gebhart/patrepeval huggingface dataset:
miRNA detection and analysis from high-throughput small RNA sequencing data (2016)

Small RNAs (sRNAs) are a broad class of short regulatory non-coding\nRNAs. microRNAs (miRNAs) are a special class of -21-22 nucleotide\nsRNAs which are derived from a stable hairpin-like secondary structure.\nmiRNAs have critical gene regulatory functions and are involved\nin many pathways including developmental timing, organogenesis and\ndevelopment in both plants and animals. Next generation sequencing\n(NGS) technologies, which are often used for identifying miRNAs,\nare continuously evolving, generating datasets containing millions of\nsRNAs, which has led to new challenges for the tools used to predict\nmiRNAs from such data. There are several tools for miRNA detection\nfrom NGS datasets, which we review in this thesis, identifying a\nnumber of potential shortcomings in their algorithms.\nIn this thesis, we present a novel miRNA prediction algorithm, miRCat2.\nOur algorithm is more robust to variations in sequencing depth\ndue to the fact that it compares aligned sRNA reads to a random uniform\ndistribution to detect peaks in the input dataset, using a new\nentropy-based approach. Then it applies filters based on the miRNA\nbiogenesis on the read alignment and on the computed secondary\nstructure.\nResults show that miRCat2 has a better specificity-sensitivity trade-off than similar tools, and its predictions also contains a larger percentage\nof sequences that are downregulated in mutants in the miRNA\nbiogenesis pathway. This con�rms the validity of novel predictions,\nwhich may lead to new miRNA annotations, expanding and contributing\nto the field of sRNA research.
The G Protein–Gated Potassium Current<i>I</i><sub>K,ACh</sub>Is Constitutively Active in Patients With Chronic Atrial Fibrillation (2005)

Our results demonstrate that larger basal inward rectifier K+ current in cAF consists of increased IK1 activity and constitutively active I(K,ACh). Blockade of I(K,ACh) may represent a new therapeutic target in AF.
Classification of Japanese Kanji using principal component analysis as a preprocessor to an artificial neural network (2002)

Applies principal component analysis (PCA) to the problem of classifying handwritten Kanji characters. PCA is a statistical tool which can yield substantial data reduction by representing each pattern in terms of a relatively small subset of orthonormal features (principal components) extracted from the input set. A PCA preprocessor to an artificial neural network has been used to reduce the dimensionality of a set of handwritten Kanji patterns to less than 5% of that of the original images. Reconstructions of the patterns from the preprocessed versions are quite impressive. Preliminary results yield nearly 90% correct classification of exemplars of 40 different Kanji characters, and also indicate that reconstruction requires more information than classification. These results demonstrate the effectiveness of PCA as a preprocessor for neural networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Laboratory study on rockbolt corrosion (2013)

Pancreatic β-cells adapt to compensate for increased metabolic demand during obesity. Although the miRNA pathway has an essential role in β-cell expansion, whether it is involved in adaptive proliferation is largely unknown. First, we report that EGR2 binding to the miR-455 promoter induced miR-455 upregulation in the pancreatic islets of obesity mouse models. Then, in vitro gain- or loss-of-function studies showed that miR-455 overexpression facilitated β-cell proliferation. Knockdown of miR-455 in ob/ob mice via pancreatic intraductal infusion prevented compensatory β-cell expansion. Mechanistically, our results revealed that increased miR-455 expression inhibits the expression of its target cytoplasmic polyadenylation element binding protein 1 (CPEB1), an mRNA binding protein that plays an important role in regulating insulin resistance and cell proliferation. Decreased CPEB1 expression inhibits elongation of the poly(A) tail and the subsequent translation of Cdkn1b mRNA, reducing the CDKN1B expression level and finally promoting β-cell proliferation. Taken together, our results show that the miR-455/CPEB1/CDKN1B pathway contributes to adaptive proliferation of β-cells to meet metabolic demand during obesity.
Retrieval of land and sea surface temperature using NOAA-11 AVHRR· data in north-eastern Brazil (1994)

Abstract The split-window method is investigated and a simple airborne atmospheric correction model for thermal data is proposed. Analysis shows that the atmospheric transmittance has a quadratic behaviour with the water vapour content in the first few kilometres of a wet atmosphere. The effect of the emissivity is evaluated for the retrieval of surface temperature using data from NOAA-11 AVHRR channels 4 and 5 for two extreme atmospheres. The results indicate that a spectral emissivity variation (Δε) in channels 4 and 5 of ±0.01 is not as important for a wet atmosphere as for a dry atmosphere. The split-window algorithm developed in this work has its parameters dependent on the atmospheric state and the values of these parameters are determined by using radiosonde profiles. Data from eighty-five radiosondes have been used to determine and check the local seasonal equatorial split-window parameters. The results of surface temperature retrieval show that the local seasonal equatorial and daily split-window parameters (given by daily radiosonde profiles) for NOAA-11 AVHRR data exhibit good agreement between their surface temperature results and the results of in situ measurements for two days. Comparisons with in situ measurements show that the maximum difference from retrieving a vegetated surface temperature using AVHRR data is less than 1.0°C in a wet atmosphere. Although the seasonal parameters have demonstrated a good performance when applied for two particular days, it does not indicate that they can be used successfully for other times when the atmospheric state differs from the average seasonal profile determined in this work. Evidence of this fact is shown through the variation of water vapour amount in the eighty-five radiosonde atmospheric profiles that have been analysed. This variation presents a wide range in water vapour from 2.8g cm-2, to 4.92g cm-2, which can significantly modify the retrieval of surface temperature using remote infrared sensors. Discussion of this problem is given in this paper.
Establishing Email-Based Social Network Trust for Vehicular Networks (2010)

We propose a vehicular network trust model that integrates cryptography-based entity trust and email-based social trust. The entity trust provides security protections such as origin integrity, data integrity, and confidentiality. The social trust provides a level of belief on the data transmitted by an entity. To achieve the email-based social trust, we require each user to run an automated agent that performs trust evaluation checks and processes trust checking requests. The requests are from their highly trusted contacts or through a trusted proxy server maintained by the email service provider. We utilize identity-based cryptography (IBC) to integrate entity trust and social trust. This allows us to use a unique identity (e.g., an email address) for each entity. Further, we use the IBC based attribute based cryptography to develop secure group communications in vehicular networks. Finally, we present research challenges and potential research directions to extend this work.
Congestion avoidance networks: CEFLAR. Congestion estimation feedback by limited acceleration-rate/-ratio (2002)

This paper shows that a network supplying variable bit rate services can be prevented from becoming congested if each terminal limits the capacity of its connection in terms of its rate of increase. Variable bit rate sources are adequately assessed with two new concepts: the bit rate increase per unit time (acceleration-rate=/spl alpha/ bit/sec/spl and/2) or the bit rate increase ratio (acceleration-ratio=exp(/spl beta/)). The dimension of the acceleration-ratio coefficient /spl beta/ is seconds/spl and/-l and the upper limits /spl alpha/ and /spl beta/ are regulated to guarantee the network's QoS. The proposed concepts allow the network state to be accurately estimated and so avoid congestion. The proposed method can be applied to ATM networks, frame relay networks, fast reservation protocol systems and so on.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hydroxyl-Directed, Stereoselective Olefination of Ketones by Transition Metal Alkylidenes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroxyl-Directed, Stereoselective Olefination of Ketones by Transition Metal AlkylidenesOsamu Fujimura, Gregory C. Fu, Paul W. K. Rothemund, and Robert H. GrubbsCite this: J. Am. Chem. Soc. 1995, 117, 8, 2355–2356Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://doi.org/10.1021/ja00113a027RIGHTS & PERMISSIONSArticle Views565Altmetric-Citations16LEARN 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 (261 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Monoclonal Antibodies against Zika Virus: Therapeutics and Their Implications for Vaccine Design (2017)

Zika virus (ZIKV) has caused global concern due to its association with neurological complications in newborns and adults. Although no vaccines or antivirals against ZIKV infection have been approved to date, hundreds of monoclonal antibodies (MAbs) have been developed in a short period. Here, we first present a complete picture of the ZIKV MAbs and then focus on the neutralizing mechanisms and immune hot spots uncovered through structural studies, which provide insight for therapeutics and vaccine design.
Ubiquitination on Nonlysine Residues by a Viral E3 Ubiquitin Ligase (2005)

Ubiquitination controls a broad range of cellular functions. The last step of the ubiquitination pathway is regulated by enzyme type 3 (E3) ubiquitin ligases. E3 enzymes are responsible for substrate specificity and catalyze the formation of an isopeptide bond between a lysine residue of the substrate (or the N terminus of the substrate) and ubiquitin. MIR1 and MIR2 are two E3 ubiquitin ligases encoded by Kaposi's sarcoma-associated herpesvirus that mediate the ubiquitination of major histocompatibility complex class I (MHC I) molecules and subsequent internalization. Here, we found that MIR1, but not MIR2, promoted down-regulation of MHC I molecules lacking lysine residues in their intracytoplasmic domain. In the presence of MIR1, these MHC I molecules were ubiquitinated, and their association with ubiquitin was sensitive to beta2-mercaptoethanol, unlike lysine-ubiquitin bonds. This form of ubiquitination required a cysteine residue in the intracytoplasmic tail of MHC I molecules. An MHC I molecule containing a single cysteine residue in an artificial glycine and alanine intracytoplasmic domain was endocytosed and degraded in the presence of MIR1. Thus, ubiquitination can occur on proteins lacking accessible lysines or an accessible N terminus.
Molecular cloning of cDNA encoding the C subunit of H(+)-ATPase from bovine chromaffin granules (1990)

A cDNA encoding subunit C of the V-ATPase from bovine chromaffin granules was cloned and sequenced. The gene encodes a hydrophilic protein of 382 amino acids with a calculated molecular weight of 43,989. Hydropathy plots revealed no apparent transmembrane segments and a rather high helix content was detected. A cDNA encoding most of the C subunit of the V-ATPase of human brain was also cloned and sequenced. The deduced amino acid sequence of this gene is almost identical to the bovine polypeptide with only one change of tyrosine 336 that was replaced by histidine in the human gene. Two polypeptide fragments derived from subunit E of V-ATPase from chromaffin granules were sequenced and found to be identical to the predicted amino acid sequence of this subunit from bovine kidney. These observations support the idea that the amino acid sequences of corresponding subunits from different V-ATPases are highly conserved. Unlike the A and B subunits of V-ATPases, that are homologous to the beta and alpha subunits of F-ATPases, subunits C and E showed no homology with analogous subunits of the F-ATPase family. It is proposed that the addition of the C and gamma subunits to the respective V- and F-ATPases during evolution defined them as two separate families of H(+)-ATPases.
The Biochemical Basis of Sports Performance (2010)

<italic>The Biochemical Basis of Sports Performance</italic> looks at this topic by type of sport. Firstly, however, it introduces with an assessment of the biochemical basis of exercise and sport. The first sport it tackles is weightlifting, for which muscle strength and function are vital. It looks at protein in enzymes and the nutritional effects on strength training and performance. Next, it turns to the sprinter, for whom anaerobic metabolism is important. Then, it looks at middle-distance events and talks the reader through the glycolytic pathway amongst other elements. After that comes the endurance athlete who needs to consider energy supply and aerobic power. The game player follows and here fatigue in sprint sports is looked into. The text then moves on to a more general discussion of what constitutes sporting talent. It ends with a look at adaptations to training: training for speed, strength, middle-distance, endurance, and training strategies.
Vaccines for immunoprevention of cancer (2021)

The immunoprevention of cancer and cancer recurrence is an important area of concern for the scientific community and society as a whole. Researchers have been working for decades to develop vaccines with the potential to alleviate these health care and economic burdens. So far, vaccines have made more progress in preventing cancer than in eliminating already established cancer. In particular, vaccines targeting oncogenic viruses, such as the human papillomavirus and the hepatitis B virus, are exceptional examples of successful prevention of virus-associated cancers, such as cervical cancer and hepatocellular carcinoma. Cancer-preventive vaccines targeting nonviral antigens, such as tumor-associated antigens and neoantigens, are also being extensively tested. Here, we review the currently approved preventive cancer vaccines; discuss the challenges in this field by covering ongoing preclinical and clinical human trials in various cancers; and address various issues related to maximizing cancer vaccine benefit.
Evidence for Neurocognitive Plasticity in At-Risk Older Adults: The Experience Corps Program (2009)

Using fMRI, we demonstrated intervention-specific short-term gains in executive function and in the activity of prefrontal cortical regions in older adults at elevated risk for cognitive impairment. These pilot results provide proof of concept for use-dependent brain plasticity in later life, and, that interventions designed to promote health and function through everyday activity may enhance plasticity in key regions that support executive function.
Fast iterative algorithm for image reconstruction from incomplete projections (2004)

A novel fast iterative algorithm for imaging reconstruction based on conjugate gradient technique was present. The real-time obtainment of the component of projection matrix and the substitution of constant step for optimal step in the one-dimension search in conjugate gradient are adopted to ensure the equality of reconstructed image from incomplete projections and shorten the reconstruction time simultaneously. The experimental results of reconstruction from computer-generated projections and real missile tomography projections have successfully shown that the fast algorithm guarantees the fitness to original image, speeds the iteration time, and can be specially used for reconstruction for incomplete projections in FAN scanning.
Simple Models For Complex Natural Surfaces: A Strategy For The Hyperspectral Era Of Remote Sensing (2005)

A two-step strategy for analyzing multispectral images is described. In the first step, the analyst decomposes the signal from each pixel (as expressed by the radiance or reflectance values in each channel) into components that are contributed by spectrally distinct materials on the ground, and those that are due to atmospheric effects, instrumental effects, and other factors, such as illumination. In the second step, the isolated signals from the materials on the ground are selectively edited, and recombined to form various unit maps that are interpretable within the framework of field units. The approach has been tested on multispectral images of a variety of natural land surfaces ranging from hyperarid deserts to tropical rain forests. Data were analyzed from Landsat MSS (multispectral scanner) and TM (Thematic Mapper), the airborne NS001 TM simulator, Viking Lander and Orbiter, AIS, and AVRIS (Airborne Visible and Infrared Imaging Spectrometer).
Second trimester levels of pregnancy associated plasma protein‐A in cases of trisomy 18 (1999)

In a study of 70 cases of trisomy 18 and 450 matched controls in the second trimester we have measured the maternal serum levels of the analytes alpha feto protein (AFP), free β-human chorionic gonadotrophin (hCG) and pregnancy associated plasma protein-A (PAPP-A). We have found the median multiple of the median (MoM) of maternal serum free β-hCG to be significantly lower (0.327) than normal, as was the level of AFP (0.600). Levels of PAPP-A were reduced even further (0.108). Of the markers associated with trisomy 18 at this time PAPP-A was the most discriminatory, being lower than the 5 per cent centile of normal in 93 per cent of cases, compared with 57 per cent of cases for free β-hCG and 32 per cent of cases for AFP. Combining free β-hCG and PAPP-A or all three markers with maternal age would have the ability to detect 74 per cent of cases at a 0.5 per cent false positive rate (or 64 per cent at a 0.1 per cent false positive rate). Unlike in cases of trisomy 21, the low PAPP-A values observed in the first trimester are continued into the second trimester. Whether the good discriminatory power of PAPP-A can be realized in second trimester screening programmes will depend on developing two stage screening algorithms. This approach is unlikely to be better than the excellent detection rates achievable with free β-hCG, PAPP-A and nuchal translucency in the first trimester. Copyright © 1999 John Wiley & Sons, Ltd.
An Endothelial Cell-Specific Requirement for the <i>UL133-UL138</i> Locus of Human Cytomegalovirus for Efficient Virus Maturation (2013)

Human cytomegalovirus (HCMV) infects a variety of cell types in humans, resulting in a varied pathogenesis in the immunocompromised host. Endothelial cells (ECs) are considered an important target of HCMV infection that may contribute to viral pathogenesis. Although the viral determinants important for entry into ECs are well defined, the molecular determinants regulating postentry tropism in ECs are not known. We previously identified the UL133-UL138 locus encoded within the clinical strain-specific ULb' region of the HCMV genome as important for the latent infection in CD34(+) hematopoietic progenitor cells (HPCs). Interestingly, this locus, while dispensable for replication in fibroblasts, was required for efficient replication in ECs infected with the TB40E or fusion-inducing factor X (FIX) HCMV strains. ECs infected with a virus lacking the entire locus (UL133-UL138(NULL) virus) complete the immediate-early and early phases of infection but are defective for infectious progeny virus production. ECs infected with UL133-UL138(NULL) virus exhibited striking differences in the organization of intracellular membranes and in the assembly of mature virions relative to ECs infected with wild-type (WT) virus. In UL133-UL138(NULL) virus-infected ECs, Golgi stacks were disrupted, and the viral assembly compartment characteristic of HCMV infection failed to form. Further, progeny virions in UL133-UL138(NULL) virus-infected ECs inefficiently acquired the virion tegument and secondary envelope. These defects were specific to infection in ECs and not observed in fibroblasts infected with UL133-UL138(NULL) virus, suggesting an EC-specific requirement for the UL133-UL138 locus for late stages of replication. To our knowledge, the UL133-UL138 locus represents the first cell-type-dependent, postentry tropism determinant required for viral maturation.
Incentive auctions and stable marriages problems solved with floor (n/2) -privacy of human preferences (2004)

Incentive auctions let several participants to cooperate for clearing a set of offers and requests, ensuring that each participant cannot do better than by inputing his true utility. This increases the social welfare by efcient allocations, and is proven to have similar outcomes as the traditional English Auctions. The desk-mates (stable matchings) problem comes from the need of placing students in pairs of two for working in projects or seating in twoseats desks. The stable marriages problem consists of nding matches of a man and a woman out of two sets of men, respectively women. Each of the persons in the previous two problems has a (hopefully stable) secret preference between every two possible partners. The participants want to nd an allocation satisfying their secret preferences and without leaking any of these secret preferences, except for what a participant can infer from the identity of the partner/spouse that was recommended to her/him. We use a distributed weighted constraint satisfaction (DisWCSP) framework where the actual constraints are secrets that are not known by any agent. They are dened by a set of functions on some secret inputs from all agents. The solution is also kept secret and each agent learns just the result of applying an agreed function on the solution. The new framework is shown to improve the efcienc y in modeling the aforementioned problems. We show how to extend our previous techniques to solve securely problems modeled with the new formalism, and exemplify with the two problems in the title.