gebhart/patrepeval huggingface dataset:
Defining the Bacteroides Ribosomal Binding Site (2013)

The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus Bacteroides are among the most abundant bacterial species in the human colon. Bacteroidetes diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in Bacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of pepI from Lactobacillus delbrueckii subsp. lactis as a novel reporter gene for Bacteroides. Furthermore, we report the identification of the 3' end of the 16S rRNA of Bacteroides ovatus and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5' untranslated region of other Bacteroidales ribosomal protein genes, we conclude that our findings are relevant to all members of this order.
All-fiber bidirectional optical parametric oscillator for precision rotation sensing (2015)

We demonstrate the first all-fiber bidirectional OPO which generates two highly coherent frequency combs in opposite directions. The OPO may find important applications in precision measurements including rotation sensing with ultra-large sensing area and sensitivity.
Local and global transformations to improve learning of medical images applied to chest radiographs (2019)

A potential drawback of computer-aided diagnosis (CAD) systems is that they tend to capture the noise characteristics along with signal variations due to a limited number of sources used in training. This leads to a decrease in performance on data from different sources. The variations in scanner settings, device manufacturers and sites pose a significant challenge to the learning capabilities of the CAD systems like chest radiographs, also called Chest X-rays (CXR). In the proposed work, we investigate if preprocessing transformations like global normalization along with local enhancements are good to tackle the variability of data from multiple sources on a supervised CXR classification system. We also propose a detail enhancement filter to enhance both finer structures and opacities in CXRs. With the proposed preprocessing improvement, experiments were performed on 13,000 images across 3 public and one private data source using Dense Convolutional Network (DenseNet). The sensitivity at equal error rate (mean ± sd) improved from 0.888 ± 0.043 to 0.931 ± 0.030 by applying a combination of global histogram equalization with the proposed detail enhancement filter when compared to the raw images. We conclude that the proposed transformations are effective in improving the learning of CXRs from different data sources.
Evaluation and Validation of a Commercially Available Enzyme-Linked Immunosorbent Assay for the Neonicotinoid Insecticide Imidacloprid in Agricultural Samples (2004)

The performance of a commercially available microtiter plate ELISA kit for the determination of the neonicotinoid insecticide imidacloprid was evaluated for sensitivity, selectivity, influence of organic solvent used for extraction procedure, matrix interference originated from agricultural sample, accuracy, and method comparison with conventional HPLC analysis. The limit of detection for the kit (0.1 or 0.5 ng/mL) was determined. The working range (1-39 ng/mL) experimentally calculated on the basis of a criterion, which is determined as the range from I(20) to I(80), was comparable to that established by the manufacturer (1-50 ng/mL). The linearity of the standard curve based on the kit-assembled standard solutions agreed with the one based on the self-made standard solutions. Specificity studies indicate that the imidacloprid monoclonal antibody can readily distinguish the target compound from other structurally related neonicotinoid analogues and some metabolites, with the exception of clothianidin, the cross-reactivity of which was approximately 12%. To extract imidacloprid from an agricultural sample (apple) as simply and rapidly as possible, some extraction methods were examined. Consequently, the extraction method with hand-shaking for 5 min was the best among the examined methods. For the analysis of imidacloprid in apple samples, it was extracted directly with methanol and the extracts were diluted 10-fold (100-fold in the well) with water prior to ELISA analysis. No significant matrix interference was observed with the dilution factor. Recoveries of imidacloprid from fortified apple samples ranged from 87.7 to 112.0%. The results obtained with the ELISA kit correlated well with those by the reference method (conventional HPLC analysis) for apple samples (r > 0.998). These findings strongly indicate that the ELISA kit may be employed routinely for an on-site imidacloprid residue analysis of apple samples.
Depletion of <i>Kcnq1ot1</i> non-coding RNA does not affect imprinting maintenance in stem cells (2011)

To understand the complex regulation of genomic imprinting it is important to determine how early embryos establish imprinted gene expression across large chromosomal domains. Long non-coding RNAs (ncRNAs) have been associated with the regulation of imprinting domains, yet their function remains undefined. Here, we investigated the mouse Kcnq1ot1 ncRNA and its role in imprinted gene regulation during preimplantation development by utilizing mouse embryonic and extra-embryonic stem cell models. Our findings demonstrate that the Kcnq1ot1 ncRNA extends 471 kb from the transcription start site. This is significant as it raises the possibility that transcription through downstream genes might play a role in their silencing, including Th, which we demonstrate possesses maternal-specific expression during early development. To distinguish between a functional role for the transcript and properties inherent to transcription of long ncRNAs, we employed RNA interference-based technology to deplete Kcnq1ot1 transcripts. We hypothesized that post-transcriptional depletion of Kcnq1ot1 ncRNA would lead to activation of normally maternal-specific protein-coding genes on the paternal chromosome. Post-transcriptional short hairpin RNA-mediated depletion in embryonic stem, trophoblast stem and extra-embryonic endoderm stem cells had no observable effect on the imprinted expression of genes within the domain, or on Kcnq1ot1 imprinting center DNA methylation, although a significant decrease in Kcnq1ot1 RNA signal volume in the nucleus was observed. These data support the argument that it is the act of transcription that plays a role in imprint maintenance during early development rather than a post-transcriptional role for the RNA itself.
CoC: Secure Supply Chain Management System Based on Public Ledger (2017)

Modern supply chain is a complex system and plays an important role for different sectors under the globalization economic integration background. Supply chain management system is proposed to handle the increasing complexity and improve the efficiency of flows of goods. It is also useful to prevent potential frauds and guarantee trade compliance. Currently, most companies maintain their own IT system for supply chain management. However, this approach has some limitations that prevent one to get most of the supply chain information. Using emerging decentralized ledger technology to build supply chain management system is a promising direction. However, decentralized ledger usually suffers from low performance and lack of capability to protect information stored on the ledger. To overcome these challenges, we propose CoC, a novel supply chain management system based on hybrid decentralized ledger. We develop an efficient block construction method with the model and security mechanism to prevent unauthorized access to data stored on the ledger.
Pedestrian-movement prediction based on mixed Markov-chain model (2011)

A method for predicting pedestrian movement on the basis of a mixed Markov-chain model (MMM) is proposed. MMM takes into account a pedestrian's personality as an unobservable parameter. It also takes into account the effects of the pedestrian's previous status. A promotional experiment in a major shopping mall demonstrated that the highest prediction accuracy of the MMM method is 74.4%. In comparison with methods based on a Markov-chain model (MM) and a hidden-Markov model (HMM) (i.e., prediction rates of about 45% and 2%, respectively), the proposed MMM-based prediction method is substantially more accurate. This pedestrian-movement prediction based on MMM using tracking data will make it possible to provide so-called "adaptive mobile services" with proactive functions.
Changes in the extents of viable and necrotic tissue, interstitial fluid pressure, and proliferation kinetics in clone A human colon tumour xenografts as a function of tumour size (1994)

Abstract. Total, viable and necrotic tumour tissue, tumour cell yields, and colony forming efficiencies were measured in clone A human colon tumour xenografts as neoplasms grew from about 100 mm 3 to about 6000 mm 3 . The volumes of the total, viable and necrotic compartments were fit using the Verhulst equation to obtain estimates of growth rates and maximal sizes of the various compartments (carrying capacities). Additionally, at four discrete tumour volumes (250, 850, 2500 and 5500 mm 3 ), hypoxic percentages, proportions of parenchymal tumour and host cells, interstitial fluid pressures, and proliferation kinetics including measurements of apoptosis were determined. There were interesting relationships between the shapes of the curves for total, viable and necrotic tissue to some of the other endpoints measured. Specifically, the volumetric growth curves for the total and viable tumour tissue compartments were identical to a volume of approximately 1000 mm 3 , but diverged at larger sizes, with the viable cell compartment exhibiting a smaller carrying capacity. The shape of the growth curve for the necrotic compartment exactly mimicked that for the total volume compartment, but was delayed in time by about 21 days. Similarity in shape to that of the overall tumour volume/necrotic volume curves was also seen for the curve for the increase in interstitial fluid pressure, and for the increase in the size of the host cell compartment. In contrast, the growth of the hypoxic compartment and of the parenchymal tumour cell compartment were similar in shape to that of the viable compartment. These data indicate that these compartments are functionally linked. Marked changes in cell kinetic parameters occurred as tumour size increased from 250–5500 mm 3 . The labelling index and growth fractions decreased from 0.256–0.125, and 0.77–0.40 respectively, and the cell loss factor increased from 0.52–0.74. The volumetric and potential doubling times increased from 4.3–17.6 and 2.1–4.6 days respectively. The cell kinetic changes could not be clearly related to the changes in shape of either the overall tumour volume or the viable tumour volume.
A formal basis for structured multimedia collaborations (2002)

A formal basis for multimedia collaborations is proposed. The formal basis establishes a precise mathematical framework for supporting a wide spectrum of structured collaborative tasks, ranging from sample meetings and conferences to classrooms and examinations, and from corporate negotiations, work flow tasks, and team design endeavours to courtroom hearings. We mechanize three levels of abstraction: streams at the lowest level, for media communication, sessions at the next level, which represent collections of semantically related media streams, and conferences, which represent temporally related sequences of sessions. The mathematical framework has been mechanized in Prototype Verification System from SRI International. The mechanization allows us to experiment with different formal models, and reason about properties of multimedia collaborations efficiently.
Understanding Kin Relationships in a Photo (2012)

There is an urgent need to organize and manage images of people automatically due to the recent explosion of such data on the Web in general and in social media in particular. Beyond face detection and face recognition, which have been extensively studied over the past decade, perhaps the most interesting aspect related to human-centered images is the relationship of people in the image. In this work, we focus on a novel solution to the latter problem, in particular the kin relationships. To this end, we constructed two databases: the first one named UB KinFace Ver2.0, which consists of images of children, their young parents and old parents, and the second one named FamilyFace. Next, we develop a transfer subspace learning based algorithm in order to reduce the significant differences in the appearance distributions between children and old parents facial images. Moreover, by exploring the semantic relevance of the associated metadata, we propose an algorithm to predict the most likely kin relationships embedded in an image. In addition, human subjects are used in a baseline study on both databases. Experimental results have shown that the proposed algorithms can effectively annotate the kin relationships among people in an image and semantic context can further improve the accuracy.
Novel molecular and bioinformatics approaches to investigate DNA methylation in human epigenome (2017)

In recent years, advances in sequencing have enabled the mapping of DNA methylation variation across many different populations of human cell types and the identification of candidate DNA methylation biomarkers for clinical applications. The clinical development of DNA methylation biomarkers has been limited, however, due to the high cost and the lack of flexibility in using the current experimental and bioinformatics tools. We made improvements to the design of bisulfite padlock probes (BSPP) to greatly increase efficiency and throughput for targeted DNA methylation quantification. The cost effectiveness and scalability of this approach was demonstrated on hundreds of samples using a set of 330,000 probes. We also developed a bioinformatics pipeline that performs SNP calling on bisulfite data and DNA methylation quantitation with reduced errors from various different assay types.Despite many available bioinformatics tools for differential DNA methylation analysis, there is a need for a more general computational tool to characterize DNA methylation variability on reference data. Therefore, we developed a new differential methylation identification method and variability score to quantify DNA methylation variation across multiple groups of samples. For simulated 5X average depth of coverage datasets, cgDMR-miner, identified 42% of simulated DMRs with 73% precision while the next best approach identified 23% of simulated DMRs with 96% precision. Thus cgDMR-miner can identify potential targets from a shallow, low accuracy initial screen that can later be validated with a deeper screen using a targeted assay.Lastly, the coordinated methylation of nearby CpG sites was investigated in order to identify more robust biomarkers for cancer. Starting with a set of identified 147,888 regions of tightly coupled CpG methylation or methylation haplotype blocks (MHBs), the linked status of CpGs within these regions were found useful for biomarker identification in human tissue samples and human cell free DNA.
Switch of CD4+ T Cell Differentiation from Th2 to Th1 by Treatment with Cathepsin B Inhibitor in Experimental Leishmaniasis (1998)

When activated, CD4+ T helper cells differentiate functionally into one of two subsets, Th1 or Th2. Before the Th differentiation, Ags must be processed into peptide epitopes and presented to CD4+ T cells in association with MHC class II molecules. However, the proteases responsible for this Ag processing have not been well defined. When BALB/c mice susceptible to infection with Leishmania major were treated with a specific inhibitor (CA074) of cathepsin B, a lysosomal cysteine protease that digests exogenous antigenic proteins, those mice acquired resistance against infection with L. major and showed the shift of immune responses from Th2 to Th1; that is, they produced specific IgG2a Ab and generated IFN-gamma in contrast to untreated and infected mice that produced IgG1 and IgE and generated IL-4. CA074 interfered with the digestion of L. major Ags with lysosomal enzymes in vivo as well as in vitro. However, this inhibitor did not show any direct influence on the growth of L. major and the functions of T cells stimulated with anti-CD3 Ab. These findings indicate that cathepsin B inhibitor could switch CD4+ T cell differentiation from Th2 to Th1, suggesting that the alteration in Ag processing modulates the polarity of Th differentiation.
The Multi-objective Dynamic Traveling Salesman Problem: Last Mile Delivery with Unmanned Aerial Vehicles Assistance (2019)

In this paper, we present an approach to optimizing the last-mile delivery route of a truck using coordination with unmanned aerial vehicles (UAVs). First, a traveling salesman problem is formulated to determine the truck's route. Then, a scheduling problem is formulated to determined the routes for the UAVs. A genetic algorithm is used to solve these problems, and simulated results are presented.
Design and Synthesis of LNA-Based Mercaptoacetamido-Linked Nucleoside Dimers (2013)

Three LNA-based mercaptoacetamido-linked nonionic nucleoside dimers TL-S-T, T-S-TL, and TL-S-TL have been synthesized by HOBT and HBTU catalyzed condensation of silyl-protected 2-S-(thymidin-5 '-yl)mercaptoacetic acid or 2-S-(2 '-O,4 '-C-methylenethymidin-5 '-yl)mercaptoacetic acid with 3 '-amino-3 '-deoxy-5 '-O-DMT-2 '-O,4 '-C-methylenethymidine or with 3 '-amino-3 '-deoxy-5 '-O-DMT-β-thymidine followed by desilylation of the protected dimers. The 3 '-O-phosphoramidite derivative of one of the nucleoside dimers was successfully prepared by condensation with [P(-Cl)(-OCH2CH2CN)-N(iPr)2}] in DCM in the presence of N,N-diisopropylethylamine (DIPEA), which is a building block for the preparation of mercaptoacetamido-linked oligonucleotides of therapeutic applications.
Gene discovery through expressed sequence tag (EST) in <i>Porphyridium</i> sp.: Search for genes of industrial and scientific importance (2002)

Conference Abstract| February 01 2002 Gene discovery through expressed sequence tag (EST) in Porphyridium sp.: Search for genes of industrial and scientific importance R. Shrestha; R. Shrestha 1Institute for Applied Biosciences and Department of Microbiology and Immunology, Ben-Gurion University, Beer-Sheva, Israel Search for other works by this author on: This Site PubMed Google Scholar M. Lapidot; M. Lapidot 1Institute for Applied Biosciences and Department of Microbiology and Immunology, Ben-Gurion University, Beer-Sheva, Israel Search for other works by this author on: This Site PubMed Google Scholar Y. Weinstein; Y. Weinstein 1Institute for Applied Biosciences and Department of Microbiology and Immunology, Ben-Gurion University, Beer-Sheva, Israel Search for other works by this author on: This Site PubMed Google Scholar S. Malis Arad S. Malis Arad 1Institute for Applied Biosciences and Department of Microbiology and Immunology, Ben-Gurion University, Beer-Sheva, Israel Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2002) 30 (1): A29. https://doi.org/10.1042/bst030a029c Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation R. Shrestha, M. Lapidot, Y. Weinstein, S. Malis Arad; Gene discovery through expressed sequence tag (EST) in Porphyridium sp.: Search for genes of industrial and scientific importance. Biochem Soc Trans 1 February 2002; 30 (1): A29. doi: https://doi.org/10.1042/bst030a029c Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2002 Biochemical Society2002 Article PDF first page preview Close Modal You do not currently have access to this content.
Development of prestriate visual projections in the monkey and human fetal cerebrum revealed by transient cholinesterase staining (1984)

Cholinesterase (ChE) staining was used to reveal the timing and pattern of development of afferents to the prestriate visual cortex (areas 18, 19, 20, and 21 of Brodmann) in a series of developing human and monkey fetal brains. This investigation was possible because the nucleus pulvinaris of the thalamus, the main source of subcortical projections to the prestriate cortex, displays positive reactivity after thiocholine incubation during the last three quarters of gestation, while neighboring thalamic nuclei that project to the adjacent neocortical areas are unstained. Staining of the pulvinar and its prestriate projections passes through six broad stages. Stage I begins in both species at the end of the first third of gestation. Positively stained fibers originate from the pulvinar and enter but do not extend beyond the hemispheric stalk. During stage II, pulvinar axons gradually invade the intermediate zone of the occipital lobe, and in stage III they reach the level of the subplate zone. In stage IV, which occurs around mid-gestation in both species, cholinesterase-positive fibers accumulate within the subplate zone subjacent to the developing prestriate cortex. During stage V, ChE-positive fibers penetrate the prospective prestriate cortex but do not yet form the alternating columnar pattern characteristic of pulvinar input to this area in the adults. Rather, ChE activity is concentrated in two continuous bands situated within prospective layers III-IV and VI; also a narrow band is visible in upper layer I. In stage V a clear histochemical border forms between prestriate and striate areas with ChE activity in prospective area 17 limited mostly to the superficial strata of layers I and II. This histochemical differentiation precedes the emergence of cytoarchitectonic landmarks. During stage VI, which begins in the last fifth of gestation in both species, the pulvinar become progressively less stainable and its projections can no longer be traced by ChE histochemistry.
Tannins and related compounds. XLV Rhubarb. 5 Isolation and characterization of flavan-3-ol and procyanidin glucosides. (1986)

A chemical examination of high-quality commercial rhubarb (Choukichio : ?? ?? ?? ) has led to the isolation and characterization of eight flavan-3-ol glucosides and three proanthocyanidin glucosides, together with several known compounds, i.e., (+)-catechin 5-O-β-D-glucopyranoside (1), (+)-catechin 7-O-β-D-glucopyranoside (2), procyanidin B-2 8-C-β-D-glucopyranoside (3) and procyanidin B-2 6-C-β-D-glucopyranoside (4). On the basis of chemical and spectroscopic evidence, the former compounds were characterized as (+)-catechin 3'-O-β-D-glucopyranoside (5), (+)-catechin 4'-O-β-D-glucopyranoside (6), (+)-catechin 7, 3'-di-O-β-D-glucopyranoside (7), (+)-catechin 5, 3'-di-O-β-D-glucopyranoside (8), (+)-catechin 3', 4'-di-O-β-D-glucopyranoside (9), (+)-catechin 5, 4'-di-O-β-D-glucopyranoside (10), (+)-catechin 8-C-β-D-glucopyranoside (11), (+)-catechin 6-C-β-D-glucopyranoside (12), procyanidin B-3 7-O-β-D-glucopyranoside (13), procyanidin B-1 8-C-β-D-glucopyranoside (14) and procyanidin B-1 6-C-β-D-glucopyranoside (15).