gebhart/patrepeval huggingface dataset:
DNA directed immobilization (DDI) for the development of an antibody fluorescent microarray for the determination of three family antibiotic residues in milk. (2019)

Misuse of antibiotics in food producing animals enhances the possibility to&#13;\ndevelop antibiotic resistance and can also lead to the appearance of these&#13;\ncompounds in derivate products. New strategies to overcome this issue are&#13;\nrequired. In this context, the FoodSmartphone project will provide analytical&#13;\ntools to ensure food quality concerning pesticides, veterinary products or&#13;\nallergens, from farm to fork. The first approach is based on fluorescent&#13;\nmicroarrays which emerge as potential screening tools to determine the&#13;\npresence of multiple analytes at the same time. In this study, we present a&#13;\nmultiplexed analytical platform based on hapten-oligonucleotide arrays to&#13;\ndetect three families of antibiotics. The use of hapten-oligonucleotide&#13;\nconjugates allows the directed immobilization (DDI) of the signal for each&#13;\nantibiotic family by immobilizing the complementary oligo-probes over the&#13;\nsurface of glass slide. After hybridization, the cocktail of primary antibodies is&#13;\nadded in the samples and this binding is elucidated by the addition of&#13;\nsecondary antibodies labeled to a fluorophore which provide the fluorescent&#13;\nsignal. Using this system a group of penicillin, sulfonamides and tylosin can be&#13;\nquantified on buffer and milk samples. The format of this assay will provide the&#13;\nbasis for its implementation on a Smartphone readout system.
Promoting Student Completion in a MOOC on Information Theory (2018)

Massive Open Online Courses (MOOCs) have become an option for convenient access to education opportunities. However, the low completion rates remain a major challenge for MOOC teachers and providers. Meanwhile, very little has been known about learner experience in MOOC on Information Theory; which is a fundamental field of interest in engineering. This work-inprogress aims at promoting student completion rate in a MOOC on Information Theory by identifying effective strategies for individualized MOOC learning. In particular, the research-to-practice study takes place in a MOOC designed and taught by the third author. We established a learning experience model by extended an existing framework in the MOOC literature. We validated our model with empirical learning data collected from our own MOOC. We identified variables that predict student learning outcomes and completion. Our model enables us to further develop an Individualized Learning Path System that generates and selects the most suitable learning path for individual students.
Signal Processing for Particle Detectors (2020)

This chapter covers the principles and basic limits of signal processing for detectors based on measurements of charge induced on predominantly capacitive electrodes. While this presents a very limited scope, it already includes a broad range of different detector technologies employed in experiments in several areas of science and in various imaging devices. Detector technologies of interest involve semiconductors, gas and liquid ionization media as well as photo detectors converting (scintillation light) into photo-electrons or ionization. One class of detectors not considered here are bolometric detectors (see Sect. 10.4).
[Long-term results of conservatively operated necroses of the lunate bone]. (1987)

The authors present a follow-up of 21 patients treated surgically for lunate bone necrosis on average 19.1 years prior to evaluation. A procedure is called conservative when the shape of the lunate is not destroyed by the operation and the mechanism of the wrist is preserved. This paper shows that these methods are indicated in early stages of Kienböck's disease, but despite some satisfied patients they show generally poor results when used for the late stages with fractured lunate and degenerative signs of the entire carpus. Emphasis should be put on the need for early diagnosis of obscure wrist pain to make early treatment possible, in order to avoid later limitation in the range of motion of the carpus. The authors also report their application to the lunate and its problems of Ficat's measurement of bone marrow pressure in necrosis of the femoral head.
Cover Picture: Upgrading Pyrolysis Oil over Ni/HZSM‐5 by Cascade Reactions (Angew. Chem. Int. Ed. 24/2012) (2012)

An active, selective, and stable catalyst (Ni in zeolite HZSM-5) was developed to convert a wide variety of CO and CO bonds in n-hexane-extracted pyrolysis oil into hydrocarbons through a cascade of hydrogenation, hydrolysis, dehydration, and dehydroaromatization reactions. In their Communication on page 5935 ff., J. Lercher and C. Zhao show that C5–C9 gasoline-range hydrocarbons are produced quantitatively from extracted crude bio-oil using Ni/HZSM-5 catalysts under mild conditions in water.
Implementation of a CDMA receiver with multiple-access noise rejection (2003)

A DS-CDMA receiver is typically implemented as a matched filter. Such a receiver, while optimum in additive white Gaussian noise, may yield poor performance when multiple-access noise is the dominant interference. Previously proposed multiple-user receivers greatly improve performance in this situation, but quickly become prohibitively complex for systems of realistic size. The authors propose a receiver which takes advantage of the colored power spectrum of the multiple-access noise to reject it. The receiver is simple to implement, can run at high rates, and can be tuned adaptively. It is designed to maximize signal-to-noise ratio, but is also shown to yield a substantial improvement over the conventional receiver in average probability of error.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An Investigation into Concurrent Expectation Propagation (2012)

As statistical machine learning becomes more and more prevalent and models become more complicated and fit to larger amounts of data, approximate inference mechanisms become more and more crucial to their success. Expectation propagation (EP) is one such algorithm for inference in probabilistic graphical models. In this work, we introduce a robustified version of EP which helps ensure convergence under a relaxed memory consistency model. The resulting algorithm can be efficiently implemented on a GPU in a straightforward way. Using a 2D Ising spin glass model, we evaluate both the original EP algorithm and our robustified version in terms of convergence, if any, and precision on a classic single core processor. We also compare the naive parallelized version of the original EP algorithm against the parallelized robustified EP on both a multicore CPU and a GPU.
Erythromyeloid tumor cells (K562) induce PGE synthesis in human peripheral blood monocytes. (1983)

Human peripheral blood monocytes were found to spontaneously produce prostaglandin of the E series (PGE) in culture medium (0.5 ng to 3.0 ng/7.5 X 10(5) cells), and the addition of K562 tumor cells enhanced the production by five- to 15-fold after 18 hr of incubation. PGE2 (10(-6) M) inhibited the cytolytic activity of freshly isolated peripheral blood monocytes against K562 target cells by 50%. The PGE production was inhibited by inhibitors of cyclo-oxygenase (indomethacin, aspirin, and ETYA) when present during the incubation. However, pretreatment of monocytes with these cyclo-oxygenase inhibitors was ineffective in preventing PGE production. Kinetic experiments showed that appreciable stimulation of PGE production occurred only after 6 hr of co-culture. Other human tumor cell lines (HSB, SB, and CEM) enhanced PGE production upon co-culture with monocytes but to a lesser extent (twofold to threefold). Monocytes treated with 0.4% formaldehyde or heat (56 degrees C) were not capable of producing PGE when cultured alone or with K526 tumor cells. In contrast, formaldehyde-treated, but not heat-treated, K562 tumor cells were able to induce monocytes to produce PGE. By using a single cell conjugation assay, K562 tumor cells were found to bind equally well to treated or untreated monocytes. In contrast, the lytic activity of treated monocytes against K562 target cells was abolished. The presence of protein synthesis inhibitor, cycloheximide, was found to inhibit PGE production by monocytes cultured alone or with K562 tumor cells. Supernatants from K562 tumor cell cultures were also capable of inducing monocytes to produce PGE, and their effect on PGE production from monocytes was suppressed by cycloheximide. In addition, pretreatment of either K562 tumor cells or monocytes with an irreversible protein synthesis inhibitor, emetine, also suppressed the production of PGE upon co-culture with the untreated counterpart. The production of PGE by monocytes in response to exposure to tumor cells may represent a mechanism whereby tumor cells subvert host immune defense against them.
Efficient CRISPR/Cas9 genome editing with Citrus embryogenic cell cultures (2020)

Both the pC-PDS1 and pC-PDS2 could successfully edit the citrus embryogenic cell cultures. However, the editing efficiency was dependent on the gRNA, confirming that the selection of a proper gRNA is essential for successful genome editing using the CRISPR/Cas9 technique. Also, utilization of embryogenic cell cultures offers another option for successful genome editing in citrus.
Treatment of Advanced Non–Small-Cell Lung Cancer With Two-Drug Combinations (2002)

Article Tools EDITORIALS Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2002.20.17.3565 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 12202651 Treatment of Advanced Non–Small-Cell Lung Cancer With Two-Drug Combinations Paul A. Bunn JrxPaul A. Bunn JrSearch for articles by this author Show More University of Colorado Cancer Center, Denver, CO https://doi.org/10.1200/JCO.2002.20.17.3565 First Page Full Text PDF Figures and Tables © 2002 by American Society of Clinical Oncology
Molecular modelling of HLA‐B*35:132 (2014)

Here we describe the molecular modelling of the new variant HLA-B*35:132. This allele shows one mismatch with B*35:01:01:01 in exon 3 at position 575 where a T is substituted by a C, which implies an amino acidic change from Leucine to Proline. This seems not to alter the molecular structure and not to compromise the HLA complex and T-cell receptor interaction.
Efficient leaky-wave antennas at terahertz frequencies generating highly directional beams (2020)

Due to their frequency-dependent angular emission, leaky-wave antennas have been recently introduced in the terahertz band to tackle many of the challenges associated with THz wireless communications. Most previous works have exploited conventional leaky-wave waveguide architectures developed for the microwave region. In this paper, we study in detail the emission characteristics of leaky-wave antennas at THz frequencies. We show that, at these high frequencies, the wavelength-scale interaction with the aperture causes a nonuniform electric field distribution at the slot interface, which is a unique regime that is not typically encountered at lower frequencies. This effect is even more pronounced as the slot width increases to a point where the sides of the slot act as secondary leaking structures, and the well-known frequency–angle relationship is not obeyed as the energy at a given frequency is radiated in a broad range of angles. Therefore, to exploit the phase matching condition, which couples frequency to emission angle, one must use very thin rectangular slots d≪λ, at the expense of device efficiency. To address this problem, we explore an alternate slot aperture design, in which the slot width increases linearly along its length (i.e., a trapezoidal shape). We show that this preserves the phase-matching constraint while allowing higher output coupling efficiencies. Moreover, since a wider effective aperture is used, the radiated beam is narrow in both angular directions, allowing the generation of true pencil-like THz beams.
Structured nonlinear crystals for visible light generation in displays and biosciences (2010)

Nonlinear conversion of diode based sources using MgO doped PPLN provides a viable route to watt level power visible laser wavelength systems with high electrical efficiency and offer a low cost solution for applications in laser projection and bio-optics. Recent developments of superior nonlinear materials together with brighter and more powerful diode sources provide an excellent opportunity for optical technology over the coming decade.
Compatible and crystallization properties of poly(lactic acid)/poly(butylene adipate‐<i>co</i>‐terephthalate) blends (2009)

Abstract Differential scanning calorimetry (DSC), wide angle X‐ray diffraction (WAXD) and dynamic mechanical analysis (DMA) properties of poly(lactic acid)/ poly(butylene adipate‐ co ‐terephthalate) (PLA/PBAT) specimens suggest that only small amounts of poor PLA and/or PBAT crystals are present in their corresponding melt crystallized specimens. In fact, the percentage crystallinity, peak melting temperature and onset re‐crystallization temperature values of PLA/PBAT specimens reduce gradually as their PBAT contents increase. However, the glass transition temperatures of PLA molecules found by DSC and DMA analysis reduce to the minimum value as the PBAT contents of PLA x PBAT y specimens reach 2.5 wt %. Further morphological and DMA analysis of PLA/PBAT specimens reveal that PBAT molecules are miscible with PLA molecules at PBAT contents equal to or less than 2.5 wt %, since no distinguished phase‐separated PBAT droplets and tan δ transitions were found on fracture surfaces and tan δ curves of PLA/PBAT specimens, respectively. In contrast to PLA, the PBAT specimen exhibits highly deformable properties. After blending proper amounts of PBAT in PLA, the inherent brittle deformation behavior of PLA was successfully improved. Possible reasons accounting for these interesting crystallization, compatible and tensile properties of PLA/PBAT specimens are proposed. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
A New Low Loss Rotman Lens Design for Multibeam Phased Arrays (2006)

The design methodology and analysis of a new low loss Rotman lens beam-forming network is presented. With the introduction of dielectric contours of varying permittivity within the lens, enhanced focusing is achieved. The varying permittivity is realized through a synthesized dielectric technique, where a periodic lattice of holes is formed within the dielectric substrate. In comparison to a conventional Rotman lens of similar shape and size, this new enhanced focused Rotman lens shows an insertion loss improvement of 1.2 to 2.0 dB. Also, the decrease in gain at the extreme scan angles is reduced from 1.5dB to 0.7dB
ChemInform Abstract: Diketopiperazines from Costa Rican Endolichenic Fungus Colpoma sp. CR1465A (2016)

Abstract isolation, structure elucidation, antifungal and antimicrobial properties of three new diketopiperazines (I)—(III) along with five known diketopiperazines
Characterization of Agrobacterium tumefaciens strains isolated from grapevine tumors in China (1987)

Thirteen strains of Agrobacterium tumefaciens isolated from grapevine tumors in northern China were surveyed. These strains varied in their host range properties, although all were tumorigenic on grapevines. Twelve of these strains belonged to Agrobacterium sp. biotype 3, and 11 strains resulted in the synthesis of the opine octopine in tumor tissue. Interestingly, one strain resulted in accumulation of arginine, a previously unrecognized opine, in tumor tissue. Although DNA in most of these strains showed homology to the previously characterized transferred DNA and vir loci, some virulent strains showed little or no homology to these loci. Thus, some of these strains represent widely divergent examples of Agrobacterium sp. The DNA in most strains exhibited little or no homology to a wide-host-range virA locus but did show strong homology to a limited-host-range virA locus. This finding further supports the idea that Agrobacterium strains associated with grapevines may have a specific virA locus.
A PCP Pincer Ligand for Coordination Polymers with Versatile Chemical Reactivity: Selective Activation of CO<sub>2</sub> Gas over CO Gas in the Solid State (2016)

Abstract A tetra(carboxylated) PCP pincer ligand has been synthesized as a building block for porous coordination polymers (PCPs). The air‐ and moisture‐stable PCP metalloligands are rigid tetratopic linkers that are geometrically akin to ligands used in the synthesis of robust metal–organic frameworks (MOFs). Here, the design principle is demonstrated by cyclometalation with Pd II Cl and subsequent use of the metalloligand to prepare a crystalline 3D MOF by direct reaction with Co II ions and structural resolution by single crystal X‐ray diffraction. The Pd−Cl groups inside the pores are accessible to post‐synthetic modifications that facilitate chemical reactions previously unobserved in MOFs: a Pd−CH 3 activated material undergoes rapid insertion of CO 2 gas to give Pd−OC(O)CH 3 at 1 atm and 298 K. However, since the material is highly selective for the adsorption of CO 2 over CO, a Pd−N 3 modified version resists CO insertion under the same conditions.
An acquired high-risk chromosome instability phenotype in multiple myeloma: Jumping 1q Syndrome (2019)

Patients with multiple myeloma (MM) accumulate adverse copy number aberrations (CNAs), gains of 1q21, and 17p deletions during disease progression. A subset of these patients develops heightened 1q12 pericentromeric instability and jumping translocations of 1q12 (JT1q12), evidenced by increased copy CNAs of 1q21 and losses in receptor chromosomes (RC). To understand the progression of these aberrations we analyzed metaphase cells of 50 patients with ≥4 CNAs of 1q21 by G-banding, locus specific FISH, and spectral karyotyping. In eight patients with ≥5 CNAs of 1q21 we identified a chromosome instability phenotype similar to that found in ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies). Strikingly, the acquired instability phenotype identified in these patients demonstrates the same transient structural aberrations of 1q12 as those found in ICF syndrome, suggesting similar underlying pathological mechanisms. Four types of clonal aberrations characterize this phenotype including JT1q12s, RC deletions, 1q12-21 breakage-fusion-bridge cycle amplifications, and RC insertions. In addition, recurring transient aberrations include 1q12 decondensation and breakage, triradials, and 1q micronuclei. The acquired self-propagating mobile property of 1q12 satellite DNA drives the continuous regeneration of 1q12 duplication/deletion events. For patients demonstrating this instability phenotype, we propose the term "Jumping 1q Syndrome."
Post-Aire Maturation of Thymic Medullary Epithelial Cells Involves Selective Expression of Keratinocyte-Specific Autoantigens (2012)

The autoimmune regulator (Aire)-directed ectopic expression of tissue-specific antigens (TSAs) by mature medullary thymic epithelial cells (mTECs) has been viewed as an essential mechanism in the induction of central tolerance. Recent data suggest that the survival of mTECs extends beyond the Aire+ cell population to form the post-Aire mTEC population and Hassall's corpuscles (HCs). The nature and function of these post-Aire epithelial cells and structures, however, have remained unidentified. In this study, we characterized in detail the end-stage development of mTECs and HCs in both Aire-sufficient and Airedeficient mice. In addition, using a transgenic mouse model in which the LacZ reporter gene is under the control of the endogenous Aire promoter, we purified and analyzed the post-Aire mTECs to characterize their function. We showed that the end-stage maturation of mTECs closely resembles that of keratinocytes and that the lack of Aire results in a marked block of mTEC differentiation, which is partially overcome by ligands for RANK and CD40. We also provide evidence that, during mTEC development, Aire is expressed only once and during a limited 1-2 day period. The following loss of Aire expression is accompanied by a quick downregulation of MHC class II and CD80, and of most of the Aire-dependent and Aire-independent TSAs, with the exception of keratinocyte-specific genes. In the final stage of maturation, the mTECs lose their nuclei to become HCs and specifically express desmogleins (DGs) 1 and 3, which, via cross-presentation by APCs, may contribute to tolerance against these pemphigus vulgaris-related TSAs.
Bile-acid-activated farnesoid X receptor regulates hydrogen sulfide production and hepatic microcirculation (2009)

These results demonstrate that CSE is an FXR-regulated gene and provide a new molecular explanation for the pathophysiology of portal hypertension.
Seam: Provably Safe Local Edits on Graphs (2017)

Algorithms that create and mutate graph data structures are challenging to implement correctly. However, verifying even basic properties of low-level implementations, such as referential integrity and memory safety, remains non-trivial. Furthermore, any extension to such a data structure multiplies the complexity of its implementation, while compounding the challenges in reasoning about correctness. We take a language design approach to this problem. We propose Seam, a language for expressing local edits to graph-like data structures, based on a relational data model, and such that data integrity can be verified automatically. We present a verification method that leverages an SMT solver, and prove it sound and precise (complete modulo termination of the SMT solver). We evaluate the verification capabilities of Seam empirically, and demonstrate its applicability to a variety of examples, most notably a new class of verification tasks derived from geometric remeshing operations used in scientific simulation and computer graphics. We describe our prototype implementation of a Seam compiler that generates low-level code, which can then be integrated into larger applications. We evaluate our compiler on a sample application, and demonstrate competitive execution time, compared to hand-written implementations.
Supplementary Figure 9 from A Naturally Derived Small Molecule Disrupts Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Human Prostate Cancer Cells (2023)

&lt;p&gt;PDF file - 95K, Determination of nuclear-cytoplasmic distribution of phosphorylated AR Ser 81 in the presence of DHT and mahanine.&lt;/p&gt;
Secondary T‐acute lymphoblastic leukaemia mimicking blast crisis in chronic myeloid leukaemia (1999)

A 34-year-old man with chronic myeloid leukaemia (CML) firstly developed a lymphoid blast crisis of B-cell type. After a second chronic phase which lasted for > 4 years with maintenance chemotherapy of hydroxyurea, 6-mercaptopurine and methotrexate, he developed a T-cell acute lymphoblastic leukaemia of TcR-gammadelta+ type. Cytogenetic analysis revealed disappearance of the t(9;22) translocation and appearance of new abnormalities consistent with the diagnosis secondary acute leukaemia. To our knowledge, secondary leukaemia in CML has not previously been reported.