How auto-differentiation can improve CT workflows: classical algorithms in a modern framework.

Many of the recent successes of deep learning-based approaches have been enabled by a framework of flexible, composable computational blocks with their parameters adjusted through an automatic differentiation mechanism to implement various data processing tasks. In this work, we explore how the same philosophy can be applied to existing "classical" (i.e.

Safe Linkage of Cohort and Population-Based Register Data in a Genomewide Association Study on Health Care Expenditure.

There are research questions whose answers require record linkage of multiple databases that may be characterized by limited options for full data sharing. For this purpose, the Open Data Infrastructure for Social Science and Economic Innovations (ODISSEI) consortium has supported the development of the ODISSEI Secure Supercomputer (OSSC) platform that allows researchers to link cohort data to data from Statistics Netherlands and run large-scale analyses in a high-performance computing (HPC) environment. Here, we report a successful record linkage genomewide association (GWA) study on expenditure for total health, mental health, primary and hospital care, and medication.

Polyphenols of Camellia sinenesis decrease mortality, hepatic injury and generation of cytokines and reactive oxygen and nitrogen species after hemorrhage/resuscitation in rats.

Background: Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are produced during hemorrhagic shock and resuscitation (H/R), which may contribute to multiple organ failure. The Aim of this study was to test the hypothesis that green tea (Camellia sinenesis) extract containing 85% polyphenols decreases injury after H/R in rats by scavenging ROS and RNS.

Methods: Female Sprague Dawley rats were given 100 mg polyphenol extract/kg body weight or vehicle 2 h prior to hemorrhagic shock.

Toxicity, DNA binding, and cell proliferation in male F344 rats following short-term gavage exposures to trans-2-hexenal.

Hexenal is a genotoxic compound to which humans are exposed daily through the consumption of foods and beverages. The present studies were conducted to examine the relationships between the dose-responses of trans-2-hexenal-induced toxicity, DNA adduct formation, and cell proliferation. Male F344 rats were exposed by gavage to single doses of up to 500 mg/kg and killed 1, 2, or 4 days after dosing or were exposed to repeat doses of up to 100 mg/kg once daily for 5 days or 5 days per week for 4 weeks and killed 1 day after the end of the dosing period.

Ski promotes tumor growth through abrogation of transforming growth factor-beta signaling in pancreatic cancer.

Objective: We hypothesized that human pancreatic cancer resists TGF-beta signaling and cell death through increased Ski expression.

Summary Background Data: Ski is an oncogenic protein that acts as a TGF-beta repressor and prevents related gene transcription. Previous work suggests that Ski acts as an oncoprotein in melanoma and esophageal cancer.

Epifluorescence microscopy and image analysis of high-level polycyclic aromatic hydrocarbon contamination in soils.

Interactions between polycyclic aromatic hydrocarbons (PAHs) and soil are an important determinant of their chemical availability and transport. Laboratory examination of microscale PAH-soil interaction is limited by the availability of methods for particle-scale observation. Inverted epifluorescence microscopy, combined with digital photography and computer image analysis, was evaluated for specificity and linearity using dissolved PAHs.

Cardiac response to pressure overload in 129S1/SvImJ and C57BL/6J mice: temporal- and background-dependent development of concentric left ventricular hypertrophy.

Left ventricular hypertrophy (LVH), a risk factor for cardiovascular morbidity and mortality, is commonly caused by essential hypertension. Three geometric patterns of LVH can be induced by hypertension: concentric remodeling, concentric hypertrophy, and eccentric hypertrophy. Clinical studies suggest that different underlying etiologies, genetic modifiers, and risk of mortality are associated with LVH geometric patterns.

Top-down and bottom-up processes in speech comprehension.

Speech comprehension includes both bottom-up and top-down processes, and imaging studies have isolated a frontal-temporal network of brain areas active during speech perception. However, the precise role of the various areas in this network during normal speech comprehension is not yet fully understood. In the present fMRI study, the signal-to-noise ratio (SNR) of spoken sentences was varied in 144 steps, and speech intelligibility was measured independently in order to study in detail its effect on the activation of brain areas involved in speech perception.

Phenotypic anchoring of acetaminophen-induced oxidative stress with gene expression profiles in rat liver.

Toxicogenomics provides the ability to examine in greater detail the underlying molecular events that precede and accompany toxicity, thus allowing prediction of adverse events at much earlier times compared to classical toxicological end points. Acetaminophen (APAP) is a pharmaceutical that has similar metabolic and toxic responses in rodents and humans. Recent gene expression profiling studies with APAP found an oxidative stress signature at a subtoxic dose that we hypothesized can be phenotypically anchored to conventional biomarkers of oxidative stress.

Correlating the alpha rhythm to BOLD using simultaneous EEG/fMRI: inter-subject variability.

Simultaneous recording of electroencephalogram/functional magnetic resonance images (EEG/fMRI) was applied to identify blood oxygenation level-dependent (BOLD) changes associated with spontaneous variations of the alpha rhythm, which is considered the hallmark of the brain resting state. The analysis was focused on inter-subject variability associated with the resting state. Data from 7 normal subjects are presented.

Early hepatic stellate cell activation is associated with advanced fibrosis after liver transplantation in recipients with hepatitis C.

Recurrent hepatitis C after liver transplantation is a serious problem faced by liver transplant recipients. Activation of hepatic stellate cells is an early step in hepatic fibrogenesis. The aim of this study was to evaluate hepatic stellate cell activation, early after liver transplantation, as a predictor for the subsequent development of advanced fibrosis.

Systemic infusion of angiotensin II exacerbates liver fibrosis in bile duct-ligated rats.

Recent evidence indicates that the renin-angiotensin system (RAS) plays a major role in liver fibrosis. Here, we investigate whether the circulatory RAS, which is frequently activated in patients with chronic liver disease, contributes to fibrosis progression. To test this hypothesis, we increased circulatory angiotensin II (Ang II) levels in rats undergoing biliary fibrosis.

DNA damage in nasal and brain tissues of canines exposed to air pollutants is associated with evidence of chronic brain inflammation and neurodegeneration.

Acute, subchronic, or chronic exposures to particulate matter (PM) and pollutant gases affect people in urban areas and those exposed to fires, disasters, and wars. Respiratory tract inflammation, production of mediators of inflammation capable of reaching the brain, systemic circulation of PM, and disruption of the nasal respiratory and olfactory barriers are likely in these populations. DNA damage is crucial in aging and in age-associated diseases such as Alzheimer's disease.

NADPH oxidase signal transduces angiotensin II in hepatic stellate cells and is critical in hepatic fibrosis.

Angiotensin II (Ang II) is a pro-oxidant and fibrogenic cytokine. We investigated the role of NADPH oxidase in Ang II-induced effects in hepatic stellate cells (HSCs), a fibrogenic cell type. Human HSCs express mRNAs of key components of nonphagocytic NADPH oxidase.

A whole head MEG study of the amplitude-modulation-following response: phase coherence, group delay and dipole source analysis.

Objective: The amplitude-modulation-following response (AMFR) is the frequency component detectable in the electroencephalogram (EEG) or magnetoencephalography (MEG) corresponding to the modulation frequency of an amplitude modulated tone used as a continuous acoustic stimulus. Various properties of the AMFR depend on modulation frequency, suggesting that different generators along the auditory pathway are involved. The present study addresses these issues on the basis of a whole head MEG experiment.

Effects of propylene oxide exposure on rat nasal respiratory cell proliferation.

Long-term exposure of rodents to propylene oxide (PO) induced inflammation, respiratory cell hyperplasia, and nasal tumors at concentrations >/= 300 ppm, suggesting a possible role for cytotoxicity and compensatory cell proliferation in PO carcinogenesis. In this study, the effects of PO exposure on histopathology and cell proliferation in nasal and hepatic tissues were studied in male F344 rats exposed by inhalation for 3 or 20 days (0, 5, 25, 50, 300, and 500 ppm). Histopathology revealed an increase in mucous cell hyperplasia in the anterior nasal passages after 20 days of exposure (>/=300 ppm).

Amplitude and phase of distortion product otoacoustic emissions in the guinea pig in an (f1 ,f2) area study.

Lower sideband distortion product otoacoustic emissions (DPOAEs), measured in the ear canal upon stimulation with two continuous pure tones, are the result of interfering contributions from two different mechanisms, the nonlinear distortion component and the linear reflection component. The two contributors have been shown to have a different amplitude and, in particular, a different phase behavior as a function of the stimulus frequencies. The dominance of either component was investigated in an extensive (f1 ,f2) area study of DPOAE amplitude and phase in the guinea pig, which allows for both qualitative and quantitative analysis of isophase contours.

Polyphenols from Camellia sinenesis attenuate experimental cholestasis-induced liver fibrosis in rats.

Accumulation of hydrophobic bile acids during cholestasis leads to generation of oxygen free radicals in the liver. Accordingly, this study investigated whether polyphenols from green tea Camellia sinenesis, which are potent free radical scavengers, decrease hepatic injury caused by experimental cholestasis. Rats were fed a standard chow or a diet containing 0.

Prolonged infusion of angiotensin II into normal rats induces stellate cell activation and proinflammatory events in liver.

Recent evidence indicates that angiotensin II (ANG II) plays an important role in liver fibrogenesis. However, the underlying mechanisms are largely unknown. In advanced chronic liver diseases, circulating levels of ANG II are frequently elevated.

Induction of transitional cell hyperplasia in the urinary bladder and aberrant crypt foci in the colon of rats treated with individual and a mixture of drinking water disinfection by-products.

Cancer of the urinary bladder and colon are significant human health concerns. Epidemiological studies have suggested a correlation between these cancers and the chronic consumption of chlorinated surface water containing disinfection by-products (DBPs). The present study was designed to determine if exposure to DBPs would cause preneoplastic or neoplastic lesions in the urinary bladder and colon of rats, and what effect a mixture of DBPs would have on these lesions.

c-Jun-N-terminal kinase drives cyclin D1 expression and proliferation during liver regeneration.

The c-Jun-N-terminal kinase (JNK) pathway is strongly activated after partial hepatectomy (PH), but its role in hepatocyte proliferation is not known. In this study, JNK activity was blocked with the small molecule inhibitor JNK SP600125 in vivo and in vitro as shown by a reduction of c-Jun phosphorylation, AP-1 DNA binding activity, and c-jun messenger RNA (mRNA) expression. SP600125 inhibited proliferating cell nuclear antigen (PCNA) expression, cyclin D1 mRNA and protein expression and reduced mitotic figures after PH.

Methods for measuring DNA adducts and abasic sites I: isolation, purification, and analysis of DNA adducts in intact DNA.

The major event involved in the formation of mutations and the initiation and progression of cancer is the induction of DNA damage by reactive intermediates arising from exposure to endogenous and exogenous chemicals. Many electrophilic metabolites of chemicals covalently bind to the bases of DNA causing specific DNA adducts. This unit includes protocols for preparing samples of intact DNA and adduct analysis to quantify the number of adducts that can potentially cause mutagenic or carcinogenic damage.

Different patterns of renal cell killing after warm and cold ischemia.

Kidneys preserved for transplantation surgery sustain injuries caused by cold ischemia during storage. Additionally, kidneys harvested from non-heart-beating donors encounter the stress of warm ischemia. The aim of this study was to determine the specific cell types losing viability after warm and cold ischemia.

Carolina rinse solution minimizes kidney injury and improves graft function and survival after prolonged cold ischemia.

Background: Kidney damage caused by cold ischemia-reperfusion injury promotes adverse outcomes after renal transplantation. The purpose of this study was to determine whether Carolina rinse solution (CRS) used at the end of cold ischemic storage decreases kidney injury and improves graft function and survival.

Methods: Inbred male Lewis rats were used as donors and recipients.