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At least 217 records · Page 12

Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

59 BASIC BIOLOGICAL SCIENCES↗

Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential

The 2009 H1N1 pandemic (pdm09) lineage of influenza A virus (IAV) crosses interspecies barriers with frequent human-to-swine spillovers each year. These spillovers reassort and drift within swine populations, leading to genetically and antigenically novel IAV that represent a zoonotic threat. We quantified interspecies transmission of the pdm09 lineage, persistence in swine, and identified how evolution in swine impacted zoonotic risk. Human and swine pdm09 case counts between 2010 and 2020 were correlated and human pdm09 burden and circulation directly impacted the detection of pdm09 in pigs. However, there was a relative absence of pdm09 circulation in humans during the 2020–21 season that was not reflected in swine. During the 2020–21 season, most swine pdm09 detections originated from human-to-swine spillovers from the 2018–19 and 2019–20 seasons that persisted in swine. We identified contemporary swine pdm09 representatives of each persistent spillover and quantified cross-reactivity between human seasonal H1 vaccine strains and the swine strains using a panel of monovalent ferret antisera in hemagglutination inhibition (HI) assays. The swine pdm09s had variable antigenic reactivity to vaccine antisera, but each swine pdm09 clade exhibited significant reduction in cross-reactivity to one or more of the human seasonal vaccine strains. Further supporting zoonotic risk, we showed phylogenetic evidence for 17 swine-to-human transmission events of pdm09 from 2010 to 2021, 11 of which were not previously classified as variants, with each of the zoonotic cases associated with persistent circulation of pdm09 in pigs. These data demonstrate that reverse-zoonoses and evolution of pdm09 in swine results in viruses that are capable of zoonotic transmission and represent a potential pandemic threat.

60 APPLIED LIFE SCIENCES↗

Forest Cover Correlation with Population Trends of the Eastern Towhee in the Mid-Eastern U.S.

The Eastern Towhee (Pipilo erythrophthalmus) is a large, ground-nesting sparrow-like bird in the Eastern United States that has shown dramatic population declines over the last 50 years. This species lives year-round in the southeastern U.S., but individuals from the northeastern U.S. migrate south in the winter and overlap with southeastern residents. The Eastern Towhee is one of the fastest-declining bird species in the eastern U.S. In this study, we compare Eastern Towhee population trends during the breeding season with winter population trends over the last three decades. Paradoxically, this species is significantly increasing in Maryland, West Virginia, New Jersey, Virginia, and Delaware during the winter, but decreasing during the summer. Using the national Breeding Bird Survey dataset, we show that the Eastern Towhee populations have been declining roughly at a rate of -11.58% in Maryland, -9.51% in West Virginia, -37.95% in New Jersey, -11.22% in Virginia, and -16.96% in Delaware per year from 1984-2015. But the populations have been increasing during winter roughly at a rate of 0.62% in Maryland, 0.05% in West Virginia, 0.33% in New Jersey, 0.08% in Virginia, and 0.51% in Delaware per year from 1984-2019, using the Christmas Bird Count. We explore a variety of hypotheses to explain this paradox, including a northward range shift in association with climate change, as well as changes in habitat availability. Our study documents how the natural world is changing in complex ways due to many stressors and will help understand how to conserve the Eastern Towhee.

Meklit Mesfin↗

Normally Expected Aberrations in the 8-hour Dynamic EKG

The establishment of norms for interpreting long term dynamic electrocardiograms is attempted by correlating a completely disease symptom and cardiac risk factor free sample with a non-pure sample in the direction of normality on various variables. Out of a population of 362 subjects exposed to dynamic electrocardiogram testing, a discrimination between normals and abnormals in terms of traditional risk factors was observed. The two groups differed significantly on the following variables: cholesterol, smoking, systolic blood pressure, white blood count, fasting blood sugar, uric acid, resting EKG, year of birth, and coronary insufficiency.

Fleck, R. L.↗

Far-infrared emission in the Rho Ophiuchi region - A comparison with molecular gas emission and visual extinction

The dust characteristics of a 40 arcmin x 40 arcmin section of the Rho Ophiuchi molecular clouds complex revealed by the IRAS satellite are compared with both molecular line and deep star count data for the region. The data reveal the cloud to be clearly visible at 12 and 25 microns, as well as at 60 and 100 microns. Modeling the infrared emission from the cloud as being due to two populations of dust grains, the short-wavelength emission is found not to reflect the internal structure of the molecular cloud. The 60 micron opacity determined using a single grain emission model correlates reasonably well with (C-13)O column density and visual extinction up to roughly 5 mag. The cloud edges appear to be heated by the interstellar radiation field. The far-infrared luminosity to mass ratio for the region is determined to be 0.9 solar luminosity/solar mass, a value much smaller than the average ratio for the inner Galaxy.

Jarrett, T. H.↗

Orbiting meteoroid and debris counting experiment

The Orbiting Meteoroid and Debris Counting Experiment (OMDC) flew for approximately 90 days in a highly elliptical earth orbit onboard the Clementine Interstage Adapter (ISA) Spacecraft. This experiment obtained data on the impact flux of natural micrometeoroids and it provided limited information on the population of small mass man-made debris as a function of altitude in near earth space. The flight of the OMDC experiment on the ISA spacecraft also demonstrated that the ultra-lightweight, low-power, particle impact detector system that was used is a viable system for flights on future spacecraft to monitor the population of small mass man-made debris particles and to map the cosmic dust environment encountered on interplanetary missions. An overview of the ISA spacecraft mission, the approach to the OMDC experiment, and the data obtained by the experiment are presented.

Kinard, William H.↗

Very low mass stars and white dwarfs in NGC 6397

Deep Wide Field/Planetary Camera 2 (WFPC2) images in wide bands centered at 606 and 802 nm were taken with the Hubble Space Telescope (HST) 4.6 min from the center of the galactic globular cluster NGC 6397. The images were used to accurately position approximately 2120 stars detected in the field on a color magnitude diagram down to a limiting magnitude m(sub 814) approximately = m(sub I) approximately = 26 determined reliably and solely by counting statistics. A white dwarf sequence and a rich, narrow cluster main sequence are detected for the first time, the latter stretching from m(sub 814) = 18.5 to m(sub 814) = 24.0 where it becomes indistinguishable from the field population. Two changes of slope of the main sequence at m(sub 814) approximately = 20 and m(sub 814) approximately = 22.5 are evident. The corresponding luminosity function increases slowly from M(sub 814) approximately = 6.5 to 8.5 are expected from ground-based observations but then drops sharply from there dwon to the measurement limit. The corresponding mass function obtained bu using the only presently available mass-luminosity function for the cluster's metallicity rises to a plateau between approximately 0.25 and approximately 0.15 solar mass, but drops toward the expected mass limit of the normal hydrogen burning main sequence at approximately 0.1 solar mass. This result is in clear contrast to that obtained from the ground and implies either a substantial modification of the cluster's initial mass function due to dynamical evolution in its lifetime, or that very low mass stars are not produced in any dynamically significant amount by clusters of this type. The white dwarf sequence is in reasonable agreement with a cooling sequence of models of mass 0.5 solar mass at the canonical distance of NGC 6397 with a scatter that is most likely due to photometric errors, but may also reflect real differences in mass or chemical composition. Contamination from unresolved galaxies, which cannot be reliably identified with our filters, makes it difficult to meaningfully compare the observed white dwarf luminosity function with its theoretical counterpart.

Paresce, Francesco↗

Probing the X-Ray Binary Populations of the Ring Galaxy NGC 1291

We present Chandra studies of the X-ray binary (XRB) populations in the bulge and ring regions of the ring galaxy NGC 1291. We detect 169 X-ray point sources in the galaxy, 75 in the bulge and 71 in the ring, utilizing the four available Chandra observations totaling an effective exposure of 179 ks. We report photometric properties of these sources in a point-source catalog. There are approx. 40% of the bulge sources and approx. 25% of the ring sources showing > 3(sigma) long-term variability in their X-ray count rate. The X-ray colors suggest that a significant fraction of the bulge (approx. 75%) and ring (approx. 65%) sources are likely low-mass X-ray binaries (LMXBs). The spectra of the nuclear source indicate that it is a low-luminosity AGN with moderate obscuration; spectral variability is observed between individual observations. We construct 0.3-8.0 keV X-ray luminosity functions (XLFs) for the bulge and ring XRB populations, taking into account the detection incompleteness and background AGN contamination. We reach 90% completeness limits of approx.1.5 x 10(exp 37) and approx. 2.2 x 10(exp 37) erg/s for the bulge and ring populations, respectively. Both XLFs can be fit with a broken power-law model, and the shapes are consistent with those expected for populations dominated by LMXBs. We perform detailed population synthesis modeling of the XRB populations in NGC 1291 , which suggests that the observed combined XLF is dominated by aD old LMXB population. We compare the bulge and ring XRB populations, and argue that the ring XRBs are associated with a younger stellar population than the bulge sources, based on the relative over-density of X-ray sources in the ring, the generally harder X-ray color of the ring sources, the overabundance of luminous sources in the combined XLF, and the flatter shape of the ring XLF.

Luo, B.↗

The Case for Optimized Edge-Centric Tractography at Scale

The anatomic validity of structural connectomes remains a significant uncertainty in neuroimaging. Edge-centric tractography reconstructs streamlines in bundles between each pair of cortical or subcortical regions. Although edge bundles provides a stronger anatomic embedding than traditional connectomes, calculating them for each region-pair requires exponentially greater computation. We observe that major speedup can be achieved by reducing the number of streamlines used by probabilistic tractography algorithms. To ensure this does not degrade connectome quality, we calculate the identifiability of edge-centric connectomes between test and re-test sessions as a proxy for information content. We find that running PROBTRACKX2 with as few as 1 streamline per voxel per region-pair has no significant impact on identifiability. Variation in identifiability caused by streamline count is overshadowed by variation due to subject demographics. This finding even holds true in an entirely different tractography algorithm using MRTrix. Incidentally, we observe that Jaccard similarity is more effective than Pearson correlation in calculating identifiability for our subject population.

59 BASIC BIOLOGICAL SCIENCES↗

Correlations in the (Sub)Mil1imeter Background from ACT x BLAST

We present measurements of the auto- and cross-frequency correlation power spectra of the cosmic (sub)millimeter background at: 250, 350, and 500 microns (1200, 860, and 600 GHz) from observations made with the Balloon-borne Large Aperture Submillimeter Telescope, BLAST; and at 1380 and 2030 microns (218 and 148 GHz) from observations made with the Atacama Cosmology Telescope, ACT. The overlapping observations cover 8.6 deg(sup 2) in an area relatively free of Galactic dust near the south ecliptic pole (SEP). The ACT bands are sensitive to radiation from the CMB, the Sunyaev-Zel'dovich (SZ) effect from galaxy clusters, and to emission by radio and dusty star-forming galaxies (DSFGs), while the dominant contribution to the BLAST bands is from DSFGs. We confirm and extend the BLAST analysis of clustering with an independent pipeline, and also detect correlations between the ACT and BLAST maps at over 25(sigma) significance, which we interpret as a detection of the DSFGs in the ACT maps. In addition to a Poisson component in the cross-frequency power spectra, we detect a clustered signal at 4(sigma), and using a model for the DSFG evolution and number counts, we successfully fit all our spectra with a linear clustering model and a bias that depends only on red shift and not on scale. Finally, the data are compared to, and generally agree with, phenomenological models for the DSFG population. This study represents a first of its kind, and demonstrates the constraining power of the cross-frequency correlation technique to constrain models for the DSFGs. Similar analyses with more data will impose tight constraints 011 future models.

Hajian, Amir↗

Probabilistic Processing of Asynchronous Geiger-Mode Avalanche Photodiode Arrays for Background Rate Measurements

A system-level performance evaluation of Geiger-mode avalanche photodiode (GmAPD) arrays requires accurate measurement and prediction of the background rate of the device due to dark counts and other spurious detection events. Since a GmAPD detector reports only a binary value and timestamp associated with an avalanche event, dark count rates are typically measured by averaging thousands of frames to support a statistically significant measurement. For both synchronous and asynchronous detector, the Poisson distributed background rates are referenced to the time each pixel is armed. Unlike for synchronous GmAPD imagers where all the pixels are armed to an array-wide arm signal, an asynchronous pixel operates independently from its neighboring pixels; requiring the background rates to be calculated using an interarrival histogram. For both types of imagers, the background rate is typically evaluated by fitting an exponential distribution to a fixed window within a measured histogram of time intervals between detection events However, if the statistics of the background rate are insufficient – whether that is due to low population sizes, saturation, or a large dynamic range of population size across the array, the pixel, or array-wide, performance metrics may report results with varying accuracy. This paper reports on an implementation of an algorithm that evaluates GmAPD background rates based on statistical metrics rather than fixed windows. The algorithm functions by determining the appropriate integration window within the interarrival time histogram based on a per-pixel count rate set by a predetermined tolerable measurement error. The implementation of the algorithm allows us to characterize GmAPD arrays with orders of magnitude spread in background rates across the detector using common statistical parameters.

Mumolo, J.↗

Cluster evolution and microwave source counts

We present the modeled counts for the expected Sunyaev-Zel'dovich microwave sources associated with clusters of galaxies, predicted for experiments with arcminute-scale spatial resolution, assuming self-similar cluster evolution, for different spectra of the primordial density fluctuations and values of the cosmological density parameter Omega. Our simulations show that the source counts should be a powerful test of the evolution of very high redshift clusters. Experiments with 1 - 2 min spatial resolution, with moderate sensitivity but covering a large area of the sky, would be most effective for studying the SZ source population. Recent arcminute-scale radio experiments, the Owens Valley Radio Observatory (OVRO) RING experiment and VLA deep imaging, achieved sensitivity and sky coverage close to that needed for the detection of negative sources associated with very distant clusters. From the absence of cluster detections in these experiments, we rule out, with 90% confidence, models with Omega less than 0.3 and n = +1 as predicting too many bright sources; or there is no hot gas in clusters more distant than z(sub max) = 5 in such models. If the single negative source detected in the RING experiment is a distant cluster, the Omega = 1, n = -2 model also may be ruled out as it predicts too few sources. The new generation of telescopes, including the new SUZIE and Ryle instruments, will soon be able to detect distant clusters. The cluster population in the past has been modeled by scaling the observed present-day sample of X-ray clusters back to high redshifts, an approach which makes the best use of the observed cluster gas parameters, and makes the simulations robust to the assumed evolution at very early epochs. Although the pure self-similar model may be incompatible with the variety of observed evolutionary effects, we show that reasonable modifications to the intracluster gas history in that model, proposed to reconcile the self-similar evolution of cluster mass and the observed evolution of their X-ray luminosity, do not considerably change our microwave predictions made using the pure self-similar model. That is, the results of our simulations are applicable to the wide class of evolutionary models in which the cluster gas mass times gas temperature evolves as the dark mass times cluster virial temperature.

Markevitch, M.↗

HEMODOSE: A Set of Multi-parameter Biodosimetry Tools

After the events of September 11, 2001 and recent events at the Fukushima reactors in Japan, there is an increasing concern of the occurrence of nuclear and radiological terrorism or accidents that may result in large casualty in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine the radiation induced changes at different biological levels. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced injury. This is due to the fact that hematopoietic system is the most vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as the most practical and best laboratory test to estimate radiation dose. The HEMODOSE web tools are built upon solid physiological and pathophysiological understanding of mammalian hematopoietic systems, and rigorous coarse-grained biomathematical modeling and validation. Using single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure, these tools can estimate absorbed doses of adult victims very rapidly and accurately. Some patient data in historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large scale radiological disaster scenario. Unlike previous dose prediction algorithms, the HEMODOSE web tools establish robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in very late phase (up to 4 weeks) after exposure

Hu, Shaowen↗

Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5–50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.

60 APPLIED LIFE SCIENCES↗

Chandra X-ray Observations of the Spiral Galaxy M81

A Chandra X-Ray Observatory ACIS-S (Advanced X-ray Astrophysics Facility (Chandra) CCD (Charge Coupled Device) Imaging Spectrometer) imaging observation is used to study the population of X-ray sources in the nearby Sab galaxy M81 (NGC 3031). A total of 177 sources are detected with 124 located within the D25 isophote to a limiting X-ray luminosity of 3e36 ergs/cm(exp 2)/s. Source positions, count rates, luminosities in the 0.3-8.0 keV band, limiting optical magnitudes, and potential counterpart identifications are tabulated. Spectral and timing analysis of the 36 brightest sources are reported including the low luminosity active galactic nucleus, SN 1993J, and the Einstein discovered ultraluminous X-ray source X6.

Swartz, Douglas A.↗

Single-cell measurement of plasmid copy number and promoter activity

Abstract Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources, all of which provide critical insights for cellular engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Single-nuclei transcriptome analysis of channel catfish spleen provides insight into the immunome of an aquaculture-relevant species

The catfish industry is the largest sector of U.S. aquaculture production. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, we performed single-cell RNA sequencing on nuclei isolated from whole spleens, a major lymphoid organ in teleost fish. Libraries were prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ reagents and sequenced on an Illumina sequencer. Each demultiplexed sample was aligned to the Coco_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. From whole spleen samples, outputs were analyzed both individually and as an integrated dataset. The three splenic transcriptome libraries generated an average of 278,717,872 reads from a mean 8,157 cells. The integrated data included 19,613 cells, counts for 20,121 genes, with a median 665 genes/cell. Cluster analysis of all cells identified 17 clusters which were classified as erythroid, hematopoietic stem cells, B cells, T cells, myeloid cells, and endothelial cells. Subcluster analysis was carried out on the immune cell populations. Here, distinct subclusters such as immature B cells, mature B cells, plasma cells, γδ T cells, dendritic cells, and macrophages were further identified. Differential gene expression analyses allowed for the identification of the most highly expressed genes for each cluster and subcluster. This dataset is a rich cellular gene expression resource for investigation of the channel catfish and teleost splenic immunome.

Science & Technology - Other Topics↗

Auger Dynamics in InP/ZnSe/ZnS Quantum Dots Having Pure and Doped Shells

In this study, we report the negative trion and biexciton Auger dynamics in very high-quality InP/ZnSe/ZnS quantum dots (QDs) having varying amounts of indium-based traps in the ZnSe shell. Negative trion times are determined by time-correlated photon-counting measurements on QDs that have been photoreduced with lithium triethylborohydride. We find that the Auger times vary from 280 to 425 ps and scale linearly with the total particle volume. Excess indium in the ZnSe shell gives rise to hole traps that are transiently populated following photoexcitation. Comparing stoichiometric and nonstoichiometric particles, we find that the negative trion lifetimes are independent of the presence of indium in the ZnSe shell. Biexciton dynamics are determined from transient absorption (TA) bleach recovery measurements. Absorption of two photons results in the formation of two types of biexcitons: those having both holes in the InP core (XX state) and those having one hole trapped in the ZnSe shell (XT state). XX state Auger times are measured in stoichiometric QDs, and for these particles, the Auger times are ~80 ps. Nonstoichiometric QDs show an additional long TA decay component, assigned to Auger recombination of the XT state. Here, a previous study (J. Phys. Chem. C 2021, 125, 4110–4118) found that hole trapping at indium-based shell traps results in a slow photoluminescence (PL) rise component. We find that the fraction of the XT state formed by the absorption of two photons correlates with the product of the fraction of slow PL rise and the rise time constant following one-photon excitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗