gebhart/patrepeval huggingface dataset:
DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin (2014)

Dynamic changes in histone modification are critical for regulating DNA double-strand break (DSB) repair. Activation of the Tip60 acetyltransferase by DSBs requires interaction of Tip60 with histone H3 methylated on lysine 9 (H3K9me3). However, how H3K9 methylation is regulated during DSB repair is not known. Here, we demonstrate that a complex containing kap-1, HP1, and the H3K9 methyltransferase suv39h1 is rapidly loaded onto the chromatin at DSBs. Suv39h1 methylates H3K9, facilitating loading of additional kap-1/HP1/suv39h1 through binding of HP1's chromodomain to the nascent H3K9me3. This process initiates cycles of kap-1/HP1/suv39h1 loading and H3K9 methylation that facilitate spreading of H3K9me3 and kap-1/HP1/suv39h1 complexes for tens of kilobases away from the DSB. These domains of H3K9me3 function to activate the Tip60 acetyltransferase, allowing Tip60 to acetylate both ataxia telangiectasia-mutated (ATM) kinase and histone H4. Consequently, cells lacking suv39h1 display defective activation of Tip60 and ATM, decreased DSB repair, and increased radiosensitivity. Importantly, activated ATM rapidly phosphorylates kap-1, leading to release of the repressive kap-1/HP1/suv39h1 complex from the chromatin. ATM activation therefore functions as a negative feedback loop to remove repressive suv39h1 complexes at DSBs, which may limit DSB repair. Recruitment of kap-1/HP1/suv39h1 to DSBs therefore provides a mechanism for transiently increasing the levels of H3K9me3 in open chromatin domains that lack H3K9me3 and thereby promoting efficient activation of Tip60 and ATM in these regions. Further, transient formation of repressive chromatin may be critical for stabilizing the damaged chromatin and for remodeling the chromatin to create an efficient template for the DNA repair machinery.
Application of MUSIC to arrays with multiple invariances (2002)

This paper describes generalizations of the MUSIC and root-MUSIC algorithms for direction of arrival (DOA) estimation to arrays composed of multiple translated subarrays. The advantage of these new approaches is that the DOAs can be estimated using either a one-dimensional search or by rooting a polynomial, as opposed to a multidimensional search as required by the multiple invariance (MI)-ESPRIT algorithm. While MI-MUSIC and root-MI-MUSIC are not statistically efficient like MI-ESPRIT, they do perform better than a single invariance implementation of ESPRIT, and are thus better suited for finding the initial conditions required by the MI-ESPRIT search.
A transformerless dual active half-bridge DC-DC converter for point-of-load power supplies (2015)

Point-of-load (POL) power supplies contribute significantly to the overall volume, weight, and cost of many electronic devices. This is mainly due to the fairly large inductor of the buck converter commonly used in these applications, which causes it to have a relatively low power density. The goal of this paper is to propose an alternative converter for POL applications which uses a much smaller inductor. The proposed converter, referred to as a transformerless dual active half-bridge (DAHB), uses an ac-link to transfer power, instead of the more conventional dc-link. Not only does the transformerless DAHB offer a significant reduction in the volume of the bulky inductor, but it also allows soft switching and 50% duty cycle operation of all active devices. The advantages of the proposed converter have been verified with a 12 V to 3.3 V, 10 A, 0.3 MHz to 1 MHz experimental prototype. The results demonstrate a reduction of approximately 50% in the volume of reactive components, while maintaining high power processing efficiency.
Unusual Catalyst Concentration Effects in the Hydrolysis of Phenyl Phosphate Esters and of DNA:  A Systematic Investigation of the Lanthanide Series<sup>1</sup> (1998)

Saturation kinetics are measured with all lanthanides and bis(nitrophenyl) phosphate BNPP as substrate. They show rather constant KM values; the kcat values, however, increase by up to 66 times for La3+ to Er3+ and decrease again for Yb3+ and Lu3+. With all lanthanides, hydrolysis of the intermediate mononitrophenyl phosphate NPP is 2−30 times faster than that of BNPP. The kcat values measured with BNPP correlate with the ion diameter of the lanthanides, in line with accepted mechanisms but with the notable exception of the higher lanthanides. A similar correlation holds for the cleavage rates with plasmid DNA, with striking differences again observed with the higher lanthanides, however. Thus, a concentration increase from 5 × 10-5 to 1 × 10-2 M leads to 64% and 84% more DNA cleavage with La3+ and Pr3+, respectively, but to up to 68% less DNA cleavage, respectively, but with Yb3+, Tm3+ or Lu3+. In contrast to the BNPP cleavage, saturation kinetics derived kcat values with DNA change little with the used cation, which on the other hand led to larger variations in the KM parameters. Preliminary UV and CD studies with plasmid DNA indicate lanthanide-induced conformational changes with pseudo-first-order rate constants 10−100 times higher than the cleavage rate under the same conditions. Again, Yb3+ shows different effects than Eu3+. The unusual behavior of the higher lanthanides is discussed on the basis of cation clustering, which, in contrast to earlier assumptions by Bamann et al., leads to diminished activities. Addition of salts such as of NaCl or MgCl2 leads to distinct decrease of catalytic effects of for instance Eu3+. The corresponding rates correlate well with Debye−Hückel ionic strength parameters. These as well as the effects of added amines are in line with a simple competition mechanism of the added cations for the anionic substrates.
Deep learning in radiology: an overview of the concepts and a survey of the state of the art (2018)

Deep learning is a branch of artificial intelligence where networks of simple interconnected units are used to extract patterns from data in order to solve complex problems. Deep learning algorithms have shown groundbreaking performance in a variety of sophisticated tasks, especially those related to images. They have often matched or exceeded human performance. Since the medical field of radiology mostly relies on extracting useful information from images, it is a very natural application area for deep learning, and research in this area has rapidly grown in recent years. In this article, we review the clinical reality of radiology and discuss the opportunities for application of deep learning algorithms. We also introduce basic concepts of deep learning including convolutional neural networks. Then, we present a survey of the research in deep learning applied to radiology. We organize the studies by the types of specific tasks that they attempt to solve and review the broad range of utilized deep learning algorithms. Finally, we briefly discuss opportunities and challenges for incorporating deep learning in the radiology practice of the future.
Investigation of Synthetic Spider Silk Crystallinity and Alignment via Electrothermal, Pyroelectric, Literature XRD, and Tensile Techniques (2017)

The processes used to create synthetic spider silk greatly affect the properties of the produced fibers. This paper investigates the effect of process variations during artificial spinning on the thermal and mechanical properties of the produced silk. Property values are also compared to the ones of the natural dragline silk of the <i>N. clavipes</i> spider, and to unprocessed (as-spun) synthetic silk. Structural characterization by scanning pyroelectric microscopy is employed to provide insight into the axial orientation of the crystalline regions of the fiber and is supported by XRD data. The results show that stretching and passage through liquid baths induce crystal formation and axial alignment in synthetic fibers, but with different structural organization than natural silks. Furthermore, an increase in thermal diffusivity and elastic modulus is observed with decreasing fiber diameter, trending towards properties of natural fiber. This effect seems to be related to silk fibers being subjected to a radial gradient during production.
A Leakage-Based Precoding Scheme for Downlink Multi-User MIMO Channels (2007)

In multiuser MIMO downlink communications, it is necessary to design precoding schemes that are able to suppress co-channel interference. This paper proposes designing precoders by maximizing the so-called signal-to-leakage-and-noise ratio (SLNR) for all users simultaneously. The presentation considers communications with both single- and multi-stream cases, as well as MIMO systems that employ Alamouti coding. The effect of channel estimation errors on system performance is also studied. Compared with zero-forcing solutions, the proposed method does not impose a condition on the relation between the number of transmit and receive antennas, and it also avoids noise enhancement. Simulations illustrate the performance of the scheme
Infrared extension of the supercontinuum generated by femtosecond terawatt laser pulses propagating in the atmosphere (2000)

We investigated the spectral behavior of a white-light continuum generated in air by 2-TW femtosecond laser pulses at 800 nm. The spectrum extends at least from 300 nm to 4.5 mum. From 1 to 1.6 mum the continuum's intensity increases strongly with the laser energy and depends on the initial chirp.
Micrometer‐Sized Spherical Assemblies of Polypeptides and Small Molecules by Acid–Base Chemistry (2004)

Spontaneous formation of microspheres is observed when charged poly(amino acid)s are combined with certain oppositely charged, multivalent organic ions. The surfaces of the spheres are chemically active and act as templates for silica condensation, and the assemblies can be made hollow or polymer-filled, depending on the silica precursor (see image; the fluorescent polymer forms a layer inside a colloidal-silica-coated sphere).
Immunization With Fc-Based Recombinant Epstein–Barr Virus gp350 Elicits Potent Neutralizing Humoral Immune Response in a BALB/c Mice Model (2018)

Epstein-Barr virus (EBV) was the first human virus proved to be closely associated with tumor development, such as lymphoma, nasopharyngeal carcinoma, and EBV-associated gastric carcinoma. Despite many efforts to develop prophylactic vaccines against EBV infection and diseases, no candidates have succeeded in effectively blocking EBV infection in clinical trials. Previous investigations showed that EBV gp350 plays a pivotal role in the infection of B-lymphocytes. Nevertheless, using monomeric gp350 proteins as antigens has not been effective in preventing infection. Multimeric forms of the antigen are more potently immunogenic than monomers; however, the multimerization elements used in previous constructs are not approved for human clinical trials. To prepare a much-needed EBV prophylactic vaccine that is potent, safe, and applicable, we constructed an Fc-based form of gp350 to serve as a dimeric antigen. Here, we show that the Fc-based gp350 antigen exhibits dramatically enhanced immunogenicity compared with wild-type gp350 protein. The complete or partial gp350 ectodomain was fused with the mouse IgG2a Fc domain. Fusion with the Fc domain did not impair gp350 folding, binding to a conformation-dependent neutralizing antibody (nAb) and binding to its receptor by enzyme-linked immunosorbent assay and surface plasmon resonance. Specific antibody titers against gp350 were notably enhanced by immunization with gp350-Fc dimers compared with gp350 monomers. Furthermore, immunization with gp350-Fc fusion proteins elicited potent nAbs against EBV. Our data strongly suggest that an EBV gp350 vaccine based on Fc fusion proteins may be an efficient candidate to prevent EBV infection in clinical applications.
Biochemical construction of specific chimeric plasmids from ColE1 DNA and unfractionated Escherichia coli DNA. (1976)

A series of chimeric plasmids was constructed using colicinigenic factor E1 (ColE1) DNA as the replicon and DNA fragments carrying the galactose or tryptophan operons from E. coli. Restriction endonuclease EcoRI digests of ColE1 DNA and various DNAs containing the trp or gal operons were joined by T4 polynucleotide ligase [polynucleotide synthetase (ATP), poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming), EC 6.5.1.1]. Chimeric plasmids carrying the desired genes were selected after transformation of Trp- or Gal- cells with ligated DNA. By using this method, we constructed ColE1-gal and ColE1-trp chimeric plasmids in which the source of the bacterial gal and trp operons was an unfractionated EcoRI digest of total E. coli DNA. The frequency of recovery of such chimeric plasmids is 10 to 20 colonies per mug of ligated DNA used in the transformation step. The method utilized in this report for constructing specific chimeric plasmids from total E. coli DNA is very simple. It requires only endonuclease R-EcoRI and T4 polynucleotide ligase, both of which are commercially available. The yield of transformants suggests that this method will be useful for cloning and amplifying a wide variety of functionally defined genes from E. coli and other prokaryotic organisms.
Specificity of the Fatty Acyl Moieties of Diacylglycerol for the Activation of Calcium-Activated, Phospholipid-Dependent Protein Kinase1 (1982)

The specificity of the fatty acyl moieties of diacylglycerol for the activation of Ca2+-activated, phospholipid-dependent protein kinase was investigated. Diacylglycerol has been previously shown to activate this enzyme by increasing the affinity for Ca2+ and phospholipid, both of which are indispensable for the enzyme activation. Diacylglycerols containing at least one unsaturated fatty acid at either position 1 or 2 are fully active in this capacity, irrespective of the chain length of the other fatty acyl moiety in the range tested, C2 to C18. Diacylglycerols containing two saturated fatty acids such as dipalmitin and distearin are far less effective. Mono- and triacylglycerols and free fatty acids are totally inactive, indicating that the diacylglycerol structure is essential.
Modulation of Respiratory TLR3-Anti-Viral Response by Probiotic Microorganisms: Lessons Learned from Lactobacillus rhamnosus CRL1505 (2014)

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract illness in infants and young children. Host immune response is implicated in both protective and immunopathological mechanisms during RSV infection. Activation of Toll-like receptor (TLR)-3 in innate immune cells by RSV can induce airway inflammation, protective immune response, and pulmonary immunopathology. A clear understanding of RSV-host interaction is important for the development of novel and effective therapeutic strategies. Several studies have centered on whether probiotic microorganisms with the capacity to stimulate the immune system (immunobiotics) might sufficiently stimulate the common mucosal immune system to improve defenses in the respiratory tract. In this regard, it was demonstrated that some orally administered immunobiotics do have the ability to stimulate respiratory immunity and increase resistance to viral infections. Moreover, during the last decade scientists have significantly advanced in the knowledge of the cellular and molecular mechanisms involved in the protective effect of immunobiotics in the respiratory tract. This review examines the most recent advances dealing with the use of immunobiotic bacteria to improve resistance against viral respiratory infections. More specifically, the article discuss the mechanisms involved in the capacity of the immunobiotic strain Lactobacillus rhamnosus CRL1505 to modulate the TLR3-mediated immune response in the respiratory tract and to increase the resistance to RSV infection. In addition, we review the role of interferon (IFN)-γ and interleukin (IL)-10 in the immunoregulatory effect of the CRL1505 strain that has been successfully used for reducing incidence and morbidity of viral airways infections in children.
BASIC SHOW STEER FEEDING and CARE (2005)

The junior livestock program is a unique opportunity to use live animals to help youth develop. Youth learn something about agriculture and livestock production and develop an appreciation for the livestock industry.
A new, versatile and stereospecific route to unusual amino acids: the enantiospecific total synthesis of statine amide and its three stereoisomers (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new, versatile and stereospecific route to unusual amino acids: the enantiospecific total synthesis of statine amide and its three stereoisomersM. Bessodes, M. Saiah, and K. AntonakisCite this: J. Org. Chem. 1992, 57, 16, 4441–4444Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://doi.org/10.1021/jo00042a026RIGHTS & PERMISSIONSArticle Views447Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (597 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Use of Serology to Detect Xanthomonas campestris pv. pelargonii in Aqueous Extracts of Geranium Plants (1989)

A direct double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) proved superior to latex bead agglutination (LBA) for rapid detection of xanthomonas campestris pv. pelargonii in aqueous extracts of geranium plants. The antisera, obtained from rabbits injected with live cells of X.c. pv. pelargonii, did not react with strains of Erwinia Pseudomonas, Clavibacter, or Agrobacterium in either the DAS-ELISA or the LBA tests
The Relation between Serum Insulin Levels and 8-Year Changes in Lipid, Lipoprotein, and Blood Pressure Levels (1992)

Hyperinsulinemia is associated with an adverse pattern of cardiovascular risk factors, including obesity, elevated triglyceride levels, low levels of high-density lipoprotein (HDL) cholesterol, and elevated blood pressure. Whether hyperinsulinemia precedes (and perhaps causes) this deterioration in the risk factors or merely accompanies the deterioration is controversial. We therefore examined the 8-year changes in lipids, lipoproteins, and blood pressure as a function of baseline levels of fasting insulin in 1,383 nondiabetic Mexican-American and non-Hispanic white subjects enrolled between October 1979 and November 1982 in the San Antonio Heart Study, a population-based longitudinal study of cardiovascular risk factors and diabetes in San Antonio, Texas. After age and concomitant changes in body mass index were adjusted for, fasting insulin at baseline was found to be correlated positively with 8-year changes in triglyceride levels and negatively with 8-year changes in HDL cholesterol levels (p less than 0.05). Among the non-Hispanic whites, insulin was more strongly correlated with a decline in HDL cholesterol levels in women than in men (p less than 0.001). Fasting insulin was also positively correlated with changes in both systolic and diastolic blood pressure in non-Hispanic whites, but not in Mexican Americans, although these correlations were slightly diminished and no longer achieved statistical significance after subjects receiving antihypertensive medications were excluded. These results support the hypothesis that in nondiabetic subjects, insulin has a direct regulatory effect on triglyceride and HDL cholesterol levels. These data provide evidence for a possible role for insulin in blood pressure regulation, at least in non-Hispanic whites, although further analysis of this issue is warranted.
Type-augmented Relation Prediction in Knowledge Graphs (2020)

Knowledge graphs (KGs) are of great importance to many real world applications, but they generally suffer from incomplete information in the form of missing relations between entities. Knowledge graph completion (also known as relation prediction) is the task of inferring missing facts given existing ones. Most of the existing work is proposed by maximizing the likelihood of observed instance-level triples. Not much attention, however, is paid to the ontological information, such as type information of entities and relations. In this work, we propose a type-augmented relation prediction (TaRP) method, where we apply both the type information and instance-level information for relation prediction. In particular, type information and instance-level information are encoded as prior probabilities and likelihoods of relations respectively, and are combined by following Bayes' rule. Our proposed TaRP method achieves significantly better performance than state-of-the-art methods on four benchmark datasets: FB15K, FB15K-237, YAGO26K-906, and DB111K-174. In addition, we show that TaRP achieves significantly improved data efficiency. More importantly, the type information extracted from a specific dataset can generalize well to other datasets through the proposed TaRP model.
Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy (2020)

Glioblastoma (GBM) is highly invasive and the deadliest brain tumor in adults. It is characterized by inter-tumor and intra-tumor heterogeneity, short patient survival, and lack of effective treatment. Prognosis and therapy selection is driven by molecular data from gene transcription, genetic alterations and DNA methylation. The four GBM molecular subtypes are proneural, neural, classical, and mesenchymal. More effective personalized therapy heavily depends on higher resolution molecular subtype signatures, combined with gene therapy, immunotherapy and organoid technology. In this review, we summarize the principal GBM molecular classifications that guide diagnosis, prognosis, and therapeutic recommendations.
Diffusion Models Beat GANs on Image Synthesis (2021)

We show that diffusion models can achieve image sample quality superior to the current state-of-the-art generative models. We achieve this on unconditional image synthesis by finding a better architecture through a series of ablations. For conditional image synthesis, we further improve sample quality with classifier guidance: a simple, compute-efficient method for trading off diversity for fidelity using gradients from a classifier. We achieve an FID of 2.97 on ImageNet 128$\times$128, 4.59 on ImageNet 256$\times$256, and 7.72 on ImageNet 512$\times$512, and we match BigGAN-deep even with as few as 25 forward passes per sample, all while maintaining better coverage of the distribution. Finally, we find that classifier guidance combines well with upsampling diffusion models, further improving FID to 3.94 on ImageNet 256$\times$256 and 3.85 on ImageNet 512$\times$512. We release our code at this https URL