gebhart/patrepeval huggingface dataset:
The extent of ribosome queuing in budding yeast (2018)

Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution, synthetic biology, gene expression regulation, intracellular biophysics, and more. However, this phenomenon hasn't been quantified yet at a genomic level. Nevertheless, methodologies for studying translation (e.g. ribosome footprints) are usually calibrated to capture only single ribosome protected footprints (mRPFs) and thus limited in their ability to detect ribosome queuing. On the other hand, most of the models in the field assume and analyze a certain level of queuing. Here we present an experimental-computational approach for studying ribosome queuing based on sequencing of RNA footprints extracted from pairs of ribosomes (dRPFs) using a modified ribosome profiling protocol. We combine our approach with traditional ribosome profiling to generate a detailed profile of ribosome traffic. The data are analyzed using computational models of translation dynamics. The approach was implemented on the Saccharomyces cerevisiae transcriptome. Our data shows that ribosome queuing is more frequent than previously thought: the measured ratio of ribosomes within dRPFs to mRPFs is 0.2-0.35, suggesting that at least one to five translating ribosomes is in a traffic jam; these queued ribosomes cannot be captured by traditional methods. We found that specific regions are enriched with queued ribosomes, such as the 5'-end of ORFs, and regions upstream to mRPF peaks, among others. While queuing is related to higher density of ribosomes on the transcript (characteristic of highly translated genes), we report cases where traffic jams are relatively more severe in lowly expressed genes and possibly even selected for. In addition, our analysis demonstrates that higher adaptation of the coding region to the intracellular tRNA levels is associated with lower queuing levels. Our analysis also suggests that the Saccharomyces cerevisiae transcriptome undergoes selection for eliminating traffic jams. Thus, our proposed approach is an essential tool for high resolution analysis of ribosome traffic during mRNA translation and understanding its evolution.
ChemInform Abstract: WANDERUNG DER METHOXY-GRUPPE BEI DER REAKTION EINIGER METHYLPYRANOSIDCHLORSULFATE MIT ALUMINIUMCHLORID (1971)

Umsetzung des Xylopyranosids (I) in CHCl3 bei 60°C mit AlCl3 liefert ein Gemisch aus dem Anomeren (II) und dem Pyranosylchlorid (III).
FRET-Based Aptasensor for the Selective and Sensitive Detection of Lysozyme (2020)

Lysozyme is a conserved antimicrobial enzyme and has been cited for its role in immune modulation. Increase in lysozyme concentration in body fluids is also regarded as an early warning of some diseases such as Alzheimer's, sarcoidosis, Crohn's disease, and breast cancer. Therefore, a method for a sensitive and selective detection of lysozyme can benefit many different areas of research. In this regard, several aptamers that are specific to lysozyme have been developed, but there is still a lack of a detection method that is sensitive, specific, and quantitative. In this work, we demonstrated a single-molecule fluorescence resonance energy transfer (smFRET)-based detection of lysozyme using an aptamer sensor (also called aptasensor) in which the binding of lysozyme triggers its conformational switch from a low-FRET to high-FRET state. Using this strategy, we demonstrated that the aptasensor is sensitive down to 2.3 picomoles (30 nM) of lysozyme with a dynamic range extending to ~2 µM and has little to no interference from similar biomolecules. The smFRET approach used here requires a dramatically small amount of aptasensor (~3000-fold less as compared to typical bulk fluorescence methods), and it is cost effective compared to enzymatic and antibody-based approaches. Additionally, the aptasensor can be readily regenerated in situ via a process called toehold mediated strand displacement (TMSD). The FRET-based aptasensing of lysozyme that we developed here could be implemented to detect other protein biomarkers by incorporating protein-specific aptamers without the need for changing fluorophore-labeled DNA strands.
Double patterning design split implementation and validation for the 32nm node (2007)

Single exposure capable systems for the 32nm 1/2 pitch (HP) node may not be ready in time for production. At the possible NA of 1.35 still using water immersion lithography, one option to generate the required dense pitches is double patterning. Here a design is printed with two separate exposures and etch steps to increase the pitch. If a 2x increase in pitch can be achieved through the design split, double patterning could thus theoretically allow using exposure systems conceived for the 65nm node to print 32nm node designs. In this paper we focus on the aspect of design splitting and lithography for double patterning the poly layer of 32nm logic cells using the Synopsys full-chip physical verification and OPC conversion platforms. All 32nm node cells have been split in an automated fashion to target different aggressiveness towards pitch reduction and polygon cutting. Every design split has gone through lithography optimization, Optical Proximity Correction (OPC) and Lithography Rule Checking (LRC) at NA values of 0.93, 1.20, and 1.35. Final comparisons are based on simulations across the process window. In addition, we have experimentally verified selected single-patterning problem areas on a 1.20 NA exposure tool (ASML XT:1700Fi at IMEC). With this information, we establish guidelines for double patterning conversions and present a new design rule for double patterning compliance checking applicable to full-chip scale.
Gastric emptying in infants with or without gastro-oesophageal reflux according to the type of milk. (1990)

The present study was designed to determine the effects of milk composition and the influence of gastro-oesophageal reflux (GOR) on gastric emptying. Cineoesogastrocintigraphy (COGS) was performed in 201 infants between 0-1 year of age in order to detect GOR, and provided a means of estimation of the gastric emptying (GE). Ninety infants appeared free from GOR and constituted the control group; 111 had GOR. There infants were fed human milk or various standard formulae. In addition, 20 infants fed a whey-hydrolysate formula were tested. An appropriate volume of milk was marked with sulfur-colloid Tc (200 microcuries). Measurements of gastric radioactivity were made 30 min and 120 min after ingestion. For the whole population, the infants with GOR had slightly more rapid GE after 30 min (P less than 0.05), but, for the same type of milk, there was no significant difference between GOR and controls. GE did not differ with age or sex, but differed mainly according to the type of milk. In the control group, gastric residual content (GRC) at 120 min was 18 +/- 11 per cent with human milk (n = 7), 16 +/- 21 per cent with whey-hydrolysate formula (n = 8), 25 +/- 17 per cent with acidified formula (n = 13), 26 +/- 19 per cent with whey-predominant formula (n = 22), 39 +/- 17 per cent with casein-predominant formulae (n = 20), 47 +/- 19 per cent with follow-up formulae (n = 16) and 55 +/- 19 per cent with cow's milk (n = 12).(ABSTRACT TRUNCATED AT 250 WORDS)
Stress-Dependent Elasticity of Rocks During the Triaxial Loading and Reloading Cycles (2019)

Summary Stress-dependent elastic properties of rocks play a significant role in the exploration and in the 4D seismic monitoring. Periodic cycles of the loading and unloading are common for the underground hydrocarbon or CO2 storages. This work presents an experimental and a theoretical study of the stress-dependent elasticity during the multistage triaxial loading and reloading cycles. The ultrasonic measurements confirmed the vertical transverse isotropy of the shale sample. Analysis of the P-wave velocities propagated in the axial and in the radial directions suggested opening of the cracks in the sample, during the first loading cycle. Application of the porosity deformation approach resulted into the description of the nonlinear stress-dependency of the elastic parameters, and moreover, was used for the quantitative and qualitative characterization of the stress-induced alterations in the rock. The created during the first loading cycle pore space was characterized as the compliant pore space with a similar stress-sensitivity as by the already existed pore space. The volumetric estimation of the created pore space is equal to 0.02%.
Inverted file partitioning schemes in multiple disk systems (1995)

Multiple-disk I/O systems (disk arrays) have been an attractive approach to meet high performance I/O demands in data intensive applications such as information retrieval systems. When we partition and distribute files across multiple disks to exploit the potential for I/O parallelism, a balanced I/O workload distribution becomes important for good performance. Naturally, the performance of a parallel information retrieval system using an inverted file structure is affected by the partitioning scheme of the inverted file. In this paper, we propose two different partitioning schemes for an inverted file system for a shared-everything multiprocessor machine with multiple disks. We study the performance of these schemes by simulation under a number of workloads where the term frequencies in the documents are varied, the term frequencies in the queries are varied, the number of disks are varied and the multiprogramming level is varied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Discovering Hierarchical Patterns in Event-Based Systems (2010)

Expressive and powerful event-pattern rules are key to successful applications of Complex Event Processing (CEP). However, the definition of complex pattern-detection logic may place heavy demands on business users. In this work we present a model for hierarchical event-patterns, allowing users to compose complex patterns from encapsulated, fully-abstracted sub-pattern definitions with a visual decision graph. Pattern definitions can be reused across business scenarios, thereby encouraging the creation of pattern libraries. In the course of this paper we give a brief overview of the event-based system SARI and describe a number of extensions to its ruling model. We present an algorithm for evaluating hierarchical ruling logic and demonstrate our approach with a use case from the fraud-detection domain.
Optical design of the UV telescope for TAUVEX (1993)

TAUVEX (Tel-Aviv Ultra Violet Explorer) is a telescope for the far UV spectral region. It will record images of the UV radiation from stars and other celestial sources from an orbiting satellite. The optical system consists of three identical and independent telescopes. The objectives of the system are based on a Ritchey-Chretien (RC) model with a field lens group to enlarge the field of view (FOV). These telescopes have been designed for the spectral region of 140 nm - 280 nm, and each has a spectral filter wheel to select a narrow spectral bandwidth. The use of different spectral bands for each telescope enables a multi spectral image to be recorded. This paper reviews the key optical design and fabrication points. The different available objective types for this program are described and analyzed to clarify the reasons for choosing the Ritchey-Chretien model.
The Effect of Dentifrice Containing Chaetomium Gracile Dextranase on the Reduction of Dental Plaque (2) (1978)

The effect of the dentifrice containing Chaetomium gracile dextranase on the reduction of dental plaque was examined and its effect was analyzed using the time series analysis of variance.Thirty male subjects and 54 female dental hygienists who aged 20 to 50 were divided into 2 groups. Each groups used dextranase (2000 units/g) and placebo dentifrices for 2 weeks.In dextranase dentifrice group reduction rates of dental plaque were 66.6 and 74.3 per cent after 1 and 2 weeks, respectively. And in placebo dentifrice group they were 42.2 and 50.7 per cent, respectively. The time series analysis of variance indicated statistically significant (p<0.012) difference between 2 groups. These results suggested that dextranase dentifrice was also effective for dental hygienists and its effect was additive to that of tooth brushing.During the experimental period no one complained bad condition of mouth and any specific change of mucosa could not be observed.
Virus-specific antibody activity of different subclasses of immunoglobulins G and A in cytomegalovirus infections (1983)

Healthy donors and patients with primary or reactivated cytomegalovirus infections were examined for antiviral antibodies of the immunoglobulin G (IgG) and IgA subclasses. For this purpose, monoclonal antibodies against the four IgG and the two IgA subclasses were used in enzyme-linked immunosorbent assays with cytomegalovirus antigen. IgG1 and IgG3 were the principal anti-cytomegalovirus subclasses in serum samples from healthy donors and patients. IgG1 was higher in reactivated than in primary disease. Cytomegalovirus-specific IgG2 was detected only in serum samples with high total cytomegalovirus IgG. A few patients with high total serum IgG4 also had cytomegalovirus-specific IgG4 antibodies. During convalescence, there was no significant increase in total IgG of any subclass. Both IgA1 and IgA2 antibodies with cytomegalovirus specificity were detected in patients who had cytomegalovirus antibodies of the IgA class.
Coarticulatory effects as an index of stylistic and regional variation in Arabic: Coarticulatory effects as an index of stylistic and regional variation in Arabic (2012)

The present chapter deals with the coarticulatory effects of the contrast of pharyngealisation in Modern Standard Arabic (MSA) and Dialectal Arabic (DA). The first study dealt with acoustic data, based on locus equation (LE) parameters extracted from the production of sixteen subjects from Yemen, Kuwait, Jordan and Morocco who spoke 24 words in MSA and 24 words in DA, with a symmetrical VCV context [iCi, uCu, aCa] where C was either pharyngealised (Ph) /t d s ð / or nonpharyngealised (n.Ph) /t d s ð/. LE parameters were very accurate to reflect pharyngealisation patterns of CV coarticulatory effects according to speech variety and geographical clustering. The second study dealt with EMA data performed on one Tunisian speaker. It provides some observations of the articulatory mechanism of pharyngealisation. This section provides also a comprehensible interpretation of coarticulatory effects of pharyngealisation revealed by locus equation parameters.
BER Performance Improvement of Data-Recycling Equalizer in Time-varing Fading Mobile Communication Channel (1997)

Time-variant mobile radio fading channels distort amplitude, frequency and phase of a transmitted signal. On channels that have time-variant spectral nulls, the conventional equalizers which have low convergence speed and high sensitiveness to phase distortion yields very poor error rate performance. In this paper, the performance of a combined structure with the data-recycling algorithm and fractionally spaced equalizer (FSE) has been investigated on time-variant mobile radio fading channels through computer simulations and compared to other kinds of equalizers. The results show that the data-recycling FSE has excellent capabilities for tracking rapidly time-variant mobile channels and effective compensation for phase distortion.
Data from Carcinomas Contain a Matrix Metalloproteinase–Resistant Isoform of Type I Collagen Exerting Selective Support to Invasion (2023)

&lt;div&gt;Abstract&lt;p&gt;Collagen fibers affect metastasis in two opposing ways, by supporting invasive cells but also by generating a barrier to invasion. We hypothesized that these functions might be performed by different isoforms of type I collagen. Carcinomas are reported to contain α1(I)&lt;sub&gt;3&lt;/sub&gt; homotrimers, a type I collagen isoform normally not present in healthy tissues, but the role of the homotrimers in cancer pathophysiology is unclear. In this study, we found that these homotrimers were resistant to all collagenolytic matrix metalloproteinases (MMP). MMPs are massively produced and used by cancer cells and cancer-associated fibroblasts for degrading stromal collagen at the leading edge of tumor invasion. The MMP-resistant homotrimers were produced by all invasive cancer cell lines tested, both in culture and in tumor xenografts, but they were not produced by cancer-associated fibroblasts, thereby comprising a specialized fraction of tumor collagen. We observed the homotrimer fibers to be resistant to pericellular degradation, even upon stimulation of the cells with proinflammatory cytokines. Furthermore, we confirmed an enhanced proliferation and migration of invasive cancer cells on the surface of homotrimeric versus normal (heterotrimeric) type I collagen fibers. In summary, our findings suggest that invasive cancer cells may use homotrimers for building MMP-resistant invasion paths, supporting local proliferation and directed migration of the cells whereas surrounding normal stromal collagens are cleaved. Because the homotrimers are universally secreted by cancer cells and deposited as insoluble, MMP-resistant fibers, they offer an appealing target for cancer diagnostics and therapy. Cancer Res; 70(11); 4366–74. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Bi-Al-Si-O glass on Si-substrates as a potential material for NIR broad band planar waveguide applications: synthesis and characterization (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text I. Hoxha, A. Bykov, M. Sharonov, and V. Petricevic, "Bi-Al-Si-O glass on Si-substrates as a potential material for NIR broad band planar waveguide applications: synthesis and characterization," in Lasers, Sources, and Related Photonic Devices, OSA Technical Digest (CD) (Optica Publishing Group, 2012), paper JTh2A.9. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Parallel adaptive algorithm for moving target indicator and its VLSI array realization (2002)

A computationally efficient adaptive algorithm for the IBDA (innovations-based detection algorithm) is devised and realized with a systolic array so that is possesses both fast adaptation and good steady-state performance. The algorithm has superior numerical properties and computational complexity. It possesses high computing parallelism and good data locality, which are preferable in VLSI arrays. One systolic array example designed for the algorithm has an iteration time of (2N+1) and ((n/sup 2/+3n)/2) processing elements, where n is the number of states.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Experimental and Computational Investigation of Hydrogen Evolution Reaction Mechanism on Nitrogen Functionalized Carbon Nanotubes (2018)

Abstract Designing earth‐abundant element based efficient and durable electrocatalysts for hydrogen evolution reaction (HER) is attracting growing attention as the renewable electricity supply sector urgently needs sustainable methods for storing energy. Nitrogen functionalized carbon nanomaterials are an interesting electrocatalysts option because of their attractive electrical properties, excellent chemical stability and catalytic activity. Hence, this study reports the HER mechanism on nitrogen functionalized few‐walled carbon nanotubes (N‐FWCNT). With this earth‐abundant element based catalyst 250 mV overpotential is required to reach 10 mA cm −2 current density and so its HER activity is comparable to other non‐noble metal catalysts, and clearly among the highest previously reported for N‐FWCNTs. To gain fundament insight on their functioning, computational analysis has been carried out to verify the effect of nitrogen and to analyze the reaction mechanism. The reaction mechanism has also been analyzed experimentally with a pH series, and both the methods suggest that the HER proceeds via the Volmer‐Heyrovský mechanism. Overall hydrogen surface coverage on N‐FWCNT is also suggested to affect the HER rate. Interestingly, in the studied structure, carbons in vicinity of nitrogen atoms, but not directly bound to nitrogen, appear to promote the HER most actively. Furthermore, durability of N‐FWCNTs has been demonstrated by operating a full electrolyzer cell for five weeks.
The Turn Of The Screw (2008)

<sc>The Story</sc> had held us, round the fire, sufficiently breathless, but except the obvious remark that it was gruesome, as on Christmas Eve in an old house a strange tale should essentially be, I remember no comment uttered till somebody happened to note it...
SU‐E‐I‐19: Local Search Clustering Algorithm for DCE‐MRI Analysis (2012)

We developed a local search clustering algorithm to segment the concentration time curves of the DCE-MRI data. The proposed clustering algorithm enhances the apparent CNR within the clustered data and reduces the errors of the permeability parameters.
Towards fully Bayesian speaker recognition: integrating out the between-speaker covariance (2011)

We propose a variational Bayes solution to integrate out the model parameters in a generative i-vector speaker recognizer. The existing state-of-the-art in generative i-vector modelling plugs in fixed maximum-likelihood point-estimates of model parameters. This recipe may suffer from over-fitting of especially the between-speaker covariance. We show how to integrate out the between-speaker covariance and demonstrate dramatic improvements on NIST SRE 2010.
A data compression technique based on reversed leading bits coding and Huffman coding (2015)

In this paper, a new test data compression technique is proposed. The compression is achieved by reversed leading bits coding together with Huffman coding (RLBC-HC). RLBC-HC fills the don't-care bit with the value of the bit before it at first. Then the test data is divided into codeword segments for pattern matching to generate corresponding symbols. With a proper number of patterns, the number of different symbols and the hardware complexity can be well balanced. Finally, Huffman coding is adopted upon those symbols to achieve high compression ratio. Experimental results demonstrate that the RLBC-HC technique can achieve better compression ratio on average over the other compression schemes.