gebhart/patrepeval huggingface dataset:
Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network (2020)

Nanopore sequencing is promising because of its long read length and high speed. During sequencing, a strand of DNA/RNA passes through a biological nanopore, which causes the current in the pore to fluctuate. During basecalling, context-dependent current measurements are translated into the base sequence of the DNA/RNA strand. Accurate and fast basecalling is vital for downstream analyses such as genome assembly and detecting single-nucleotide polymorphisms and genomic structural variants. However, owing to the various changes in DNA/RNA molecules, noise during sequencing, and limitations of basecalling methods, accurate basecalling remains a challenge. In this paper, we propose Causalcall, which uses an end-to-end temporal convolution-based deep learning model for accurate and fast nanopore basecalling. Developed on a temporal convolutional network (TCN) and a connectionist temporal classification decoder, Causalcall directly identifies base sequences of varying lengths from current measurements in long time series. In contrast to the basecalling models using recurrent neural networks (RNNs), the convolution-based model of Causalcall can speed up basecalling by matrix computation. Experiments on multiple species have demonstrated the great potential of the TCN-based model to improve basecalling accuracy and speed when compared to an RNN-based model. Besides, experiments on genome assembly indicate the utility of Causalcall in reference-based genome assembly.
Molecular cloning of human angiotensinogen cDNA and evidence for the presence of its mRNA in rat heart. (1987)

Human angiotensinogen cDNA clone was isolated from a liver cDNA library using a 32-nucleotide-long, synthetic oligonucleotide. The cDNA insert was 1,030 bp long and coded for the secretory and biologically active angiotensin II regions of the angiotensinogen molecule. The RNA from rat liver, brain, and heart was analyzed by the Northern hybridization procedure using nick translated angiotensinogen cDNA as a probe. In addition to liver, the angiotensinogen mRNA is present in the brain and the heart. The angiotensinogen mRNA in the heart is at least fourfold to fivefold more abundant as compared with the liver. We also provide evidence that angiotensinogen mRNA is present in the rat atria and right ventricle but not detectable in the left ventricle. The size of the angiotensinogen mRNA is the same from all three of the tissues, as judged by their electrophoretic mobilities.
Real-Time Control of Wastewater Treatment Systems Using ORP (1993)

Oxidation-Reduction Potential (ORP) can be used as a process control parameter for real-time automated control of batch sewage treatment systems. Results suggest that ORP has great potential for the control of anoxic sequences, since the distinct breakpoint in the ORP-time curve correlates to the disappearance of nitrates.
Highly conserved repetitive DNA sequences are present at human centromeres. (1992)

Highly conserved repetitive DNA sequence clones, largely consisting of (GGAAT)n repeats, have been isolated from a human recombinant repetitive DNA library by high-stringency hybridization with rodent repetitive DNA. This sequence, the predominant repetitive sequence in human satellites II and III, is similar to the essential core DNA of the Saccharomyces cerevisiae centromere, centromere DNA element (CDE) III. In situ hybridization to human telophase and Drosophila polytene chromosomes shows localization of the (GGAAT)n sequence to centromeric regions. Hyperchromicity studies indicate that the (GGAAT)n sequence exhibits unusual hydrogen bonding properties. The purine-rich strand alone has the same thermal stability as the duplex. Hyperchromicity studies of synthetic DNA variants indicate that all sequences with the composition (AATGN)n exhibit this unusual thermal stability. DNA-mobility-shift assays indicate that specific HeLa-cell nuclear proteins recognize this sequence with a relative affinity greater than 10(5). The extreme evolutionary conservation of this DNA sequence, its centromeric location, its unusual hydrogen bonding properties, its high affinity for specific nuclear proteins, and its similarity to functional centromeres isolated from yeast suggest that this sequence may be a component of the functional human centromere.
CD16 (FcRγIII) as a potential marker of osteoclast precursors in psoriatic arthritis (2010)

An increased frequency of circulating CD14+CD16+ cells was noted in PsA compared to controls, and intermediate levels of CD16 may suggest a transitional state of OCP during osteoclastogenesis. Intriguingly, TNFalpha blocked CD16 expression on a subset of CD14+ monocytes. Collectively, our data suggest that CD16 has the potential to serve as an OCP marker in inflammatory arthritis.
Controlling stereochemistry during oxidative coupling. Preparation of Rp or Sp phosphoramidates from one P-chiral precursor (2004)

Stereochemical outcome of oxidative coupling of H-phosphonate diesters with amines, promoted by iodine, can be controlled to obtain the corresponding phosphoramidate diesters with inversion or with retention of configuration at the phosphorus centre.
A 1V 24GHz 17.5mW PLL in 0.18μm CMOS (2005)

A 1V 24GHz fully integrated PLL is designed in a 0.18/spl mu/m. CMOS process using a transformer-feedback VCO and a stacked frequency divider. The PLL measures an in-band phase noise of -106.3dBc/Hz at 100kHz offset and an out-of-band phase noise of -119.1dBc/Hz at 10MHz offset. It consumes 17.5mW from a 1V supply and occupying an area of 0.55mm/sup 2/.
Effect of noble metal buffer layers on superconducting YBa2Cu3O7 thin films (1987)

Superconducting YBa2Cu3O7 thin films have been prepared by using a magnetron sputtering system in the single-source mode. Samples deposited on [100] single-crystal MgO with and without a Au buffer layer all show high transition temperatures (82–87 K). The use of a Au buffer layer significantly improves the superconducting properties, particularly the Meissner effect and critical current density (3.3×106 A/cm2 at T=2 K and 3.5×104 A/cm2 at T=77 K). The Au films remain metallic after high-temperature annealing in an oxygen atmosphere. We propose to use Au buffer layers as current shunts to protect superconducting films and devices.
Mechanisms of etch hillock formation (1996)

We have studied the formation of etch hillock defects during anisotropic etching of (100) silicon in KOH. Defect density is correlated with low etchant concentration and high etch temperature. Cathodic etch experiments indicate that hillocks form under conditions of decreased OH/sup -/ ion concentration. The activation energy for defect formation is 1.2 eV, considerably higher than the energy associated with silicon removal. We propose a mechanism to explain hillock formation that involves nucleation by silicon redeposited from the etch solution. The incidence of hillocks in this model is the result of a competition between the forward and reverse etch reactions. Examination of defects by electron microscopy suggests that growth occurs preferentially on slow-etching planes, in agreement with the model predictions.
A physical mobile radio channel model (1991)

A model is presented for the time- and frequency-selective outdoor mobile radio channel. which is based on the physical process of wave propagation in a statistical fluctuating medium. The reduction of this complex scattering problem to a set of relations containing the pertinent statistics for conducting communications system analysis is developed. Characteristics of the propagation process, e.g., delay power spectra, amplitude distribution (Nakagami-m-distribution), and correlation functions, are derived in parameterized form from physical considerations. The method allows a classification of real configurations (environments) into several classes and the extraction of the relevant parameters in direct comparison with measured data. The method is applied to typical channel situations in Switzerland. The mathematical modeling of the classes is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PCR-based assessment of the recovery rate of exfoliated colonocytes or cancer cells from fecal samples depends on the storage conditions after defecation. (2007)

The present data provided important clinical knowledge regarding the storage of fecal samples for future mass screening tests.
A Role for Class A Scavenger Receptor in Dendritic Cell Nibbling from Live Cells (2003)

Monocyte-derived dendritic cells (DC) possess the unique capacity to capture Ag from live cells through intimate cell contact, a process referred to as nibbling. We sought to define the receptor(s) mediating DC nibbling. Uptake of fluorescently labeled plasma membrane from live cells by DC was inhibited by protease treatment and by a panel of polyanionic ligands, implicating scavenger receptors (SR) in this process. Differential expression of SR on DC and macrophages correlated with the capacity to acquire membrane from live cells. Internalized membrane colocalized with SR ligand and entered the endosomal pathway. DC very efficiently acquired and internalized gp100 tumor Ag expressed at the surface of viable adenocarcinoma cells via recombinant adenoviral infection. Cross-presentation of gp100 by DC to MHC class I-restricted T cells was inhibited by polyanionic SR ligand and an Ab to type A SR (SR-A), whereas Ab to the class B SR CD36, which mediates uptake of apoptotic cells, induced no inhibition. DC capture of fluorescently labeled membrane from live cells was partially blocked by SR-A-specific Ab, suggesting that other SR may also be contributing to nibbling. DC maturation resulted in a switch in expression from type II SR-A (SR-AII) to the SR-AI splice variant. Finally, SR-A was identified on interdigitating DC isolated from monkey lymph nodes. These findings define a novel role for SR-A, and suggest that Ag uptake from live cells by DC may be important in the generation of immunity and in the maintenance of peripheral tolerance in vivo.
Two lipases from <i>Candida antarctica</i>: cloning and expression in <i>Aspergillus oryzae</i> (1995)

The basidiomycetous yeast Candida antarctica expresses two lipases that possess widely different properties. The genes LIPA and LIPB encoding both lipases were cloned and sequenced. Both lipases were secreted efficiently from Aspergillus oryzae transformed with lipase expression plasmids. N-Glycosylation was slightly more extensive in the heterologously expressed enzymes than in those purified from C. antarctica, but the enzymatic characteristics were retained. Both enzymes are encoded as preproenzymes. Proteolytic processing of the primary translation product was efficient in A. oryzae and resulted in the same N-terminals as in C. antarctica. Modifications or deletions of the propeptide of lipase component B did not prevent efficient secretion of active lipase from A. oryzae. Alternative proteolytic processing of the modified propeptides was detected. Key words: Lipase, Candida, cloning, Aspergillus, expression, propeptide.
A 55-ns 16-Mb DRAM with built-in self-test function using microprogram ROM (1990)

A single 5-V power supply 16-Mb dynamic random-access memory (DRAM) has been developed using high-speed latched sensing and a built-in self-test (BIST) function with a microprogrammed ROM, in which automatic test pattern generation procedures were stored by microcoded programs. The chip was designed using a double-level Al wiring, 0.55- mu m CMOS technology. As a result, a 16-Mb CMOS DRAM with 55-ns typical access time and 130-mm/sup 2/ chip area was attained by implementing 4.05- mu m/sup 2/ storage cells. The installed ROM was composed of 18 words*10 b, where the marching test and checkerboard scan write/read test procedures were stored, resulting in successful self-test operation. As the BIST circuit occupies 1 mm/sup 2/ and the area overhead is about 1%, it proves to be promising for large-scale DRAMs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Leveraging knowledge graphs for web-scale unsupervised semantic parsing (2013)

The past decade has seen the emergence of web-scale structured and linked semantic knowledge resources (e.g., Freebase, DBPedia). These semantic knowledge graphs provide a scalable “schema for the web”, representing a significant opportunity for the spoken language understanding (SLU) research community. This paper leverages these resources to bootstrap a web-scale semantic parser with no requirement for semantic schema design, no data collection, and no manual annotations. Our approach is based on an iterative graph crawl algorithm. From an initial seed node (entity-type), the method learns the related entity-types from the graph structure, and automatically annotates documents that can be linked to the node (e.g., Wikipedia articles, web search documents). Following the branches, the graph is crawled and the procedure is repeated. The resulting collection of annotated documents is used to bootstrap webscale conditional random field (CRF) semantic parsers. Finally, we use a maximum-a-posteriori (MAP) unsupervised adaptation technique on sample data from a specific domain to refine the parsers. The scale of the unsupervised parsers is on the order of thousands of domains and entity-types, millions of entities, and hundreds of millions of relations. The precision-recall of the semantic parsers trained with our unsupervised method approaches those trained with supervised annotations. Index Terms: semantic parsing, semantic web, semantic search, dialog, natural language understanding
Stimulating Concepts in Chemistry (2000)

Design and synthesis - theozymes and catalyst design organic synthesis in aqueous media domino reactions asymmetric two-center catalysis organic reactions in supercritical CO2 separation-built-in organic synthesis catalytic asymmetric synthesis of natural products combinatorial libraries architecture, organization and assembly - carbon - from fullerenes to new allotropes dendritic architecture constructive binding and slippage inclusion phenomena molecular organization molecular devices and material properties - molecular wires molecular devices and machines electron and energy transfer crystal engineering nano technology chemical sensors biological aspects - enzyme mimitics enzyme inhibitors organic synthesis and cell biology.
Use of interference lithography to pattern arrays of submicron resist structures for field emission flat panel displays (1997)

We report on the fabrication of square arrays of submicron resist dots and holes using interference lithography—a relatively simple and inexpensive way of generating periodic structures over large areas. The arrays are formed by exposing a layer of resist to a two-beam interference pattern followed by a second exposure after rotating the sample by 90°. Arrays with periods of 0.67–3.2 μm were fabricated. The size of the structures is accurately controlled by varying the exposure dose. The exposure latitude for patterning arrays of dots is ±16% for a ±10% change in structure width when an optimum size-to-period ratio is chosen. Compared to dots, holes are patterned with a smaller process window. We show that arrays of dots with diameters as small as 0.20 μm, sidewall slopes of 88°, and aspect ratios as high as 3:1 can be produced. These structures are well suited for the production of field emission flat panel displays.
Effect of Contrast Material Injection Duration and Rate on Aortic Peak Time and Peak Enhancement at Dynamic CT Involving Injection Protocol with Dose Tailored to Patient Weight (2004)

Aortic peak time, aortic peak enhancement, and T200 were closely related to injection duration in the protocol with contrast material dose determined according to patient weight.
Efficient updates in highly available distributed random access memory (2006)

With increased network speeds and throughputs, multicomputers (a system of computers connected by a high-speed network) have become an attractive alternative to store important data in their collective random access memory. Erasure codes provide space-optimal data redundancy to protect this type of storage from node unavailability. They have been used in LH*RS, the scalable high availability, distributed version of linear hashing. We present and evaluate a technique that uses the property of linear erasure correcting codes to make updates transactional and concurrent with recovery from one or more node availabilities without locks or two-phase commits. The technique significantly improves on previous work in update speed and also allows for serializable updates to a bucket that is in the process of being recovered
Semantic Grid-Based Road Model Estimation for Autonomous Driving. (2019)

For autonomous driving, knowledge about the current environment and especially the driveable lanes is of utmost importance. Currently this information is often extracted from meticulously (hand-)crafted offline high-definition maps, restricting the operation of autonomous vehicles to few well-mapped areas and making it vulnerable to temporary or permanent environment changes. This paper addresses the issues of map-based road models by building the road model solely from online sensor measurements. Based on Dempster-Shafer theory and a novel frame of discernment, sensor measurements, such as lane markings, semantic segmentation of drivable and non-drivable areas and the trajectories of other observed traffic participants are fused into semantic grids. Geometrical lane information is extracted from these grids via an iterative path-planning method. The proposed approach is evaluated on real measurement data from German highways and urban areas.
Cre-loxP mediated marker elimination and gene reactivation at the waxy locus created in rice genome based on strong positive-negative selection (2010)

The combination of homologous and site-specific recombination, if possible, could create mutants, such as tissue- or growth phase- specific gene knockout. In higher plants, there is no information on the site-specific recombination of the endogenous gene locus modified by gene targeting (GT) because of still limited success of reproducible GT for the endogenous gene. Our method of rice GT mediated by a strong positive–negative selection is appropriate for combined use with site-specific recombination because, in our method, it is possible to manipulate genome sequence variously without any unintentional random transformation, including ectopic targeting. We had previously created a targeted-waxy mutant by inserting the hygromycin phospho transferase (hpt) with ΔEn (a functional transcriptional stop sequence from En/Spm transposon), into the Waxy intron 1 region upstream of the translational initiation site. Since this inserted sequence was sandwiched by a pair of loxP in the same orientation, here, we tested Cre-loxP mediated elimination of this targeted insertion. The Cre was transiently expressed by a highly active promoter of CaMV 35S with the castor bean catalase intron 1 in the calli of the targeted-waxy homozygote. Cells derived from the treated calli were grown independently and applied to PCR screening as a bulk of calli clumps. Although the efficiency was quite low, Cre-loxP mediated hpt-ΔEn elimination and Waxy reactivation in the pollen of regenerated plants were detected as expected in some cells.
Enhanced Antioxidant Activity After Chlorination of Quercetin by Hypochlorous Acid (2001)

These data suggest that under certain pathological conditions in vivo (e.g., inflammation), flavonols may be converted to chlorinated derivates, which exhibit an enhanced antioxidant potential and thereby play a role in cardioprotection.
A Proactive Secret Sharing Scheme in matrix projection method (2009)

Proactive Secret Sharing (PSS) scheme is a method to periodically renew n secret shares in a (k, n) threshold-based Secret Sharing Scheme (SSS) without modifying the secret, or reconstructing the secret to reproduce new shares. Traditionally, PSS schemes are developed for the Shamir's SSS which is a single SSS. Bai (2006) developed a multiple-secret sharing scheme using matrix projection. This paper presents a distributed PSS method for the matrix projection SSS. Once the new shares are updated, adversaries cannot discover the secrets from k shares which are mixed with past and present shares.
A Ka-band 3-bit RF MEMS true-time-delay network (2003)

A monolithic Ka-band true-time-delay (TTD) switched-line network containing 12 metal-to-metal contact RF microelectromechanical system switches has been successfully fabricated and characterized on a 75-/spl mu/m-thick GaAs substrate. The compact 9.1-mm/sup 2/ TTD network was designed to produce flat delay time over a dc-to-40-GHz bandwidth with full 360/spl deg/ phase control at 45/spl deg/ intervals at 35 GHz. Measurements show a match to within 2% to the designed delay times at 35 GHz for all eight switch states with 2.2-dB average insertion loss over all states. Peak rms phase error is 2.28/spl deg/ and peak rms amplitude error is 0.28 dB from dc to 40 GHz. Return loss better than 15 dB from dc to 40 GHz for all eight states confirms the circuit's broad-band operation.
Amino-functionalization of large-pore mesoscopically ordered silica by a one-step hyperbranching polymerization of a surface-grown polyethyleneimine (2006)

A simple method for surface functionalization of large-pore mesoporous silica by hyperbranching polymerization resulting in a high loading of amine groups is presented.
Polymeric Memory Elements and Logic Circuits that Store Multiple Bit States (2010)

The ever-increasing flow of information requires new approaches for high-density data storage (HDDS). Here, we present a novel solution that incorporates the easily accessible polymer poly(3,4-ethylenedioxythiophene) (PEDOT) with multistate memory. The electrical addressable polymer is able to store up to five different memory states, which are stable up to 20 min. The observed memory states are generated by the optical output signature of the PEDOT deposited on indium tin oxide (ITO) coated glass, upon applying specific electrical inputs. Moreover, the demonstrated platforms can be represented by a general logic circuit, which allows the construction of multistate memory, such as flip-flops and flip-flap-flop logic circuits.
The Dual Effects of Δ<sup>9</sup>-Tetrahydrocannabinol on Cholangiocarcinoma Cells: Anti-Invasion Activity at Low Concentration and Apoptosis Induction at High Concentration (2010)

Currently, only gemcitabine plus platinum demonstrates the considerable activity for cholangiocarcinoma. The anticancer effect of Δ 9-tetrahydrocannabinol (THC), the principal active component of cannabinoids has been demonstrated in various kinds of cancers. We therefore evaluate the antitumor effects of THC on cholangiocarcinoma cells. Both cholangiocarcinoma cell lines and surgical specimens from cholangiocarcinoma patients expressed cannabinoid receptors. THC inhibited cell proliferation, migration and invasion, and induced cell apoptosis. THC also decreased actin polymerization and reduced tumor cell survival in anoikis assay. pMEK1/2 and pAkt demonstrated the lower extent than untreated cells. Consequently, THC is potentially used to retard cholangiocarcinoma cell growth and metastasis.
Finding bugs in spreadsheets using reference counting (2015)

Spreadsheets are considered one of the most widely used end-user programming environments. Just as it is important for software to be free of bugs, spreadsheets need to be free of errors. This is important because in some cases, errors in spreadsheets can cost a financial entity thousands of dollars. In this work, we formulate a class of commonplace errors based on our manual inspection of real life spreadsheets, and further provide an analysis algorithm to detect these errors. We introduce ``reference counting'' as a simple yet effective algorithm to detect range errors. We finally demonstrate how reference counting can effectively point out erroneous cells in faulty spreadsheets.