gebhart/patrepeval huggingface dataset:
Integrated-optic implementation of a confocal scanning optical microscope (1993)

A confocal scanning optical microscope implemented in an integrated-optic structure is demonstrated. The compact nature of the device proves to be more suitable for environments where mechanical shock can result in optical misalignment of discrete components. The device is implemented in a thin-film optical waveguide with optical fiber connections for light input and output. An objective lens and focusing beam splitter are incorporated into the waveguide structure to form the sensing head of the microscope. The fabrication of the device is discussed, and both intensity and differential contrast images are presented to demonstrate the device operation. The confocal imaging characteristics of the microscope are also demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Strategic use of Iranian bread wheat landrace accessions for genetic improvement: Core set formulation and validation (2020)

Abstract Iranian wheat landrace accessions (IWAs) were collected from country‐wide farm fields and market places in 1935 by a professor at the University of Tehran and shared with University of California at Davis, California. IWAs were further submitted to the genebank of International Maize and Wheat Improvement Center (CIMMYT), Mexico. 2,403 IWAs from CIMMYT’s genebank were assayed by DArT‐seq technology to assess genetic diversity. No apparent ecogeographic patterns related to genetic diversity were detected, probably due to long‐term transport and frequent interchange of landraces among farmers. A multivariate clustering procedure combining genotypic and phenotypic information was used in selecting a core‐set, which represented 15% of the hexaploid wheat accessions included in this study. This subset captured an estimated 93% of rare (frequency &lt;0.05) alleles. Multisite phenotypic data (India, Mexico) validated the ability of the core‐set in detecting useful variants. Potential donor accessions for multiple traits (disease resistance, zinc concentration) were identified from the core‐set for wheat‐breeding. This report illustrates a breeder friendly robust core‐set formulation strategy for harnessing the useful genetic variation stored in the genebanks.
A five‐nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis (1998)

Homologous recombination in Bacillus subtilis requires the product of the addA and addB genes, the AddAB enzyme. This enzyme, which is both a helicase and a powerful nuclease, is thought to be the counterpart of the Escherichia coli RecBCD enzyme. From this analogy, it is expected that the nuclease activity of AddAB can be downregulated by a specific DNA sequence, which would correspond to the chi site in E. coli. Using protection of linear double-stranded DNA as a criterion, we identified the five-nucleotide sequence 5'-AGCGG-3', or its complement 5'-CCGCT-3', as being sufficient for AddAB nuclease attenuation. We have shown further that this attenuation occurs only if the sequence is properly oriented with respect to the translocating AddAB enzyme. Finally, inspection of the complete B. subtilis genome revealed that this five-nucleotide sequence is over-represented and is, in a majority of cases, co-oriented with DNA replication. Based on these observations, we propose that 5'-AGCGG-3', or its complement, is the B. subtilis analogue of the E. coli chi sequence.
Vaccination potential of B and T epitope-enriched NP and M2 against Influenza A viruses from different clades and hosts (2018)

To avoid outbreaks of influenza virus epidemics and pandemics among human populations, modern medicine requires the development of new universal vaccines that are able to provide protection from a wide range of influenza A virus strains. In the course of development of a universal vaccine, it is necessary to consider that immunity must be generated even against viruses from different hosts because new human epidemic virus strains have their origins in viruses of birds and other animals. We have enriched conserved viral proteins-nucleoprotein (NP) and matrix protein 2 (M2)-by B and T-cell epitopes not only human origin but also swine and avian origin. For this purpose, we analyzed M2 and NP sequences with respect to changes in the sequences of known T and B-cell epitopes and chose conserved and evolutionarily significant epitopes. Eventually, we found consensus sequences of M2 and NP that have the maximum quantity of epitopes that are 100% coincident with them. Consensus epitope-enriched amino acid sequences of M2 and NP proteins were included in a recombinant adenoviral vector. Immunization with Ad5-tet-M2NP induced strong CD8 and CD4 T cells responses, specific to each of the encoded antigens, i.e. M2 and NP. Eight months after immunization with Ad5-tet-M2NP, high numbers of M2- and NP-responding "effector memory" CD44posCD62neg T cells were found in the mouse spleens, which revealed a long-term T cell immune memory conferred by the immunization. In all, the challenge experiments showed an extraordinarily wide-ranging efficacy of protection by the Ad5-tet-M2NP vaccine, covering 5 different heterosubtypes of influenza A virus (2 human, 2 avian and 1 swine).
Mode-locking in a network of kuramoto-like oscillators (2015)

In this paper we consider a network of phase oscillators. We develop the equations that model the time evolution of the phase of each oscillator in the network. The oscillator represents a modified Kuramoto oscillator and in this study we discuss how these modifications are obtained. In the context of this study, we use this network to model a network of PLLs for distributed clock applications. We analyse analytically and numerically the synchronisation modes of this system for different types of the coupling function. We show that depending on the properties of the coupling function, the network displays either multiple coexisting synchronisation modes or only a single synchronisation mode. While in the context of clock generation, multiple synchronisation modes coexisting in the system at the same parameters are a parasitic phenomenon. However in the context of other application such as associative memory models, mode-locking can be seen a useful phenomenon. The results provide a deeper understanding of globally synchronised clock networks with applications in microprocessor design.
Targeting muscle stem cell intrinsic defects to treat Duchenne muscular dystrophy (2016)

Duchenne muscular dystrophy (DMD) is a genetic disease characterised by skeletal muscle degeneration and progressive muscle wasting, which is caused by loss-of-function mutations in the <i>DMD</i> gene that encodes for the protein dystrophin. Dystrophin has critical roles in myofiber stability and integrity by connecting the actin cytoskeleton to the extracellular matrix. Absence of dystrophin leads to myofiber fragility and contributes to skeletal muscle degeneration in DMD patients, however, accumulating evidence also indicate that muscle stem cells (also known as satellite cells) are defective in dystrophic muscles, which leads to impaired muscle regeneration. Our recent work demonstrated that dystrophin is expressed in activated satellite cells, where it regulates the establishment of satellite cell polarity and asymmetric cell division. These findings indicate that dystrophin-deficient satellite cells have intrinsic dysfunctions that contribute to muscle wasting and progression of the disease. This discovery suggests that satellite cells could be targeted to treat DMD. Here we discuss how these new findings affect regenerative therapies for muscular dystrophies. Therapies targeting satellite cells hold great potential and could have long-term efficiency owing to the high self-renewal ability of these cells.
A Memory Fault Simulator for Radiation-Induced Effects in SRAMs (2010)

This paper introduces a simulator that allows analyzing the radiation induced errors on memory devices. The simulator takes all the radiation effects on SRAM into account and can be easily tuned on the base of data gained during radiation experiments and/or presented in literature. We also present a case study application in which the proposed simulator is used to validate a low-cost hardware platform for soft error detection in avionic environment by the mean of atmospheric balloons in the context of HAMLET project.
Numerical and quantitative analysis of HIV/AIDS model with modified Atangana-Baleanu in Caputo sense derivative (2022)

Fractional calculus plays an important role in the development of control strategies, the study of the dynamical transmission of diseases, and some other real-life problems nowadays. The time-fractional HIV/AIDS model is examined using a novel method in this paper. Based on the Atangana-concept Baleanu’s of a derivative in the Caputo sense, the current modified fractional derivative operator uses singular and non-local kernels. This new modified fractional operator is given a numerical approximation and applied to the HIV/AIDS model. In the presence of this novel operator, we present some significant analysis for the HIV/AIDS epidemic model. The uniqueness and stability criteria of the model have been demonstrated using the Picard successive approximation approach and Banach’s fixed point theory. The Laplace Adomian decomposition method (LADM) was used to obtain the numerical solution for the modified Atangana-Baleanu Caputo derivative model. The convergence analysis is verified for the proposed scheme. Finally, numerical results and simulations are derived with the proposed scheme for HIV/AIDS model. On the dynamics of HIV/AIDS transmission, the effects of many biological parameters are examined.
Robust watermarking scheme based on RDWT-SVD: Embedding data in all subbands (2011)

In this paper, a new method for non-blind image watermarking presented that is robust against affine transformation and ordinary image manipulation. The proposed method presents a watermarking scheme based on redundant discrete wavelet transform (RDWT) and Singular Value Decomposition (SVD). After applying RDWT to cover image, we apply SVD to each subband. Then we modify singular values of the cover image using singular values of the visual watermark. The advantage of the proposed technique is its robustness against most common attacks. Analysis and experimental results show higher performance of the proposed method in comparison to the DWT-SVD method.
Targeting CD47 in lymphoid malignancies with CAR T cells. (2023)

2513 Background: Despite major therapeutic advances of chimeric antigen receptor (CAR) T cells directed against CD19 in relapsed and refractory non-Hodgkin lymphoma (NHL), two thirds of patients experience relapse within the first two years. Nearly one third of these relapses are associated with CD19 antigen-loss escape thus leveraging alternate CAR targets may improve outcomes. CD47, an anti-phagocytic “don’t eat me” receptor known to be overexpressed in NHL, is an ideal CAR target as it is potentially indispensable for tumor progression. Methods: CD47-CAR binding domains were engineered either as a camelid single variable heavy chain nanobody (CD47-VHH-CAR) or as the CD47 binding domain of cognate receptor SIRPα (SIRPα-CAR), each combined with a CD28 costimulatory domain and a CD3ζ activation domain with two mutated ITAMs (1XX). In vitro co-culture assays were performed with lymphoid mouse tumor cell lines BM185 and A20. For in vivo experiments, syngeneic BALB/c mice were sublethally irradiated for lymphodepletion then injected intravenously with 1x10 5 luciferase + BM185 cells. Two days later, mice were injected with 2x10 6 CAR T cells, and bioluminescence imaging was performed to monitor tumor progression. For bio-localization experiments, CAR T cells were co-transduced with a separate vector encoding luciferase. Results: CD47-CAR T cell expansion in vitro was hindered due to fratricide, which can be rescued by CD47 CRISPR knockout. Both CD47-VHH-CAR and SIRPa-CAR T cells exhibited potent and specific in vitro lysis of BM185 and A20 cells. CD47-VHH-CAR T cells showed transient anti-leukemia activity, however, survival was not significantly prolonged. T cell bio-localization analysis revealed that, compared to CD19-CAR T cells, CD47-VHH-CAR T cells exhibited prolonged retention in the thorax with minimal bone marrow trafficking, suggesting CD47 antigen-specific pulmonary sequestration, and inferior expansion. SIRPα-CAR T cells engineered to secrete pro-inflammatory cytokine IL-18 significantly improved CAR T cell expansion, resulting in bone marrow trafficking and clearance of BM185 tumor. However, recipients of IL-18-secreting SIRPa-CAR T cells experienced lethal CAR T cell-related toxicity. To improve the safety of CD47-CAR T cells, we engineered an NFAT-responsive vector expressing the CD47-CAR modified with E. coli-derived dihydrofolate reductase drug destabilization domain to limit CD47-CAR expression to T cells exposed to the stabilizing antibiotic trimethoprim and receiving a licensing NFAT signal from a CD19-CAR. Conclusions: In vivo activity of CD47-targeting CAR T cells is limited by thoracic retention and limited expansion, which can be partially overcome by overexpression of IL-18, though enhanced toxicity precludes survival prolongation. Our findings suggest that strategies to spatiotemporally restrict CAR expression or activation will be necessary to achieve safe and efficacious CD47-CAR T cell activity.
Funcionalització d' o -carborans iodats per obtenir estructures dendrimèriques útils en aplicacions mèdiques (2011)

L'1,2-dicarba-closo-dodecaborà, l'o-carborà, és un clúster icosaèdric format per deu vèrtexs de borahidrogen i dos vèrtexs de carbonihidrogen en posició adjacent. Aquesta molècula és químicament molt versàtil, ja que presenta una reactivitat diferenciada segons el tipus de vèrtex, la qual cosa en permet la derivatització en funció de l'aplicació mèdica desitjada. Al nostre grup de recerca, tenim una gran experiència en reaccions de substitució electrofílica sobre els àtoms de bor, sobretot per tal d'obtenir derivats B-iodats de l'o-carborà que continguin un elevat nombre d'àtoms de iode per molècula. Aquesta condició els converteix en bons candidats per ser usats com a agents de contrast opacs als raigs X en ciments ossis polimèrics de metilmetacrilat. Els enllaços de boriode d'aquests carborans poden ser posteriorment derivatitzats amb diferents grups orgànics funcionals, tot formant nous vèrtex de bor carboni i obtenint, així, molècules útils com a nuclis d'estructures de tipus dendró. El creixement dendrimèric d'aquests nuclis es du a terme mitjançant reaccions d'acoblament amb altres clústers de carborà funcionalitzats, tot obtenint molècules amb un elevat contingut en àtoms de bor, molt útils com a agents anticancerosos en la tècnica BNCT (Boron Neutron Capture Therapy).
Entity based Q&A Retrieval (2012)

Bridging the lexical gap between the user's question and the question-answer pairs in the Q&A archives has been a major challenge for Q&A retrieval. State-of-the-art approaches address this issue by implicitly expanding the queries with additional words using statistical translation models. While useful, the effectiveness of these models is highly dependant on the availability of quality corpus in the absence of which they are troubled by noise issues. Moreover these models perform word based expansion in a context agnostic manner resulting in translation that might be mixed and fairly general. This results in degraded retrieval performance. In this work we address the above issues by extending the lexical word based translation model to incorporate semantic concepts (entities). We explore strategies to learn the translation probabilities between words and the concepts using the Q&A archives and a popular entity catalog. Experiments conducted on a large scale real data show that the proposed techniques are promising.
New Concepts in Cancer Biomarkers: Circulating miRNAs in Liquid Biopsies (2016)

The effective and efficient management of cancer patients relies upon early diagnosis and/or the monitoring of treatment, something that is often difficult to achieve using standard tissue biopsy techniques. Biological fluids such as blood hold great possibilities as a source of non-invasive cancer biomarkers that can act as surrogate markers to biopsy-based sampling. The non-invasive nature of these "liquid biopsies" ultimately means that cancer detection may be earlier and that the ability to monitor disease progression and/or treatment response represents a paradigm shift in the treatment of cancer patients. Below, we review one of the most promising classes of circulating cancer biomarkers: microRNAs (miRNAs). In particular, we will consider their history, the controversy surrounding their origin and biology, and, most importantly, the hurdles that remain to be overcome if they are really to become part of future clinical practice.
Danazol for heavy menstrual bleeding (2002)

Danazol appears to be an effective treatment for heavy menstrual bleeding compared to other medical treatments, though it is uncertain whether it is acceptable to women. The use of danazol may be limited by its side effect profile, its acceptability to women and the need for continuing treatment. Overall no strong recommendations can be made due to the small number of trials, and the small sample sizes of the included trials.
Characterization of Nuclear Materials in Extreme Conditions: Raman Spectroscopy Approach (2014)

A review is given of our last advances on Raman spectroscopy characterization of irradiated and/or leached UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , PuO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and (U,Pu)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> samples. For this purpose, three original Raman setups dedicated to the study of nuclear materials were involved. In every case, irradiation-induced Raman defect bands in the 500 - 750 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> range was observed. For UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , an annealing temperature experiment suggests that these defect bands could be the signatures of medium-range structured defects. Besides, the leaching experiments show different behavior between the irradiated in situ probed UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ceramic and post mortem probed [UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> + (U,Pu)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ] sample: The growth of an altered layer made of studtite and schoepite phases was monitored at the surface of UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ceramic, while post-mortem studies reveal the presence of U <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> and studtite phases at the surface of the UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> grains of the binary sample. No alteration layer was observed at the surface of the leached (U,Pu)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> grains.
Risk Factors for Dislocation After Revision Total Hip Arthroplasty (2012)

Level IV, therapeutic study. See Instructions for Authors for a complete description of levels of evidence.
Coplanar Oligo(p-phenylenedisilenylene)s as Si═Si Analogues of Oligo(p-phenylenevinylene)s: Evidence for Extended π-Conjugation through the Carbon and Silicon π-Frameworks (2015)

A series of oligo(p-phenylenedisilenylene)s (Si-OPVs 1-4), silicon analogues of oligo(p-phenylenevinylene)s, up to the tetramer have been synthesized and isolated by the introduction of a newly developed protecting group [(HexO)MEind] for improving their solubility. The experimental and theoretical studies of the Si-OPVs 1-4 demonstrate the fully extended π-conjugation of the Si-OPV main chains. Single crystal X-ray analyses of the monomer 1 and the dimer 2 revealed the highly coplanar Si-OPV backbones facilitating the effective extension of the π-conjugation, which has further been validated by the significant increases in the absorption maxima from 465 nm for the monomer 1 to 610 nm for the tetramer 4. The absorption maxima exhibit an excellent fit to Meier's equation, leading to the estimation of an effective conjugation length (ECL) of 9 repeat units (nECL = 9) and the absorption maximum of 635 nm for the infinite chain (λ∞ = 635 nm). In sharp contrast to other nonemissive disilenes, the Si-OPVs 2-4 show an intense fluorescence from 613 to 668 nm at room temperature with the quantum yields up to 0.48. All the data presented here provide the first evidence for the efficient extended π-conjugation between the Si═Si double bonds and the carbon π-electron systems over the entire Si-OPV skeleton. This study reveals the possibility for developing the conjugated disilene π-systems, in which the Si═Si double bonds would be promising building blocks, significantly optimizing the intrinsic photophysical and electrochemical properties of the carbon-based π-conjugated materials.
Hawk: The Blockchain Model of Cryptography and Privacy-Preserving Smart Contracts. (2015)

Emerging smart contract systems over decentralized cryptocurrencies allow mutually distrustful parties to transact safely without trusted third parties. In the event of contractual breaches or aborts, the decentralized blockchain ensures that honest parties obtain commensurate compensation. Existing systems, however, lack transactional privacy. All transactions, including flow of money between pseudonyms and amount transacted, are exposed on the blockchain. We present Hawk, a decentralized smart contract system that does not store financial transactions in the clear on the blockchain, thus retaining transactional privacy from the public’s view. A Hawk programmer can write a private smart contract in an intuitive manner without having to implement cryptography, and our compiler automatically generates an efficient cryptographic protocol where contractual parties interact with the blockchain, using cryptographic primitives such as zero-knowledge proofs. To formally define and reason about the security of our protocols, we are the first to formalize the blockchain model of cryptography. The formal modeling is of independent interest. We advocate the community to adopt such a formal model when designing applications atop decentralized blockchains.