gebhart/patrepeval huggingface dataset:
A benchmark and an algorithm for detecting germline transposon insertions and measuring <i>de novo</i> transposon insertion frequencies (2021)

Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo 'singleton' insertion frequencies in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by de-repressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2.
Using Jupyter Tools to Design an Interactive Textbook to Guide Undergraduate Research in Materials Informatics (2022)

With the growing desire to incorporate data science and informatics into STEM curricula, there is an opportunity to integrate research-based software and tools (e.g., Python) within existing pedagogical methods to craft new, accessible learning experiences. We show how the open-source Jupyter Book software can achieve this goal by creating a digital, interactive textbook compiled from Jupyter notebooks, which are already commonplace in research. Using Jupyter Book, we design an open-source, introductory materials informatics research curriculum where the Python programming exercises are supplemented with prose, graphics, slides, and discussion questions, all of which are embedded into a uniform web interface for streamlined access. Interactive programming capabilities, enabled through the JupyterHub cloud infrastructure, provide opportunities in these digital spaces for students to interrogate the code, test their own hypotheses, and deepen their comprehension. These authentic learning experiences demonstrate the broad utility of the Jupyter ecosystem in sustaining the growth of materials informatics education.
Multisensor data fusion for enhanced respiratory rate estimation in thermal videos (2016)

Scientific studies have demonstrated that an atypical respiratory rate (RR) is frequently one of the earliest and major indicators of physiological distress. However, it is also described in the literature as "the neglected vital parameter", mainly due to shortcomings of clinical available monitoring techniques, which require attachment of sensors to the patient's body. The current paper introduces a novel approach that uses multisensor data fusion for an enhanced RR estimation in thermal videos. It considers not only the temperature variation around nostrils and mouth, but the upward and downward movement of both shoulders. In order to analyze the performance of our approach, two experiments were carried out on five healthy candidates. While during phase A, the subjects breathed normally, during phase B they simulated different breathing patterns. Thoracic effort was the gold standard elected to validate our algorithm. Our results show an excellent agreement between infrared thermography (IRT) and ground truth. While in phase A a mean correlation of 0.983 and a root-mean-square error of 0.240 bpm (breaths per minute) was obtained, in phase B they hovered around 0.995 and 0.890 bpm, respectively. In sum, IRT may be a promising clinical alternative to conventional sensors. Additionally, multisensor data fusion contributes to an enhancement of RR estimation and robustness.
Crystal-structure-matched FePO&lt;sub&gt;4&lt;/sub&gt; Surface-coating on LiCoPO&lt;sub&gt;4&lt;/sub&gt;/MWCNT Nanocomposites for Long Lifecycle 5 V Class Lithium Ion Batteries (2019)

Stable high-voltage operation of LiCoPO4 (LCP) was successfully achieved via crystal-structure-matched surface coating using FePO4 (FP) with an identical olivine structure to the LCP. The efficient formation of Fe3+-rich surface together with the partial dissolution of Fe3+ into LCP matrix yielded the excellent cycle performance with 99% of capacity retention at 100th cycle, with a minimized Fe3+ dosage compared to the methods previously reported. This work confirms that the existence of the Fe3+ on the LCP surface is an important factor to bring about the stability of electrode/electrolyte interface.
Plenary Lectures (2010)

Evolution tinkers with odds and ends, but the resulting systems look like circuits designed according to good engineering principles. This talk will discuss several design principles, and how they can be used to make sense of complex transcription and signalling networks in cells.
Effectofphosphorus availabilityon basal rootshallownessin common (2001)

Root gravitropism ma y bean importantelementofplant ro phosphorusavailabilitybecauseit determine s root foraging in fertile t opsoil horizon s, and thereb y phosphoru s ac quisition. In thi s study we seek to test this hypothesisin both t dimensionalpaper growth pouch and three -dimen sional s olid media of sand andsoil cultures. Fi ve common bean (Phaseo lus vulgaris L. ) genotypeswith contrasting ad aptationto low phosphorus availability wereevaluatedin growth pouches ove r 6 days of growth,and in sand cultureand soil culture o ver 4 weeks of growth. Inall three media,phosphorusavailabilityregulatedthe gravitropic r esponse ofbasalrootsin a genotype-dependent mann er.In pouches, s soil, the phosphorus-inefficient ge notype DOR 364 had deeper roots with phosphorus stress, whereas the ph osphoru s-efficient ge notype G 198 33 respondedto phosphorus stress by producing shallower ro ots.Genotype sweremostresponsiveto phosphorus stress insand culture,where rel ative rootallocationto the 0-3- and 3- 6-cm horizonsincreased50% with phosphorus s varied 300% (3- 6 cm) to 500% (0-3 em) among genotypes. Our re sultsindicatethat(1) phosphorusavailabilityregulates roo tgravitropic growth in both paper and solid media , ( responses o bservedin young seedlingscontinue thr oughout ve getative growth,(3) the rof rootgravitropi smto phosphorus availabilityvaries amon g genotypes,and (4) genotypic adaptation t o low phosphorus a vailability i s correlated with the ability to allocate root s to shallowsoil horizons under phosphorus stress.
Controlling the start of combustion on an HCCI diesel engine (2008)

In this paper we propose a control strategy to improve stability of the combustion of HCCI engines during sharp transients. This approach complements existing airpath and fuelpath controllers, and aims at accurately controlling the start of combustion ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">soc</i> ). For that purpose, injection time is adjusted based on a simple Knock Integral Model and real time intake manifold signals. Experimental results are presented, which stress the relevance of the approach.
The structure of a GH149 β‐(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide‐specific GH94 glucose‐β‐(1 → 3)‐glucose (laminaribiose) phosphorylase (2019)

Glycoside phosphorylases (GPs) with specificity for β-(1 → 3)-gluco-oligosaccharides are potential candidate biocatalysts for oligosaccharide synthesis. GPs with this linkage specificity are found in two families thus far-glycoside hydrolase family 94 (GH94) and the recently discovered glycoside hydrolase family 149 (GH149). Previously, we reported a crystallographic study of a GH94 laminaribiose phosphorylase with specificity for disaccharides, providing insight into the enzyme's ability to recognize its' sugar substrate/product. In contrast to GH94, characterized GH149 enzymes were shown to have more flexible chain length specificity, with preference for substrate/product with higher degree of polymerization. In order to advance understanding of the specificity of GH149 enzymes, we herein solved X-ray crystallographic structures of GH149 enzyme Pro_7066 in the absence of substrate and in complex with laminarihexaose (G6). The overall domain organization of Pro_7066 is very similar to that of GH94 family enzymes. However, two additional domains flanking its catalytic domain were found only in the GH149 enzyme. Unexpectedly, the G6 complex structure revealed an oligosaccharide surface binding site remote from the catalytic site, which, we suggest, may be associated with substrate targeting. As such, this study reports the first structure of a GH149 phosphorylase enzyme acting on β-(1 → 3)-gluco-oligosaccharides and identifies structural elements that may be involved in defining the specificity of the GH149 enzymes.
Evaluation of neutralizing antibodies in patients treated with recombinant interferon-beta ser. (1989)

Patients receiving recombinant interferon-beta ser (rIFN-beta ser) for cancer and viral diseases were evaluated for formation of antibodies with IFN-neutralizing activity. The assay for serum neutralizing activity measures the ability of the sample to neutralize the antiviral activity of rIFN-beta ser. Neutralizing antibody incidence was route dependent. Of 335 patients treated intravenously, 3 were positive, representing an incidence of 0.9%. The remaining 13 antibody-positive patients had been treated subcutaneously, representing an incidence of 9.6% (13/136). In general, peak titers for neutralizing activity were low to moderate; 15 of the 16 patients (94%) had titers between 100 and 2,000 neutralizing units/ml. The incidence of neutralizing antibodies was higher in patients who had been under study for longer periods of time. Mean time of onset of neutralizing activity for the 16 positive patients was about 5 months. Because length of time on study appeared to be a possible predisposing factor for development of neutralizing antibodies, we recalculated the incidence of this activity for all patients on study for 5 months or longer (90 i.v., 71 s.c.). All of the 16 neutralizing-positive patients were on study for more than 150 days, whereas the remaining 87 in the i.v. group and 58 in the s.c. group were negative. Thus, a longer time on study appears to increase incidence, but in only a portion of subjects treated. No adverse clinical effects could be directly associated with neutralizing antibodies.
Efficacy and Safety of an Extravascular Implantable Cardioverter–Defibrillator (2022)

In this prospective global study, we found that extravascular ICDs were implanted safely and were able to detect and terminate induced ventricular arrhythmias at the time of implantation. (Funded by Medtronic; ClinicalTrials.gov number, NCT04060680.).
Ear Acoustic Biometrics Using Inaudible Signals and Its Application to Continuous User Authentication (2018)

This paper presents an improved version of a previously-proposed ear-acoustic biometric system for personal authentication. Even though the previous system provided a fast, accurate, and easy means of authentication, it employed noticeably audible probe signals to extract ear acoustic-features, signals which might interrupt user activities. To overcome this problem, this paper presents silent user authentication by employing inaudible signals in the place of audible signals for capturing ear acoustic-features. A comparative study using a number of audible and inaudible signals demonstrates that inaudible signals provide accurate authentication under the condition that the relative position of the earphone device against the ear canal is constant, which is a requirement for continuous user authentication. On the other hand, audible signals offer better accuracy when the earphone position changes, which is often the case in initial user authentication. This suggests the idea of a hybrid system that employs both audible and inaudible signals for, respectively, accurate initial authentication and user-friendly continuous authentication.
Strengthening Mg‐Al‐Zn Alloy by Repetitive Oblique Shear Strain (2011)

This chapter contains sections titled: Grain Refinement of Mg for Strengthening Repetitive Shear Straining by Caliber Rolling Caliber Rolling for AZ31 alloy Effect of Repetitive Shear Straining Summary Acknowledgement
EPR study of hydrated anatase under UV irradiation (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEPR study of hydrated anatase under UV irradiationRussell F. Howe and Michael. GratzelCite this: J. Phys. Chem. 1987, 91, 14, 3906–3909Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/j100298a035https://doi.org/10.1021/j100298a035research-articleACS PublicationsRequest reuse permissionsArticle Views1956Altmetric-Citations398LEARN 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 options Get e-Alerts
An algorithm for automatic crystal identification in pixelated scintillation detectors using thin plate splines and Gaussian mixture models (2016)

A typical positron emission tomography detector is comprised of a scintillator crystal array coupled to a photodetector array or other position sensitive detector. Such detectors using light sharing to read out crystal elements require the creation of a crystal lookup table (CLUT) that maps the detector response to the crystal of interaction based on the x-y position of the event calculated through Anger-type logic. It is vital for system performance that these CLUTs be accurate so that the location of events can be accurately identified and so that crystal-specific corrections, such as energy windowing or time alignment, can be applied. While using manual segmentation of the flood image to create the CLUT is a simple and reliable approach, it is both tedious and time consuming for systems with large numbers of crystal elements. In this work we describe the development of an automated algorithm for CLUT generation that uses a Gaussian mixture model paired with thin plate splines (TPS) to iteratively fit a crystal layout template that includes the crystal numbering pattern. Starting from a region of stability, Gaussians are individually fit to data corresponding to crystal locations while simultaneously updating a TPS for predicting future Gaussian locations at the edge of a region of interest that grows as individual Gaussians converge to crystal locations. The algorithm was tested with flood image data collected from 16 detector modules, each consisting of a 409 crystal dual-layer offset LYSO crystal array readout by a 32 pixel SiPM array. For these detector flood images, depending on user defined input parameters, the algorithm runtime ranged between 17.5-82.5 s per detector on a single core of an Intel i7 processor. The method maintained an accuracy above 99.8% across all tests, with the majority of errors being localized to error prone corner regions. This method can be easily extended for use with other detector types through adjustment of the initial template model used.
The AdaptiSPECT imaging aperture (2012)

In this paper, we present the imaging aperture of an adaptive SPECT imaging system being developed at the Center for Gamma Ray Imaging (AdaptiSPECT). AdaptiSPECT is designed to automatically change its configuration in response to preliminary data, in order to improve image quality for a particular task. In a traditional pinhole SPECT imaging system, the characteristics (magnification, resolution, field of view) are set by the geometry of the system, and any modification can be accomplished only by manually changing the collimator and the distance of the detector to the center of the field of view. Optimization of the imaging system for a specific task on a specific individual is therefore difficult. In an adaptive SPECT imaging system, on the other hand, the configuration can be conveniently changed under computer control. A key component of an adaptive SPECT system is its aperture. In this paper, we present the design, specifications, and fabrication of the adaptive pinhole aperture that will be used for AdaptiSPECT, as well as the controls that enable autonomous adaptation.
Hydrogen Storage in Palladium: Magnetically Improved Interfacial Kinetics (2013)

Abstract not Available.
Avidin-biotin complex-based capture coating platform for universal Influenza virus immobilization and characterization (2021)

Influenza virus mutates quickly and unpredictably creating emerging pathogenic strains that are difficult to detect, diagnose, and characterize. Conventional tools to study and characterize virus, such as next generation sequencing, genome amplification (RT-PCR), and serological antibody testing, are not adequately suited to rapidly mutating pathogens like Influenza virus where the success of infection heavily depends on the phenotypic expression of surface glycoproteins. Bridging the gap between genome and pathogenic expression remains a challenge. Using sialic acid as a universal Influenza virus binding receptor, a novel virus avidin-biotin complex-based capture coating was developed and characterized that may be used to create future diagnostic and interrogation platforms for viable whole Influenza virus. First, fluorescent FITC probe studies were used to optimize coating component concentrations. Then atomic force microscopy (AFM) was used to profile the surface characteristics of the novel capture coating, acquire topographical imaging of Influenza particles immobilized by the coating, and calculate the capture efficiency of the coating (over 90%) for all four representative human Influenza virus strains tested.
Newt A1 cell-derived extracellular vesicles promote mammalian nerve growth (2023)

Newts have the extraordinary ability to fully regenerate lost or damaged cardiac, neural and retinal tissues, and even amputated limbs. In contrast, mammals lack these broad regenerative capabilities. While the molecular basis of newts' regenerative ability is the subject of active study, the underlying paracrine signaling factors involved remain largely uncharacterized. Extracellular vesicles (EVs) play an important role in cell-to-cell communication via EV cargo-mediated regulation of gene expression patterns within the recipient cells. Here, we report that newt myogenic precursor (A1) cells secrete EVs (A1EVs) that contain messenger RNAs associated with early embryonic development, neuronal differentiation, and cell survival. Exposure of rat primary superior cervical ganglion (SCG) neurons to A1EVs increased neurite outgrowth, facilitated by increases in mitochondrial respiration. Canonical pathway analysis pinpointed activation of NGF/ERK5 signaling in SCG neurons exposed to A1EV, which was validated experimentally. Thus, newt EVs drive neurite growth and complexity in mammalian primary neurons.
NHE-1 inhibition-induced cardioprotection against ischaemia/reperfusion is associated with attenuation of the mitochondrial permeability transition (2007)

The beneficial effect of NHE-1 inhibition in hearts subjected to IR is associated with attenuation of mitochondrial PTP opening and apoptosis and the resultant mitochondrial dysfunction. The effect of AVE on PTP opening most likely is indirect, as pore opening was not affected by direct administration of AVE to mitochondrial suspensions.
Characterization of malignant tissue cells using laser induced breakdown spectroscopy (2004)

Laser induced breakdown spectroscopy (LIBS) has been used to distinguish malignant and normal tissue of the dogs. Preliminary LIBS spectra of tissue samples were analyzed and the results have compared with the ICP analysis.
The effect of displacement on the mechanical properties of human cadaver subsynovial connective tissue (2012)

The subsynovial connective tissue (SSCT) in the carpal tunnel may participate in the origin of carpal tunnel syndrome (CTS), yet material properties of the SSCT have not been well-characterized. We investigated the response of the SSCT to repeated ramp stretch tests. Eight human cadaver wrists were used. The physiological excursion of the flexor digitorum superficialis of the third digit (FDS 3) was measured, starting from a neutral position to maximal flexion of the metacarpophalangeal and proximal interphalangeal joints. The FDS 3 tendon was pulled to 40%, 60%, 90%, and 120% of the physiological excursion. Two "ramp stretch" cycles were performed at every excursion level, except for 120% of excursion, where three cycles were performed. The ratio of energy absorbed between the second (E2) and first (E1) ramp stretch was 0.94 (SD = 0.07) for 60%, 0.84 (SD = 0.11) for 90%, and 0.68 (SD = 0.11) for 120% of the physiological excursion. A significant decrease occurred in energy absorbed after the first ramp stretch cycle at 90% and 120% of the physiological excursion, which was not seen at 60%. Our data are consistent with a stepwise damage occurring in the SSCT. Furthermore, the damage seems to initiate within the physiological range of tendon excursion. This finding may be important in understanding the pathophysiology of conditions that are associated with SSCT pathology, such as carpal tunnel syndrome.