenuated LTP in Hippocampal Dentate Gyrus Neurons of Mice Deficient in the PAF Receptor (2001)

Platelet-activating factor (PAF), a bioactive lipid (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) derived from phospholipase A(2) and other pathways, has been implicated in neural plasticity and memory formation. Long-term potentiation (LTP) can be induced by the application of PAF and blocked by a PAF receptor (PAF-R) inhibitor in the hippocampal CA1 and dentate gyrus. To further investigate the role of PAF in synaptic plasticity, we compared LTP in dentate granule cells from hippocampal slices of adult mice deficient in the PAF-R and their age-matched wild-type littermates. Whole cell patch-clamp recordings were made in the current-clamp mode. LTP in the perforant path was induced by a high-frequency stimulation (HFS) and defined as >20% increase above baseline of the amplitude of excitatory postsynaptic potentials (EPSPs) from 26 to 30 min after HFS. HFS-induced enhancement of the EPSP amplitude was attenuated in cells from the PAF-R-deficient mice (163 +/- 14%, mean +/- SE; n = 32) when compared with that in wild-type mice (219 +/- 17%, n = 32). The incidence of LTP induction was also lower in the cells from the deficient mice (72%, 23 of 32 cells) than in the wild-type mice (91%, 29 of 32 cells). Using paired-pulse facilitation as a synaptic pathway discrimination, it appeared that there were differences in LTP magnitudes in the lateral perforant path but not in the medial perforant path between the two groups. BN52021 (5 microM), a PAF synaptosomal receptor antagonist, reduced LTP in the lateral path in the wild-type mice. However, neither BN52021, nor BN50730 (5 microM), a microsomal PAF-R antagonist, reduced LTP in the lateral perforant path in the receptor-deficient mice. These data provide evidence that PAF-R-deficient mice are a useful model to study LTP in the dentate gyrus and support the notion that PAF actively participates in hippocampal synaptic plasticity.
(R)‐(+)‐ and (S)‐(−)‐2,2′‐Bis(Diphenylphosphino)‐1,1′‐Binaphthyl (BINAP) (2003)

Abstract (R)‐(+)‐ and (S)‐(−)‐2,2′‐bis(diphenylphosphino)‐1,1′‐binaphthyl (BINAP) product: (R)‐(+)‐BINAP intermediate: ditriflate of binaphthol (11.0 g, 20 mmol)
A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome (2012)

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.
Chikungunya Virus Envelope-Specific Human Monoclonal Antibodies with Broad Neutralization Potency (2011)

Chikungunya virus (CHIKV) is an alphavirus responsible for numerous epidemics in Africa and Asia. Infection by CHIKV is often characterized by long-lasting, incapacitating arthritis, and some fatal cases have been described among elderly and newborns. Currently, there is no available vaccine or specific treatment against CHIKV. Blood B cells from a donor with history of CHIKV infection were activated, immortalized, amplified, and cloned. Two human mAbs against CHIKV, 5F10 and 8B10, were identified, sequenced, and expressed in recombinant form for characterization. In a plaque reduction neutralization test, 5F10 and 8B10 show mean IC(50) of 72 and 46 ng/ml, respectively. Moreover, both mAbs lead to a strong decrease in extracellular spreading of infectious viral particles from infected to uninfected cells. Importantly, the mAbs neutralize different CHIKV isolates from Singapore, Africa, and Indonesia, as well as O'nyong-nyong virus, but do not recognize other alphaviruses tested. Both mAbs are specific for the CHIKV envelope: 5F10 binds to the E2 glycoprotein ectodomain and 8B10 to E1 and/or E2. In conclusion, these two unique human mAbs strongly, broadly, and specifically neutralize CHIKV infection in vitro and might become possible therapeutic tools against CHIKV infection, especially in individuals at risk for severe disease. Importantly, these mAbs will also represent precious tools for future studies on host-pathogen interactions and the rational design of vaccines against CHIKV.
Laser spectroscopic characterization of negatively charged nitrogen-vacancy (NV−) centers in diamond (2019)

We report on the spectroscopic and laser characterization of negatively charged nitrogen-vacancy (NV−) centers in diamond. Spectroscopic properties such as absorption and emission spectra as well as kinetics were studied, and parameters such as cross-sections and lifetimes were estimated. A vibronic band of NV0 with zero phonon line (ZPL) at 575 nm was detected under 532 nm pulsed excitation due to the photoionization of NV−. Transmission of 532 nm pump pulses saturate around ∼10%, which is much smaller than the theoretical level. Δk/k0 kinetics revealed slow recovery of NV− centers after photoionization under 532 nm pumping, which involved different relaxation channels depending on the probe beam wavelengths. Localization of the electrons in the metastable state of NV0 centers resulted in higher saturated transmission of 632 nm pump.
Pharmacodynamic Markers for Choline Kinase Down-regulation in Breast Cancer Cells (2009)

High levels of choline kinase (ChoK) expression and choline phospholipid metabolites are often associated with malignant transformation, invasion, and metastasis, particularly in breast cancer. These findings have led to the development of novel pharmacologic or gene therapeutic interventions for ChoK-targeted inhibition. To identify pharmacodynamic markers for the therapeutic evaluation of ChoK down-regulation, we investigated the uptake and efflux of [(3)H]choline, a natural substrate of ChoK, and two other important metabolic indicators of malignancy, namely, [(3)H]thymidine and [(3)H]fluorodeoxyglucose, which measure proliferation and glucose metabolic changes, respectively, in ChoK-downregulated cells. Choline uptake in nonmalignant and malignant breast epithelial cell lines expressing graded levels of ChoK showed a ChoK-dependent uptake, retention, and efflux of [(3)H]choline. Reduced proliferation observed because of ChoK down-regulation resulted in reduced [(3)H]thymidine uptake and incorporation into DNA within 48 hours of treatment. Reduced [(3)H]thymidine incorporation levels were consistent with a decreased cell cycle S-phase fraction. No change in [(3)H]fluorodeoxyglucose uptake was observed between ChoK-downregulated and control cells in any of the three cell lines tested. These results demonstrate the utility of radiolabeled choline or choline analogs and proliferation imaging agents as pharmacodynamic markers for ChoK-targeted therapies and suggest a ChoK-mediated mechanism for tumor sequestration of choline-based imaging agents.