gebhart/patrepeval huggingface dataset:
Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product (1996)

To facilitate the scanning of large genomic regions for the presence of exonic gene segments we have constructed a cosmid-based exon trap vector. The vector serves a dual purpose since it is also suitable for contig construction and physical mapping. The exon trap cassette of vector sCOGH1 consists of the human growth hormone gene driven by the mouse mettallothionein-1 promoter. Inserts are cloned in the multicloning site located in intron 2 of the hGH gene. The efficiency of the system is demonstrated with cosmids containing multiple exons of the Duchenne Muscular Dystrophy gene. All exons present in the inserts were successfully retrieved and no cryptic products were detected. Up to seven exons were isolated simultaneously in a single spliced product. The system has been extended by a transcription-translation-test protocol to determine the presence of large open reading frames in the trapped products, using a combination of tailed PCR primers directing protein synthesis in three different reading frames, followed by in vitro transcription-translation. Having larger stretches of coding sequence in a single exon trap product rather than small single exons greatly facilitates further analysis of potential genes and offers new possibilities for direct mutation analysis of exon trap material.
Design and fabrication of SOI micro-ring resonators based on sub-wavelength grating waveguides (2015)

Standard silicon photonic strip waveguides offer a high intrinsic refractive index contrast; this permits strong light confinement, leading to compact bends, which in turn facilitates the fabrication of devices with small footprints. Sub-wavelength grating (SWG) based waveguides can allow the fabrication of low loss devices with specific, engineered optical properties. The combination of SWG waveguides with optical micro-resonators can offer the possibility of achieving resonators with properties different from the traditional SOI rings. One important property that SWG rings can offer is decreased light confinement in the waveguide core; this improves the resonator's sensitivity to changes in the cladding refractive index, making the rings ideal for refractive index sensing applications. In this paper, we present the design and experimental characterization of SWG based rings realized on SOI chips without upper cladding (permitting their use as sensors). The fabricated rings offer quality factors in the range of ~1k-6k, depending on SWG parameters. Based on the comparison of experimental and simulated data we expect sensitivities exceeding 383 nm/RIU in water and 270 nm/RIU in air, showing excellent potential for use in sensing applications.
Decoupled software pipelining with the synchronization array (2004)

Despite the success of instruction-level parallelism (ILP) optimizations in increasing the performance of microprocessors, certain codes remain elusive. In particular, codes containing recursive data structure (RDS) traversal loops have been largely immune to ILP optimizations, due to the fundamental serialization and variable latency of the loop-carried dependence through a pointer-chasing load. To address these and other situations, we introduce decoupled software pipelining (DSWP), a technique that statically splits a single-threaded sequential loop into multiple nonspeculative threads, each of which performs useful computation essential for overall program correctness. The resulting threads execute on thread-parallel architectures such as simultaneous multithreaded (SMT) cores or chip multiprocessors (CMP), expose additional instruction level parallelism, and tolerate latency better than the original single-threaded RDS loop. To reduce overhead, these threads communicate using a synchronization array, a dedicated hardware structure for pipelined inter-thread communication. DSWP used in conjunction with the synchronization array achieves an 11% to 76% speedup in the optimized functions on both statically and dynamically scheduled processors.
Dimensions in solution of pyridoxylated apohemoglobin (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDimensions in solution of pyridoxylated apohemoglobinJanusz Kowalczyck and Enrico BucciCite this: Biochemistry 1983, 22, 20, 4805–4809Publication Date (Print):September 27, 1983Publication History Published online1 May 2002Published inissue 27 September 1983https://pubs.acs.org/doi/10.1021/bi00289a029https://doi.org/10.1021/bi00289a029research-articleACS PublicationsRequest reuse permissionsArticle Views21Altmetric-Citations6LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
NRZ timing recovery technique for band-limited channels (1997)

Nonreturn-to-zero (NRZ) data, when transmitted over band-limited channels, suffer from the lack of zero crossings because the elongated tail of each pulse interferes with subsequent ones, causing intersymbol interference (ISI). An NRZ timing recovery technique working with a decision-feedback equalizer (DFE) recovers the clock from the equalized waveform and enables data transmission at a rate ten times higher than the channel bandwidth. The proposed timing recovery technique uses a data-triggered low-jitter phase detector to sustain phase locking even with 600 missing transitions, A data rate of 30 Mb/s in 3-MHz bandwidth is demonstrated with a peak-peak clock jitter of 2 ns using 2-/spl mu/m CMOS.
NCBI Viral Genomes Resource (2014)

Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.
Latent Space Policies for Hierarchical Reinforcement Learning (2018)

We address the problem of learning hierarchical deep neural network policies for reinforcement learning. In contrast to methods that explicitly restrict or cripple lower layers of a hierarchy to force them to use higher-level modulating signals, each layer in our framework is trained to directly solve the task, but acquires a range of diverse strategies via a maximum entropy reinforcement learning objective. Each layer is also augmented with latent random variables, which are sampled from a prior distribution during the training of that layer. The maximum entropy objective causes these latent variables to be incorporated into the layer's policy, and the higher level layer can directly control the behavior of the lower layer through this latent space. Furthermore, by constraining the mapping from latent variables to actions to be invertible, higher layers retain full expressivity: neither the higher layers nor the lower layers are constrained in their behavior. Our experimental evaluation demonstrates that we can improve on the performance of single-layer policies on standard benchmark tasks simply by adding additional layers, and that our method can solve more complex sparse-reward tasks by learning higher-level policies on top of high-entropy skills optimized for simple low-level objectives.
Analysis of 65 tuberous sclerosis complex (TSC) patients byTSC2DGGE,TSC1/TSC2MLPA, andTSC1long-range PCR sequencing, and report of 28 novel mutations (2005)

Tuberous sclerosis complex (TSC) is a severe autosomal-dominant disorder characterized by the development of benign tumors (hamartomas) in many organs. It can lead to intellectual handicap, epilepsy, autism, and renal or heart failure. An inactivating mutation in either of two tumor-suppressor genes-TSC1 and TSC2-is the cause of this syndrome, with TSC2 mutations accounting for 80-90% of all mutations. Molecular diagnosis of TSC is challenging, since TSC1 and TSC2 consist of 21 and 41 coding exons, respectively, and the mutation spectrum is very heterogeneous. Here we report a new approach for detecting mutations in TSC: a denaturing gradient gel electrophoresis (DGGE) analysis for small TSC2 mutations, a multiplex ligation-dependent probe amplification (MLPA) analysis for large deletions and duplications in TSC1 or TSC2, and a long-range PCR/sequencing-based analysis for small TSC1 mutations. When applied in this order, the three methods provide a new sensitive and time- and cost-efficient strategy for the molecular diagnosis of TSC. We analyzed 65 Danish patients who had been clinically diagnosed with TSC, and identified pathogenic mutations in 51 patients (78%). These included 36 small TSC2 mutations, four large deletions involving TSC2, and 11 small TSC1 mutations. Twenty-eight of the small mutations are novel. For the missense mutations, we established a functional assay to demonstrate that the mutations impair TSC2 protein function. In conclusion, the strategy presented may greatly help small- and medium-sized laboratories in the pre- and postnatal molecular diagnosis of TSC.
A novel binarization algorithm for ballistics imaging systems (2010)

The identification of ballistics specimens from imaging systems is of paramount importance in criminal investigation. Binarization plays a key role in preprocess of recognizing cartridges in the ballistic imaging systems. Unfortunately, it is very difficult to get the satisfactory binary image using existing binary algorithms. In this paper, we utilize the global and local thresholds to enhance the image binarization. Importantly, we present a novel criterion for effectively detecting edges in the images. Comprehensive experiments have been conducted over sample ballistic images. The empirical results demonstrate the proposed method can provide a better solution than existing binary algorithms.
Complete Rations for Dairy Cattle. II. Sugarcane Bagasse Pellets as Roughage in Blended Rations for Lactating Cows (1975)

Three groups of six lactating cows were allotted to complete rations containing either 25% sugarcane bagasse pellets, 25% cottonseed hulls, or 12.5% of each which were fed ad libitum for 10 wk in a continuous trial. Covariance adjusted dry matter intake as percent of body weight, kg milk/day, kg solids corrected milk/day and milk fat percent on the respective rations averaged 3.9, 4. 1, 4.0; 21.7, 22.8, 21.7; 22.0, 20.6, 21.1; and 4.1, 3.8 and 3.8. Sugarcane bagasse pellets were a satisfactory roughage substitute for cottonseed hulls. In Experiment II 36 lactating cows were assigned to complete rations containing 20, 25, or 30% sugarcane bagasse pellets fed ad libitum for 15 wk. Within each bagasse percent Coastal bermuda hay (1.36 kg offered~cow daily), sodium bentonite (3.7% of complete ration) or the control ration for that bagasse percent was fed for 5-wk periods (3 3 Latin square design). Covariance adjusted means for dry matter intake as percent of body weight, kg milk/day, milk fat percent; kg solids corrected milk/day, solids-not-fat percent, and protein percent were 3.5, 3.6, 3.5; 18.6, 18.5, 18.1: 4.3, 4.7, 4.6; 18.8, 20.1, 19.2: 9.09, 9.15, 9.20; and 3.6, 3.6 and 3.6 for the 20, 25, and 30% bagasse rations. Cows on the 20% bagasse ration produced more solids corrected milk when hay was fed, and solids-not-fat
Dynamic channel allocation for vehicle-to-vehicle communications in automated highway systems (2002)

Efficient channel allocation for the purpose of vehicle-to-vehicle communications in automated highway system (AHS) is an unsolved problem. The extension of cellular mobile framework to the AHS is inefficient and faulty. We propose two algorithms in this paper: 1) a centralized algorithm that allocates channels by keeping track of the vehicles through a network of detectors; and 2) a mixed-control algorithm that combines vehicle-based channel interference measurements with the centralized algorithm.
Oxidation of Maltodextrins and Starch by the System Tungstate‐Hydrogen Peroxide (1989)

Abstract The potential of the aqueous system sodium tungstate‐hydrogen peroxide for glycol‐cleavage oxidation of maltodextrins, starch and trans ‐1,2‐cyclohexanediol as a model compound has been evaluated. The peroxotungstate species formed in this medium effect oxidation of the glucose units via two major pathways: ( i ) glycol‐cleavage of the C2–C3 diol moieties in internal glucose units, followed by (undesired) hydrolysis of the ring‐opened intermediate and ( ii ) stepwise decarboxylation at the reducing terminal glucose unit until the glycosidic bond is reached. Both reaction types yield glucose oligomers terminated by erythronic acid at the former reducing end, which is an important fraction (up to 40%) of the oxidation product. Decomposition of hydrogen peroxide to oxygen and water is an inevitable side reaction.
A novel Schottky/2-DEG diode for millimeter- and submillimeter-wave multiplier applications (1992)

A high-frequency diode is proposed for use as a frequency multiplier element in the millimeter- and submillimeter-wavelength regions. The Schottky/2-DEG diode utilizes a Schottky contact along the edge of a two-dimensional electron gas (2-DEG) structure. This geometry allows one to combine a very low series resistance due to the excellent transport properties of the 2-DEG with a high breakdown voltage caused by the 2-D electric field spreading in the depletion region (compared to a 1-D field variation in the conventional Schottky diode). The higher Fermi velocity of the 2-DEG leads to a less severe transit-time limitation of the frequency response.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The expression in E. coli of synthetic repeating polymeric genes coding for poly(L-aspartyl-L-phenylalanine) (1980)

Two dodecadeoxynucleotides of defined sequence have been synthesised by phosphotriester methodology. They can be polymerised to give a double stranded DNA which codes, when read in the correct phase, for the repeating dipeptide poly(aspartyl-phenylalanine). This polymeric DNA has been cloned in E. coli K12 using as vector a plasmid having a controllable bacterial promoter upstream of the insertion site. Clones containing genes coding for up to 150 repeats of (aspartyl-phenylalanine) have been isolated and characterised. The polymeric inserts appear to be stable over many generations and are expressed in E. coli under the control of the bacterial promoter, to give a polymer of phenylalanine and aspartic acid which may be broken down enzymically to yield aspartyl-phenylalanine.
Analysis of consensus molecular subtypes (CMS) classification in the TRICOLORE trial: A randomized phase III trial of S-1 and irinotecan (IRI) plus bevacizumab (Bmab) versus mFOLFOX6 or CapeOX plus Bmab as first-line treatment for metastatic colorectal cancer (mCRC). (2020)

169 Background: The TRICOLORE trial previously demonstrated that S-1+IRI+Bmab (Arm B) was non-inferior to mFOLFOX6/CapeOX+Bmab (Arm A) in terms of progression-free survival (PFS) as first-line treatment for mCRC, irrespective of RAS status. CMS was reported to be a prognostic factor for mCRC. Previously, it was reported that the CMS could be a predictive factor for the efficacy of oxaliplatin (OX) and IRI (Okita A, et al. Oncotarget. 2018). In this exploratory study of TRICOLORE trial, we examined if the CMS could be a predictive factor of OX and IRI regimen. Methods: We collected formalin-fixed paraffin-embedded (FFPE) primary tumor tissues and performed gene expression analysis by microarray. The subtype of CMS was determined by the CMS classifier (Guinney et al. Nature Med. 2015). PFS and overall survival (OS) were compared between arm A and B in each subtypes of CMS. Results: Total of 308 FFPE samples from 487 cases who were enrolled in the TRICOLORE study were collected. Number of patients classified into CMS1 to CMS4 were 47, 72, 99 and 90, respectively. Similar to the previous reports, the proportion of RAS mutant cases was highest in CMS3 and the most of BRAF mutant cases were classified into CMS1. The median PFS (mPFS) of arm A and B were almost same in CMS2 (16.1m vs. 17.6m, HR = 1.10, p = 0.79) and CMS3 (10.6 vs. 11.4, HR = 0.95, p = 0.81). In CMS1, mPFS of arm A was worse than that of arm B, although not statistically significant (7.4m vs. 13.2m, HR = 0.73, p = 0.35). In CMS4, mPFS of arm B was better than that of arm A, although not statistically significant again (9.7m vs. 14.1m, HR = 0.72, p = 0.15). The median OS (mOS) of both arm in CMS2-CMS4 and arm B in CMS1 were good and were 29.0m or more. On the other hand, mOS of arm A in CMS1 (18.1m) was worse than the others. Conclusions: From these results, it was not concluded that CMS was a predictor of mFOLFOX6/CapeOX+Bmab and S-1+IRI+Bmab. However, mPFS and mOS of mFOLFOX6/CapeOX+Bmab in CMS1 were poor unlike other CMS subtypes, and these were consistent with a previous report. Whereas S-1+IRI+Bmab was effective in all subtypes of CMS. Clinical trial information: UMIN000007834.
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes (2007)

Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
Mathematical model of influenza A virus production in large‐scale microcarrier culture (2005)

A mathematical model that describes the replication of influenza A virus in animal cells in large-scale microcarrier culture is presented. The virus is produced in a two-step process, which begins with the growth of adherent Madin-Darby canine kidney (MDCK) cells. After several washing steps serum-free virus maintenance medium is added, and the cells are infected with equine influenza virus (A/Equi 2 (H3N8), Newmarket 1/93). A time-delayed model is considered that has three state variables: the number of uninfected cells, infected cells, and free virus particles. It is assumed that uninfected cells adsorb the virus added at the time of infection. The infection rate is proportional to the number of uninfected cells and free virions. Depending on multiplicity of infection (MOI), not necessarily all cells are infected by this first step leading to the production of free virions. Newly produced viruses can infect the remaining uninfected cells in a chain reaction. To follow the time course of virus replication, infected cells were stained with fluorescent antibodies. Quantitation of influenza viruses by a hemagglutination assay (HA) enabled the estimation of the total number of new virions produced, which is relevant for the production of inactivated influenza vaccines. It takes about 4-6 h before visibly infected cells can be identified on the microcarriers followed by a strong increase in HA titers after 15-16 h in the medium. Maximum virus yield Vmax was about 1x10(10) virions/mL (2.4 log HA units/100 microL), which corresponds to a burst size ratio of about 18,755 virus particles produced per cell. The model tracks the time course of uninfected and infected cells as well as virus production. It suggests that small variations (<10%) in initial values and specific rates do not have a significant influence on Vmax. The main parameters relevant for the optimization of virus antigen yields are specific virus replication rate and specific cell death rate due to infection. Simulation studies indicate that a mathematical model that neglects the delay between virus infection and the release of new virions gives similar results with respect to overall virus dynamics compared with a time delayed model.
Linear programmable nanophotonic processors (2018)

Advances in photonic integrated circuits have recently enabled electrically reconfigurable optical systems that can implement universal linear optics transformations on spatial mode sets.This review paper covers progress in such "programmable nanophotonic processors" as well as emerging applications of the technology to problems including classical and quantum information processing and machine learning.
Random evolution in massive graphs (2001)

Many massive graphs (such as the WWW graph and Call graphs) share certain universal characteristics which can be described by the so-called "power law." In this paper, we, examine three important aspects of power law graphs, (1) the evolution of power law graphs, (2) the asymmetry of in-degrees and out-degrees, (3) the "scale invariance" of power law graphs. In particular, we give three increasingly general directed graph models and one general undirected graph model for generating power law graphs by adding at most one node and possibly one or more edges at a time. We show that for any given edge density and desired power laws for in-degrees and out-degrees, not necessarily the same, the resulting graph will almost surely have the desired edge density and the power laws for the in-degrees and out-degrees. Our most general directed and undirected models include nearly all known power law evolution models as special cases. Finally, we show that our evolution models generate "scale invariant" graphs. We describe a method for scaling the time in our evolution model such that the power law of the degree sequences remains invariant.