gebhart/patrepeval huggingface dataset:
Experimental Ixodes ricinus-Sheep Cycle of Anaplasma phagocytophilum NV2Os Propagated in Tick Cell Cultures (2020)

The causative agent of tick-borne fever and human granulocytic anaplasmosis, <i>Anaplasma phagocytophilum</i>, is transmitted by <i>Ixodes ricinus</i>, and is currently considered an emerging disease throughout Europe. In this study, we established a model of <i>A. phagocytophilum</i> sheep infection and <i>I. ricinus</i> transmission using the European Norway variant 2 ovine strain (NV2Os) propagated in both IDE8 and ISE6 tick cells. Two sheep were inoculated with IDE8 tick cells infected with NV2Os. Both sheep developed <i>A. phagocytophilum</i> infection as determined by qPCR and PCR, the presence of fever 4 days post inoculation (dpi), the observation of morulae in granulocytes at 6 dpi, and the detection of <i>A. phagocytophilum</i> antibodies at 14 dpi. <i>A. phagocytophilum</i> was detected by PCR in skin, lung, small intestine, liver, spleen, uterus, bone marrow, and mesenteric lymph node from necropsies performed at 14 and 15 dpi. One sheep was infested during the acute phase of infection with <i>I. ricinus</i> nymphs from a pathogen-free colony. After molting, <i>A. phagocytophilum</i> transstadial transmission in ticks was validated with qPCR positive bacterial detection in 80% of salivary glands and 90% of midguts from female adults. Infected sheep blood collected at 14 dpi was demonstrated to be able to infect ISE6 tick cells, thus enabling the infection of two additional naive sheep, which then went on to develop similar clinical signs to the sheep infected previously. One of the sheep remained persistently infected until 115 dpi when it was euthanized, and transmitted bacteria to 70 and 2.7% of nymphs engorged as larvae during the acute and persistent infection stages, respectively. We then demonstrated that these infected nymphs were able to transmit the bacteria to one of two other naive infested sheep. As expected, when <i>I. ricinus</i> females were engorged during the acute phase of infection, no <i>A. phagocytophilum</i> transovarial transmission was detected. The development of this new experimental model will facilitate future research on this tick-borne bacterium of increasing importance, and enable the evaluation of any new tick/transmission control strategies.
Fault Detection and Classification in Industrial IoT in Case of Missing Sensor Data (2021)

This article addresses the issue of reliability in the Industrial Internet of Things (IIoT) in case of missing sensors measurements due to network or hardware problems. We propose to support the fault detection and classification modules, which are the two critical components of a monitoring system for IIoT, with a generative model. The latter is responsible for imputing missing sensor measurements so that the monitoring system performance is robust to missing data. In particular, we adopt generative adversarial networks (GANs) to generate missing sensor measurements and we propose to fine-tune the training of the GAN based on the impact that the generated data have on the fault detection and classification modules. We conduct a thorough evaluation of the proposed approach using the extended Tennessee Eastman Process data set. Results show that the GAN-imputed data mitigate the impact on the fault detection and classification even in the case of persistently missing measurements from sensors that are critical for the correct functioning of the monitoring system.
Supplementary Figure 5 from Engineered Fusokine GIFT4 Licenses the Ability of B Cells to Trigger a Tumoricidal T-cell Response (2023)

&lt;p&gt;PDF file - 98K, B6 mice treated with GIFT4 protein or implanted with B16-GIFT4 cells do not produce anti-GIFT4 antibodies.&lt;/p&gt;
Phytotoxicity of Graphene Family Nanomaterials and Its Mechanisms: A Review (2019)

Graphene family nanomaterials (GFNs) have experienced significant development in recent years and have been used in many fields. Despite the benefits, they bring to society and the economy, their potential for posing environmental and health risks should also be considered. The increasing release of GFNs into the ecosystem is one of the key environmental problems that humanity is facing. Although most of these nanoparticles are present at low concentrations, many of them raise considerable toxicological concerns, particularly regarding their accumulation in plants and the consequent toxicity introduced at the bottom of the food chain. Here, we review the recent progress in the study of toxicity caused by GFNs to plants, as well as its influencing factors. The phytotoxicity of GFNs is mainly manifested as a delay in seed germination and a severe loss of morphology of the plant seedling. The potential mechanisms of phytotoxicity were summarized. Key mechanisms include physical effects (shading effect, mechanical injury, and physical blockage) and physiological and biochemical effects (enhancement of reactive oxygen species (ROS), generation and inhibition of antioxidant enzyme activities, metabolic disturbances, and inhibition of photosynthesis by reducing the biosynthesis of chlorophyll). In the future, it is necessary to establish a widely accepted phytotoxicity evaluation system for safe manufacture and use of GFNs.
Crispr/Cas9 Targeted Capture of Mammalian Genomic Regions for Characterization by NGS (2018)

ABSTRACT The robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We explore the potential of the CRISPR/Cas9 system for the targeted capture of genomic loci containing integrated vectors in CHO-K1-based cell lines, and compare it to popular target-enrichment methods and to whole genome sequencing (WGS). The CRISPR/Cas9-based techniques allow for amplification-free capture of genomic regions, which reduces the possibility of sequencing artifacts. Other advantages of these methods are the ease of bioinformatics analysis, potential for multiplexing, and the production of longer sequencing templates for real-time sequencing. The utility of these protocols has been proven by identification of transgene integration sites and flanking sequences in a number of CHO cell lines. However, data produced by these and other targeted capture methods are not always sufficient to analyze complex genomic rearrangements (CGRs) or unexpected sequences introduced into genome by vector integration events. In contrast, WGS provides complete information about vector integration sites, vector copy number, CGRs, and foreign DNA-but despite these benefits, WGS is not easily implemented due to the cost and complexity of the analysis.
A Novel Bonding Method for Ionic Wafers (2007)

A novel method for bonding sapphire, quartz, and glass wafers with silicon using the modified surface activated bonding (SAB) method is described. In this method, the mating surfaces were cleaned and simultaneously coated with nano-adhesion Fe layers using a low energy argon ion beam. The optical images show that the entire area of the 4-in wafers of LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /Si was bonded. Such images for other samples show particle induced voids across the interface. The average tensile strength for all of the mating pairs was much higher than 10 MPa. Prolonged irradiation reduced polarization in sapphire, quartz, and Al-silicate glasses. Fe and Ar ion-induced charge deposition result in the formation of an electric field, which was responsible for the depolarization. The lattice mismatch induced local strain was found in LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /Si. No such strain was observed in the Al-silicate glass/Si interface probably because of annealing at 300 for 8 h. The Al-silicate glass/Si interface showed an interfacial layer of 2 nm thick. A 5-nm-thick amorphous layer was observed with the other layer across the /Si interface. The EELS spectra confirmed the presence of nano-adhesion Fe layers across the interface. These Fe layers associated with the electric field induced by ion beam irradiation for prolonged period of time, particularly in LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /Si, might be responsible for the high bonding strength between Si/ionic wafers at low temperatures.
A New Exponentially Weighted Moving Average Control Chart for Monitoring Process Dispersion (2014)

Exponentially weighted moving average (EWMA) control charts have been widely recognized as an advanced statistical process monitoring tool due to their excellent performance in detecting small to moderate shifts in process parameters. In this paper, we propose a new EWMA control chart for monitoring the process dispersion based on the best linear unbiased absolute estimator (BLUAE) obtained under paired ranked set sampling (PRSS) scheme, which we name EWMA‐PRSS chart. The performance of the EWMA‐PRSS chart is evaluated in terms of the average run length and standard deviation of run length, estimated using Monte Carlo simulations. These control charts are compared with their existing counterparts for detecting both increases and decreases in the process dispersion. It is observed that the proposed EWMA‐PRSS chart performs uniformly better than the EWMA dispersion charts based on simple random sampling and ranked set sampling (RSS) schemes. We also construct an EWMA chart based on imperfect PRSS (IPRSS) scheme, named EWMA‐IPRSS chart, for detecting overall changes in the process variability. It turns out that, with reasonable assumptions, the EWMA‐IPRSS chart outperforms the existing EWMA dispersion charts. A real data set is used to explain the construction and operation of the proposed EWMA‐PRSS chart. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Whole-Genome Sequences of Two Kazachstania barnettii Strains Isolated from Anthropic Environments (2022)

Recent studies have suggested that species of the Kazachstania genus may be interesting models of yeast domestication. Among these, Kazachstania barnettii has been isolated from various microbially transformed foodstuffs such as sourdough bread and kefir. In the present work, we sequence, assemble, and annotate the complete genomes of two K. barnettii strains: CLIB 433, being one of the two reference strains for K. barnettii that was isolated as a spoilage organism in soft drink, and CLIB 1767, recently isolated from artisan bread-making sourdough. Both assemblies are of high quality with N50 statistics greater than 1.3 Mb and BUSCO score greater than 99%. An extensive comparison of the two obtained genomes revealed very few differences between the two K. barnettii strains, considering both genome structure and gene content. The proposed genome assemblies will constitute valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.
Localization of vertebrae on DXA VFA images using constrained local models with random forest regression voting (2014)

Osteoporotic fractures are associated with significant morbidity, mortality and public health costs, and will increase with an ageing population. Many osteoporotic vertebral fractures (VF) present on images do not come to clinical attention or lead to fracture prevention treatment. Furthermore, DXA vertebral fracture assessments (VFA) are often reported subjectively by a radiologist or other clinician. VFA computer-aided systems offer potential advantages. Methods based on statistical shape models (e.g. active appearance models, AAMs) have been used to segment vertebrae in radiographs and DXA VFA. However, results achieved using AAMs exhibit significant numbers of large errors due to model fitting failure, particularly on more severely fractured vertebrae. We evaluate an alternative algorithm, the Random Forest Regression Voting Constrained Local Model (RFRV-CLMs), which has proved more robust and generalizable than AAMs in annotation of landmarks on various clinical images; we investigate whether this will reduce the number of fitting failures in vertebral segmentation.320 DXA VFA images obtained on various Hologic (Bedford MA) scanners had manual annotations of 405 landmark points of vertebrae T7 to L4, with fracture classifications from an expert radiologist. RFRV-CLMs were applied to these data in a leave-1/4-out fashion. Figure 1 shows an example image with manual annotations (left; grade 3 severe and grade 1 mild fractures of L1 and L2, respectively), with automatic annotations for L1 to L3 (right). Errors were calculated as the mean, across each vertebra, of the minimum distances between the automatic annotations and a Bezier spline passing through the manual annotations. Figure 2 shows a cumulative distribution function of errors in ten vertebral levels in all 320 images, for each vertebral classification. Mean errors of \textless4mm were achieved for 95\% of grade 3 fractures, and 100\% of other classifications. Mean errors above 2mm were observed on 3.84\% and 10.48\% of vertebra with grade 2 and 3 fractures, respectively, compared to 10.2\% and 16.5\% obtained with AAMs. We conclude that the RFRV-CLM produces fewer large errors due to fitting failures than the AAM in vertebral segmentation, and so is more suitable for automatic analysis of DXA VFA.
Differential Regulation of Akt Kinase Isoforms by the Members of the TCL1 Oncogene Family (2002)

The members of the TCL1 proto-oncogene family (TCL1, MTCP1, and TCL1b) bind to Akt1, increasing its phosphorylation status and kinase activity. This is thought to be secondary to the formation of TCL1-Akt oligomers within which Akt is preferentially phosphorylated. Here we show that, in contrast to Akt1 and Akt2, which bind to all members of the TCL1 family, Akt3 specifically interacts with TCL1 but not with MTCP1 or TCL1b. This association is functional, as the presence of TCL1 but not MTCP1 or TCL1b increased Akt3 kinase activity in in vitro kinase assays. Functional specificity is determined by the Akt pleckstrin homology domain as chimeric Akt1, where Akt1 PH domain was replaced by that of Akt3 was no longer able to interact with MTCP1 or TCL1b and its kinase activity was solely enhanced by TCL1. Moreover, we show that, in TCL1-overexpressing SUPT-11 T-cell leukemia and P3HR-1 Burkitt's lymphoma cell lines, TCL1 interacts with endogenous Akt1, Akt2, and Akt3. TCL1 enhanced hetero-oligomerization of Akt1 with Akt3 and as a consequence facilitated transphosphorylation of Akt molecules, which may contribute to Akt activation and TCL1-induced leukemogenesis in vivo.
Biosensors in the body : continuous in vivo monitoring (1997)

An Introduction to in vivo Biosensing: progress and problems Electrochemical Sensors for in vivo Glucose Sensing Near-infrared Spectrometry for in vivo Glucose Sensing Fully-implantable Sensor Devices - Special Considerations Biocompatability of Active Implantable Devices Neurochemical Analysis Using Sensors Techniques for Fabrication of Implantable Sensors Electrochemical and Optical Sensors for in vivo Monitoring of Blood Gases and Electrolytes.
STAT3 Target Genes Relevant to Human Cancers (2014)

Since its discovery, the STAT3 transcription factor has been extensively studied for its function as a transcriptional regulator and its role as a mediator of development, normal physiology, and pathology of many diseases, including cancers. These efforts have uncovered an array of genes that can be positively and negatively regulated by STAT3, alone and in cooperation with other transcription factors. Through regulating gene expression, STAT3 has been demonstrated to play a pivotal role in many cellular processes including oncogenesis, tumor growth and progression, and stemness. Interestingly, recent studies suggest that STAT3 may behave as a tumor suppressor by activating expression of genes known to inhibit tumorigenesis. Additional evidence suggested that STAT3 may elicit opposing effects depending on cellular context and tumor types. These mixed results signify the need for a deeper understanding of STAT3, including its upstream regulators, parallel transcription co-regulators, and downstream target genes. To help facilitate fulfilling this unmet need, this review will be primarily focused on STAT3 downstream target genes that have been validated to associate with tumorigenesis and/or malignant biology of human cancers.
Treatment of diarrhea in patients with inflammatory bowel disease: concepts and cautions. (2007)

Diarrhea continues to be a prevalent symptom in patients with inflammatory bowel disease (IBD), requiring a wide differential diagnosis to define the pathophysiologic mechanisms in individual patients. It is essential that physicians properly evaluate complaints of diarrhea by assessing both patient symptoms and potential physiologic impacts on fluid and electrolyte status. Underlying mechanisms of diarrhea with IBD are the location, extent, and severity of inflammation; malabsorption; altered motility; and iatrogenic causes such as medications, diet, and antibiotic-associated colitis (eg, Clostridium difficile). When treating diarrhea, physicians need to control inflammatory activity using appropriate treatment algorithms. Therapies include aminosalicylates, corticosteroids, immune modifiers, and, most recently, biologic treatment. Other medications, including loperamide, diphenoxylate, codeine sulfate, and tinctures of opium, slow motility and increase the absorption of fluids and nutrients. For iatrogenic issues, medications that cause diarrhea should be withdrawn and individual diets modified. Not all diarrheas in the IBD patient are the same; therefore, it is essential to tailor therapies according to presumed etiologies. Antidiarrheal agents are not recommended in extremely ill patients and those with known hypersensitivity or evidence of obstruction or colonic dilation, fever, or abdominal tenderness. Concomitant use of loperamide with diphenoxylate and atropine should be avoided in early pregnancy.
The Production and Qualification of Scintillator Tiles for the ATLAS Hadronic Calorimeter (2007)

The production of the scintillator tiles for the ATLAS Tile Calorimeter is presented. In addition to the manufacture and production, the properties of the tiles will be presented including light yield, uniformity and stability.
Sexual Hyperactivity and Reduced Longevity of dunce Females of Drosophila melanogaster (1987)

The dunce gene of Drosophila melanogaster codes for a cyclic adenosine-3',5'-monophosphate-specific phosphodiesterase. Mutations of dunce alter or abolish the activity of this enzyme, produce elevated cAMP levels, cause recessive female sterility, and produce learning deficiencies in both sexes. Aberrant male sexual behavior has also been associated with the memory defects of dunce mutants. Here we show that the longevity of dunce mutant females, homozygous for null-enzyme alleles, is reduced by 50% in the presence of males compared to control dunce females kept without males. Mutant dunce females, mate every 22-24 hr. We propose a cause-effect relationship between mating and reduced longevity. Pheromones or peptides transferred during mating may activate adenylate cyclase and create an increase in cAMP levels that cannot be damped in dunce females. This increase may affect basic physiological functions and lead to reduced longevity.
Gain Broadening of Two-Stage Tapered Gyrotron Traveling Wave Tube Amplifier (1995)

The first operation of a two-stage tapered gyrotron traveling wave amplifier employing two tapered waveguide circuits and tapered magnetic fields is reported. Small-signal gain of 30 dB and saturated gain of 25 dB over a 20% bandwidth at an efficiency of 16% have been observed using a 33 kV, 1.5 A electron beam. Comparison with supporting theory is satisfactory.
Cationic Photoinitiators: Solid State Photochemistry of Triphenylsulfonium Salts (1990)

Abstract Triphenylsulfonium bromide, triflate, tetrafluoroborate, hexafluoroarsenate, hexafluorophosphate and hexafluoroantimonate were irradiate in solution and in the solid state. The photoproducts, 2-, 3- and 4-phenylthiobiophenyl are formed by an in-cage fragmentation-recombination mechanism, whereas diphenylsulfide is formed by a cage-escape reaction. In dilute solution, the ratio of cage to escape products is approximately one for each salt. Also in concentrated solutions, an identical cage : escape ratio is observed for all salts except for the bromide, which favors the escape reaction. Photolysis of the salts in the solid state shows remarkable counter ion dependence and cage : escape ratios as high as 5 : 1 are observed. The mechanism for both in-cage and escape reactions is described.
PCFGs with syntactic and prosodic indicators of speech repairs (2006)

A grammatical method of combining two kinds of speech repair cues is presented. One cue, prosodic disjuncture, is detected by a decision tree-based ensemble classifier that uses acoustic cues to identify where normal prosody seems to be interrupted (Lickley, 1996). The other cue, syntactic parallelism, codifies the expectation that repairs continue a syntactic category that was left unfinished in the reparandum (Levelt, 1983). The two cues are combined in a Treebank PCFG whose states are split using a few simple tree transformations. Parsing performance on the Switchboard and Fisher corpora suggests that these two cues help to locate speech repairs in a synergistic way.
Very quick audio searching: introducing global pruning to the Time-Series Active Search (2002)

Previously, we proposed a histogram-based quick signal search method called Time-Series Active Search (TAS). TAS is a method of searching through long audio or video recordings for a specified segment, based on signal similarity. TAS is fast; it can search through a 24-hour recording in 1 second after a query-independent preprocessing. However, an even faster method is required when we consider a huge amount of audio archives, for example a month's worth of recordings. Thus, we propose a preprocessing method that significantly accelerates TAS. The core part of this method comprises a global histogram clustering of long signals and a pruning scheme using those clusters. Tests using broadcast recording indicate that the proposed algorithm achieves a search speed approximately 3 to 30 times faster than TAS. In these tests, the search results are exactly the same as with TAS.
Linearization of modal parameters in Duffing oscillator using the random decrement technique (2018)

In this study, it is investigated how the random decrement (RD) technique can be used to linearize the nonlinear stiffness of a single degree of freedom system with a hardening spring, known as a Duffing oscillator. The linearization is implemented by using a set of trigger levels in the response signal to define RD signatures. The modal parameters are estimated at the same response level for various excitation force levels, from the RD signatures describing the system at that specific level, and extracting the modal parameters using time domain parameter extraction methods. The system described by the RD signature is assumed to behave as a linear system with an equivalent stiffness depending on the trigger level. Various triggering conditions for the RD technique are investigated, to study their applicability in linearizing the nonlinear system. The results of the study show that, with the Local Extremum, and Envelope triggering condition, the RD technique can be successfully used to linearize the modal parameters of the Duffing oscillator.