gebhart/patrepeval huggingface dataset:
Replication of prophage P1 is cell-cycle specific (1992)

P1 prophage replication during the Escherichia coli division cycle has been analyzed by using the membrane-elution technique to produce cells labelled at different times during the division cycle and scintillation counting for quantitative analysis of radioactive prophage DNA. P1 prophage replicates during a restricted portion of the bacterial division cycle, like the minichromosome, but at a time during the division cycle different than the time at which the minichromosome replicates in the same cell. A high-copy mini-R6K plasmid present in the same cell replicates throughout the division cycle. Over a wide range of growth rates, the P1 prophage replicates approximately one-half generation after the minichromosome replicates. Thus, the mechanisms underlying P1 replication are similar to those for the F plasmid and the chromosome. Replication occurs when some property related to cell size or cell mass reaches a constant value per origin.
Molecular Addition Compounds of Iodine. II. Recalculation of Thermodynamic Data on Lewis Base-Iodine Systems Using an Absolute Equation (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Addition Compounds of Iodine. II. Recalculation of Thermodynamic Data on Lewis Base-Iodine Systems Using an Absolute EquationRussell S. Drago and Norman J. RoseCite this: J. Am. Chem. Soc. 1959, 81, 23, 6141–6145Publication Date (Print):December 1, 1959Publication History Published online1 May 2002Published inissue 1 December 1959https://pubs.acs.org/doi/10.1021/ja01532a010https://doi.org/10.1021/ja01532a010research-articleACS PublicationsRequest reuse permissionsArticle Views328Altmetric-Citations50LEARN 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
Carcinoembryonic antigen and cytokeratin 20 in peritoneal cells of cancer patients: are we aware of what we are detecting by mRNA examination? (2008)

Carcinoembryonic antigen and cytokeratin 20 in peritoneal cells of cancer patients: are we aware of what we are detecting by mRNA examination?
Palladium(II)-Catalyzed Enantioselective Aerobic Dialkoxylation of 2-Propenyl Phenols:  A Pronounced Effect of Copper Additives on Enantioselectivity (2007)

A direct O2-coupled Pd(II)-catalyzed enantioselective dialkoxylation of 2-propenylphenols has been developed by utilizing chiral quinoline oxazoline ligands. A detrimental effect of added copper salts on enantioselectivity was observed which is attributed to the displacement of the chiral ligand off of Pd(II).
Age and Gender Affect Epiphyseal Closure in White-tailed Deer (2013)

Timing of epiphyseal closure determines length of long bones and thus body size, but factors affecting epiphyseal closure in Odocoileus virginianus (White-tailed Deer) have not been conclusively quantified. We collected morphometric data and radiographic images of the distal humerus, proximal radius, distal radius, and metacarpus on approximately 0.5-, 1.5-, 2.5-, and 3.5-year-old optimally nourished captive deer. Age affected closure of distal radial and metacarpal epiphyseal plates (P < 0.001), with all individuals exhibiting epiphyseal closure by 3.5 years of age. Gender affected closure of the distal radial epiphyseal plates (P = 0.036), with females closing prior to males. Differential bone growth rate prior to epiphyseal closure may be one mechanism by which individual and cohort phenotypic effects are manifested in cervids.
MARTX toxins as effector delivery platforms (2015)

Bacteria frequently manipulate their host environment via delivery of microbial 'effector' proteins to the cytosol of eukaryotic cells. In the case of the multifunctional autoprocessing repeats-in-toxins (MARTX) toxin, this phenomenon is accomplished by a single, >3500 amino acid polypeptide that carries information for secretion, translocation, autoprocessing and effector activity. MARTX toxins are secreted from bacteria by dedicated Type I secretion systems. The released MARTX toxins form pores in target eukaryotic cell membranes for the delivery of up to five cytopathic effectors, each of which disrupts a key cellular process. Targeted cellular processes include modulation or modification of small GTPases, manipulation of host cell signaling and disruption of cytoskeletal integrity. More recently, MARTX toxins have been shown to be capable of heterologous protein translocation. Found across multiple bacterial species and genera--frequently in pathogens lacking Type 3 or Type 4 secretion systems--MARTX toxins in multiple cases function as virulence factors. Innovative research at the intersection of toxin biology and bacterial genetics continues to elucidate the intricacies of the toxin as well as the cytotoxic mechanisms of its diverse effector collection.
Improving Power Density of Free-Piston Stirling Engines (2016)

Analyses and experiments demonstrate the potential benefits of optimizing piston and displacer motion in a free piston Stirling Engine. Isothermal analysis shows the theoretical limits of power density improvement due to ideal motion in ideal Stirling engines. More realistic models based on nodal analysis show that ideal piston and displacer waveforms are not optimal, often producing less power than engines that use sinusoidal piston and displacer motion. Constrained optimization using nodal analysis predicts that Stirling engine power density can be increased by as much as 58 using optimized higher harmonic piston and displacer motion. An experiment is conducted in which an engine designed for sinusoidal motion is forced to operate with both second and third harmonics, resulting in a maximum piston power increase of 14. Analytical predictions are compared to experimental data showing close agreement with indirect thermodynamic power calculations, but poor agreement with direct electrical power measurements.
Bias Temperature Instability Characterization of Advanced Gate Stacks (2007)

We performed a physical and electrical characterization of the defects that would cause negative and positive bias temperature instability (NBTI, PBTI) in gate stacks that use SiO2, plasma-nitrided SiO2, HfSiON, and HfSiON with Ni- silicide electrodes. The characterization shows that the influence of impurities, damages and mechanical stress, derived from the newly incorporated materials and process technologies on the insulator bulk and insulator/Si interface must be suppressed to cope with the problems of NBTI and PBTI in the advanced gate stacks.
Improving RGB Image Consistency for Depth-Camera based Reconstruction through Image Warping (2020)

Figure 1: A partial room reconstruction using InfiniTAMv3. Left: result without applying a warping function.
Pictorial communication: pictures and the synthetic universe (1991)

Principles for the design of dynamic spatial instruments for communicating quantitative information to viewers are considered through a brief review of the history of pictorial communication. Pictorial communication is seen to have two directions: (1) from the picture to the viewer and (2) from the viewer to the picture. Optimization of the design of interactive instruments using pictorial formats requires an understanding of the manipulative, perceptual and cognitive limitations of human viewers.
Electro-Thermal Model for Thyristor for HVDC Valve (2012)

To enhance the electricity grid's capacity of resource allocation, long-distance, large capacity (Ultra) high-voltage DC transmission technology is widely used. Significantly increased voltage and current levels affect both electric and thermal characteristics of the thyristors in a DC converter valve. This paper aims to establish a thyristor electro-thermal model to analyze the interaction between electrical and thermal stresses under various steady and transient operation conditions. Thyristor junction temperature prediction method was investigated to ensure its long-term reliability in applications.
Coxsackievirus Aggregates in Muscle Cells of a Polymyositis Patient (1978)

Muscle biopsy specimens of a patient with polymyositis showed crystalline structures resembling picornavirus aggregates within muscle cells. The patient's serum reacted in an indirect immunofluorescence assay with autologous muscle cells. A strongly positive immunofluorescence staining was also noted when a section of muscle tissue was reacted with coxsackievirus A9 antiserum, and a weakly positive reaction was noted with coxsackievirus B2 antiserum. No staining was observed after treatment with antiserum to poliovirus type 1 or echovirus types 11 and 22.
ALKBH4-dependent demethylation of actin regulates actomyosin dynamics (2013)

Regulation of actomyosin dynamics by post-transcriptional modifications in cytoplasmic actin is still poorly understood. Here we demonstrate that dioxygenase ALKBH4-mediated demethylation of a monomethylated site in actin (K84me1) regulates actin–myosin interaction and actomyosin-dependent processes such as cytokinesis and cell migration. ALKBH4-deficient cells display elevated K84me1 levels. Non-muscle myosin II only interacts with unmethylated actin and its proper recruitment to and interaction with actin depend on ALKBH4. ALKBH4 co-localizes with the actomyosin-based contractile ring and midbody via association with methylated actin. ALKBH4-mediated regulation of actomyosin dynamics is completely dependent on its catalytic activity. Disorganization of cleavage furrow components and multinucleation associated with ALKBH4 deficiency can all be restored by reconstitution with wild-type but not catalytically inactive ALKBH4. Similar to actin and myosin knock-out mice, homozygous Alkbh4 mutant mice display early embryonic lethality. These findings imply that ALKBH4-dependent actin demethylation regulates actomyosin function by promoting actin-non-muscle myosin II interaction. The division of a single eukaryotic cell into two requires actomyosin-dependent contraction. Here the authors show that lysine methylation of actin inhibits contractility during cytokinesis by blocking its association with myosin, and this modification is reversed at the contractile ring by the demethylase ALKBH4.
Interrogating the Role of Chromatin Regulator BRD4 in the DNA Damage Response in Medulloblastoma (2019)

Medulloblastoma (MB) is the most common malignant brain tumor in children. MYC-driven tumors make up 40% of MBs and display the poorest prognosis. Treatment often has debilitating effects on patients, thus, novel molecularly targeted therapies could minimize adverse effects and improve treatment. Bromodomain and Extra-terminal domain (BET) inhibitors were introduced as an alternative strategy for targeting MYC proteins, by impairing epigenetic regulation of MYC transcription. Emerging data show that MYC repression is not the only effect that BET inhibition has on various cancers. We interrogated the role of chromatin regulator BRD4 in the DNA damage response in MB. We showed that small-molecule BET inhibition can down-regulate key DNA repair proteins of various DNA repair pathways, and that BET inhibitors and BET degraders synergize with other established chemotherapeutic compounds in MB cell lines. We further demonstrated that transcriptional repression results in defective DNA repair, suggesting that the development of drug-combination therapies including BET-inhibitors and established first-line MB agents may enhance drug efficacy in MB patients.
Quantitative Imaging Detection of Additive Manufactured Parts Using Laser Ultrasonic Testing (2020)

Selective laser melting (SLM) is an important method of additive manufacturing, however it has some disadvantages such as poor surface qualities of the formed parts and the appearances of small surface defects. In this article, 360L stainless steel with artificial defects in different lengths are processed by SLM processing. A full noncontact laser ultrasonic-based B-scan detection system is built to detect the surface defects. The interaction between the scattered surface wave and the surface defect is verified through 3-dimension (3D) finite element simulation. In order to improve the signal-to-noise ratio (SNR) of laser ultrasonic signal in AM 316L part, Variational Mode Decomposition (VMD) algorithm based particle swarm optimization (PSO) is applied to denoise signals. Meanwhile, wavelet transform (WT) algorithm is used to compare SNR with VMD algorithm. Then, the time and amplitude parameters of different positions are extracted to realize B-scan imaging, and the lengths of defects are further accurately quantified through the time-amplitude-position imaging images. Otherwise, we find that the size of laser spot affects the precise quantification of defects. The smaller the spot is, the more precise the quantitative effect is. The results show that this method can quantitatively detect surface defects of AM 316L parts.
Comparable specimen collection from both ends of at-home mid-turbinate swabs (2020)

Unsupervised upper respiratory specimen collection is a key factor in the ability to massively scale SARS-CoV-2 testing. But there is concern that unsupervised specimen collection may produce inferior samples. Across two studies that included unsupervised at-home mid-turbinate specimen collection, ~1% of participants used the wrong end of the swab. We found that molecular detection of respiratory pathogens and a human biomarker were comparable between specimens collected from the handle of the swab and those collected correctly. Older participants were more likely to use the swab backwards. Our results suggest that errors made during home-collection of nasal specimens do not preclude molecular detection of pathogens and specialized swabs may be an unnecessary luxury during a pandemic.
P2‐239: POTENTIAL DIAGNOSTIC VALUE OF RED BLOOD CELLS α‐SYNUCLEIN HETEROAGGREGATES IN ALZHEIMER'S DISEASE (2019)

A plethora of complex misfolded protein combinations have been found in Alzheimer disease (AD) brains besides the classical pathological hallmarks. Recently, α-synuclein (α-syn) and its heterocomplexes with amyloid-β (Aβ) and tau have been suggested to be involved in the pathophysiological processes of neurodegenerative diseases. These pathological features are not limited to the brain, but can be also found in peripheral fluids. In this respect, Red Blood Cells (RBCs) have been suggested as a good model to investigate the biochemical alterations of neurodegeneration. Our aim is to find whether RBC concentrations of α-syn and its heterocomplexes (i.e., α-syn/Aβ and α-syn/tau) were different in AD patients compared with healthy controls (HC) and to assess their potential diagnostic accuracy in discriminating AD from HC individuals. The levels of homo- and hetero-aggregates of α-syn, Aβ and tau were analysed in a cohort of AD patients at early stage either with dementia or prodromal symptoms (N=39) and age-matched HC (N=39). All AD patients showed a typical hippocampal phenotype and received a biomarker-based diagnosis (low cerebrospinal fluid levels of Aβ peptide combined with high cerebrospinal fluid concentrations of total-tau and/or phospho-tau proteins; alternatively, a positivity to cerebral amyloid-PET scan). We found lower concentrations of α-syn and its heterocomplexes (i.e., α-syn/Aβ and α-syn/tau) in RBCs of AD patients compared to HC. RBC α-syn/Aβ as well as RBC α-syn/tau heterodimers discriminated AD participants from HC with fair accuracy (Area under receiver operating characteristic, AUROC=0.76, 0.72, respectively), whereas RBC α-syn concentrations differentiated poorly the two groups (AUROC=0.63). RBC Aβ and RBC α-syn/Aβ heterocomplex moderately correlated with CSF Aβ (ρs=0.435 and 0.368, respectively; P=0.015 and 0.042) in a subset of 32 AD patients. Although additional investigations are required, these data suggest α-syn heteroaggregates in RBCs as potential tool in the diagnostic work-up of early AD diagnosis. Finally, RBCs may represent interesting peripheral in vivo models of neurodegeneration since they likely to be involved in the accumulation and clearance of the misfolded proteins.
Absolute quantification strategies in proteomics based on mass spectrometry (2004)

The strong need for quantitative information in proteomics has fueled the development of mass spectrometry-based analytical methods that are able to determine protein abundances. This article reviews mass spectrometry experiments aimed at providing an absolute quantification of proteins. The experiments make use of the isotope-dilution concept by spiking a known amount of synthetic, isotope-labeled reference peptide into the analyte sample. Quantification is achieved by comparing the mass spectrometry signal intensities of the reference with an endogenous peptide that is generated upon proteolytic cleavage of the target protein. In an analogous manner, the level of post-translational modification at a distinct residue within a target protein can be determined. Among the strengths of absolute quantification are low detection limits reaching subfemtomole levels, a high dynamic range spanning approximately five orders of magnitude, low requirements for sample clean-up, and a fast and straightforward method development. Recent studies have demonstrated the compatibility of absolute quantification with various mass spectrometry readout techniques and sample purification steps such as 1D gel electrophoresis, size-exclusion chromatography, isoelectric peptide focusing, strong cation exchange and reversed phase or affinity chromatography. Under ideal conditions, quantification errors and coefficients of variation below 5% have been reported. However, the fact that at the start of the experiment the analyte is a protein and the internal standard is a peptide, severe quantification errors may result due to the selection of unsuitable reference peptides and/or imperfect protein proteolysis. Within the ensemble of mass spectrometry-based quantification methods, absolute quantification is the method of choice in cases where absolute numbers, many repetitive experiments or precise levels of post-translational modifications are required for a few, preselected species of interest. Consequently, prominent application areas include biomarker quantification, the study of post-translational modifications such as phosphorylation or ubiquitination and the comparison of concentrations of interacting proteins.
Reproducible research within the datanet federation consortium (2014)

The DataNet Federation Consortium (DFC) is an NSF funded project that provides cyberinfrastructure for federating data management systems into a collaboration environment. Researchers are able to build a shared collection, apply analysis workflows, and manage the analysis results. The shared collections may span storage resources at multiple institutions, and multiple types of data management systems. The analysis workflows may include staging of files to remote compute platforms, and in-place analysis at the remote data storage location. The workflows can be captured as shareable objects, with automatic capture of input files, input parameters, and output files. A key feature is support for interoperability mechanisms for accessing data from remote repositories, using an appropriate external protocol. It is possible to automate acquisition of data from external resources, transform the data sets into required formats, and save results within the collaboration environment. The interoperability mechanisms can be controlled by policies that automate data acquisition steps, automate validation of collection properties such as integrity, and automate execution of administrative tasks such as data migration. Researchers can share a workflow, modify input parameters, re-execute the workflow, and share the output results. This enables reproducible data-driven research. The DFC builds upon the integrated Rule Oriented Data System, which is open source software middleware available from http://irods.org. The DFC web site is http://datafed.org.
Automated recognition of the iliac muscle and modeling of muscle fiber direction in torso CT images (2016)

The iliac muscle is an important skeletal muscle related to ambulatory function. The muscles related to ambulatory function are the psoas major and iliac muscles, collectively defined as the iliopsoas muscle. We have proposed an automated recognition method of the iliac muscle. Muscle fibers of the iliac muscle have a characteristic running pattern. Therefore, we used 20 cases from a training database to model the movement of the muscle fibers of the iliac muscle. In the recognition process, the existing position of the iliac muscle was estimated by applying the muscle fiber model. To generate an approximation mask by using a muscle fiber model, a candidate region of the iliac muscle was obtained. Finally, the muscle region was identified by using values from the gray value and boundary information. The experiments were performed by using the 20 cases without abnormalities in the skeletal muscle for modeling. The recognition result in five cases obtained a 76.9% average concordance rate. In the visual evaluation, overextraction of other organs was not observed in 85% of the cases. Therefore, the proposed method is considered to be effective in the recognition of the initial region of the iliac muscle. In the future, we will integrate the recognition method of the psoas major muscle in developing an analytical technique for the iliopsoas area. Furthermore, development of a sophisticated muscle function analysis method is necessary.
Highly Transparent Mg 0.27 Al 2.58 O 3.73 N 0.27 Ceramic Prepared by Pressureless Sintering (2013)

A novel aluminum magnesium oxynitride transparent ceramic with the chemical formula Mg 0.27 Al 2.58 O 3.73 N 0.27 was firstly prepared by pressureless sintering of fine single‐phase powders at 1875°C for 24 h in nitrogen atmosphere. The ceramic was fully dense with the average grain size of 57.5 μm. The sample showed excellent in‐line transmission from the visible to middle‐infrared wavelengths with the maximum transmittance of 84%, which could be attributed to rare pores in the sintering body. The material also exhibited good mechanical properties of Vickers hardness (13.39 ± 0.18 GPa), fracture toughness (2.46 ± 0.3 MPa/m 1/2 ), and flexural strength (274 ± 6 MPa).