MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics.

Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimension datasets and several open-source software packages are available to facilitate analysis and visualization. Spatial results are typically imperfect.

Extremely rapid, yet noncatastrophic, preservation of the flattened-feathered and 3D dinosaurs of the Early Cretaceous of China.

Northeast China's Early Cretaceous Yixian Formation preserves spectacular fossils that have proved extraordinarily important in testing evolutionary hypotheses involving the origin of birds and the distribution of feathers among nonavian dinosaurs. These fossils occur either flattened with soft tissue preservation (including feathers and color) in laminated lacustrine strata or as three-dimensional (3D) skeletons in "life-like" postures in more massive deposits. The relationships of these deposits to each other, their absolute ages, and the origin of the extraordinary fossil preservation have been vigorously debated for nearly a half century, with the prevailing view being that preservation was linked to violent volcanic eruptions or lahars, similar to processes that preserved human remains at Pompeii.

Correlation of sub-centennial-scale pulses of initial Central Atlantic Magmatic Province lavas and the end-Triassic extinctions.

The end-Triassic extinction (ETE) on land was synchronous with the initial lavas of the Central Atlantic Magmatic Province (CAMP) and occurred just after the brief 26 thousand year (kyr) reverse geomagnetic polarity Chron E23r that can be used for global correlation. Lava-by-lava paleomagnetic secular variation data, previously reported from Morocco and northeastern United States combined with our data for the North Mountain Basalt from the Fundy Basin of Canada show that the initial phase of CAMP volcanism occurred in only five directional groups or pulses each occupying less than a century. The first four directional groups occur during a ~40 kyr period based on available astrochronology and U-Pb geochronology.

Integrated multimodal cell atlas of Alzheimer's disease.

Alzheimer's disease (AD) is the leading cause of dementia in older adults. Although AD progression is characterized by stereotyped accumulation of proteinopathies, the affected cellular populations remain understudied. Here we use multiomics, spatial genomics and reference atlases from the BRAIN Initiative to study middle temporal gyrus cell types in 84 donors with varying AD pathologies.

Diagnostics, treatment and outcomes of cardiac sarcoidosis in a Norwegian cohort.

Background: Evidence-based guidelines for cardiac sarcoidosis (CS) regarding use of second- and third-line agents, treatment duration, surveillance and prognostic factors are lacking.

Objective: To analyze the clinical presentation, diagnostics, treatment, monitoring and clinical outcomes in a Norwegian cohort.

Methods: Using discharge diagnoses between 2017 through 2020 from a large tertiary center, we identified 52 patients with CS.

Integrated multimodal cell atlas of Alzheimer's disease.

Alzheimer's disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms driving AD progression and vulnerable cell populations affected by disease remain coarsely understood. The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types.

Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and CO[Formula: see text].

Orbital cyclicity is a fundamental pacemaker of Earth's climate system. The Newark-Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period.

Arctic ice and the ecological rise of the dinosaurs.

Abundant lake ice-rafted debris in Late Triassic and earliest Jurassic strata of the Junggar Basin of northwestern China (paleolatitude ~71°N) indicates that freezing winter temperatures typified the forested Arctic, despite a persistence of extremely high levels of atmospheric co (partial pressure of CO). Phylogenetic bracket analysis shows that non-avian dinosaurs were primitively insulated, enabling them to access rich deciduous and evergreen Arctic vegetation, even under freezing winter conditions. Transient but intense volcanic winters associated with massive eruptions and lowered light levels led to the end-Triassic mass extinction (201.

Hematite reconstruction of Late Triassic hydroclimate over the Colorado Plateau.

Hematite is the most abundant surficial iron oxide on Earth resulting from near-surface processes that make it important for addressing numerous geologic problems. While red beds have proved to be excellent paleomagnetic recorders, the early diagenetic origin of hematite in these units is often questioned. Here, we validate pigmentary hematite ("pigmentite") as a proxy indicator for the Late Triassic environment and its penecontemporaneous origin by analyzing spectrophotometric measurements of a 14.

Molecular and isotopic evidence reveals the end-Triassic carbon isotope excursion is not from massive exogenous light carbon.

The negative organic carbon isotope excursion (CIE) associated with the end-Triassic mass extinction (ETE) is conventionally interpreted as the result of a massive flux of isotopically light carbon from exogenous sources into the atmosphere (e.g., thermogenic methane and/or methane clathrate dissociation linked to the Central Atlantic Magmatic Province [CAMP]).

Mapping Solar System chaos with the Geological Orrery.

The Geological Orrery is a network of geological records of orbitally paced climate designed to address the inherent limitations of solutions for planetary orbits beyond 60 million years ago due to the chaotic nature of Solar System motion. We use results from two scientific coring experiments in Early Mesozoic continental strata: the Newark Basin Coring Project and the Colorado Plateau Coring Project. We precisely and accurately resolve the secular fundamental frequencies of precession of perihelion of the inner planets and Jupiter for the Late Triassic and Early Jurassic epochs (223-199 million years ago) using the lacustrine record of orbital pacing tuned only to one frequency (1/405,000 years) as a geological interferometer.

Empirical evidence for stability of the 405-kiloyear Jupiter-Venus eccentricity cycle over hundreds of millions of years.

The Newark-Hartford astrochronostratigraphic polarity timescale (APTS) was developed using a theoretically constant 405-kiloyear eccentricity cycle linked to gravitational interactions with Jupiter-Venus as a tuning target and provides a major timing calibration for about 30 million years of Late Triassic and earliest Jurassic time. While the 405-ky cycle is both unimodal and the most metronomic of the major orbital cycles thought to pace Earth's climate in numerical solutions, there has been little empirical confirmation of that behavior, especially back before the limits of orbital solutions at about 50 million years before present. Moreover, the APTS is anchored only at its younger end by U-Pb zircon dates at 201.

The postcranial skeleton of (Cynodontia: Traversodontidae) from the Upper Triassic of North Carolina, USA and the comparison with other traversodontids.

Postcranial remains of from the Upper Triassic of North Carolina are described and compared to those of other known traversodontid cynodonts. The postcranial skeleton of is characterized by four sacral ribs, simple ribs lacking costal plates, the extension of the scapular neck below the acromion process, a short scapular facet on the procoracoid, a concave anterior margin of the procoracoid, humerus entepicondyle with smooth corner, and the presence of a fifth distal carpal. Four types of ribs are identified among traversodontids: 'normal' form, tubercular rib, costal plate, and Y-shaped rib.

Integrative Approach for a Transformative Freshman-Level STEM Curriculum.

In 2014 Wesley College adopted a unified undergraduate program of evidence-based high-impact teaching practices. Through foundation and federal and state grant support, the college completely revised its academic core curriculum and strengthened its academic support structures by including a comprehensive early alert system for at-risk students. In this core, science, technology, engineering, and mathematics (STEM) faculty developed fresh manifestations of integrated concept-based introductory courses and revised upper-division STEM courses around student-centered learning.

Triassic-Jurassic climate in continental high-latitude Asia was dominated by obliquity-paced variations (Junggar Basin, Ürümqi, China).

Empirical constraints on orbital gravitational solutions for the Solar System can be derived from the Earth's geological record of past climates. Lithologically based paleoclimate data from the thick, coal-bearing, fluvial-lacustrine sequences of the Junggar Basin of Northwestern China (paleolatitude ∼60°) show that climate variability of the warm and glacier-free high latitudes of the latest Triassic-Early Jurassic (∼198-202 Ma) Pangea was strongly paced by obliquity-dominated (∼40 ky) orbital cyclicity, based on an age model using the 405-ky cycle of eccentricity. In contrast, coeval low-latitude continental climate was much more strongly paced by climatic precession, with virtually no hint of obliquity.

Fecal calprotectin in patients with suspected small bowel disease--a selection tool for small bowel capsule endoscopy?

Objective: Fecal calprotectin (FC) has been proposed as a selection tool for gastrointestinal examinations, but the use of FC in the diagnosis of small bowel disease in particular is less studied. The aim of this study was to assess if FC could be used to predict findings on small bowel capsule endoscopy (SBCE).

Material And Methods: We retrospectively collected FC values, SBCE findings and clinical data in 161 patients with suspected small bowel disease referred for SBCE.

Zircon U-Pb geochronology links the end-Triassic extinction with the Central Atlantic Magmatic Province.

The end-Triassic extinction is characterized by major losses in both terrestrial and marine diversity, setting the stage for dinosaurs to dominate Earth for the next 136 million years. Despite the approximate coincidence between this extinction and flood basalt volcanism, existing geochronologic dates have insufficient resolution to confirm eruptive rates required to induce major climate perturbations. Here, we present new zircon uranium-lead (U-Pb) geochronologic constraints on the age and duration of flood basalt volcanism within the Central Atlantic Magmatic Province.

Climatically driven biogeographic provinces of Late Triassic tropical Pangea.

Although continents were coalesced into the single landmass Pangea, Late Triassic terrestrial tetrapod assemblages are surprisingly provincial. In eastern North America, we show that assemblages dominated by traversodont cynodonts are restricted to a humid 6° equatorial swath that persisted for over 20 million years characterized by "semiprecessional" (approximately 10,000-y) climatic fluctuations reflected in stable carbon isotopes and sedimentary facies in lacustrine strata. More arid regions from 5-20 °N preserve procolophonid-dominated faunal assemblages associated with a much stronger expression of approximately 20,000-y climatic cycles.

Compound-specific carbon isotopes from Earth's largest flood basalt eruptions directly linked to the end-Triassic mass extinction.

A leading hypothesis explaining Phanerozoic mass extinctions and associated carbon isotopic anomalies is the emission of greenhouse, other gases, and aerosols caused by eruptions of continental flood basalt provinces. However, the necessary serial relationship between these eruptions, isotopic excursions, and extinctions has never been tested in geological sections preserving all three records. The end-Triassic extinction (ETE) at 201.

Potential on-shore and off-shore reservoirs for CO2 sequestration in Central Atlantic magmatic province basalts.

Identifying locations for secure sequestration of CO(2) in geological formations is one of our most pressing global scientific problems. Injection into basalt formations provides unique and significant advantages over other potential geological storage options, including large potential storage volumes and permanent fixation of carbon by mineralization. The Central Atlantic Magmatic Province basalt flows along the eastern seaboard of the United States may provide large and secure storage reservoirs both onshore and offshore.

Ethnic divergence and linkage disequilibrium of novel SNPs in the human NLI-IF gene: evidence of human origin and lack of association with tuberculosis susceptibility.

Sequence variation in the human genome has been used as a tool in studying human diseases and the evolutionary history of man. A human inherited predisposition to tuberculosis has been suggested and studied; however. genetic mechanisms are still ambiguous.