Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay of tectonism and eustasy during the Early Permian icehouse: Southern Sydney Basin, southeast Australia

This investigation presents an outcrop‐based integrated study of sedimentological analysis and sequence stratigraphy applied to the Lower Permian sedimentary succession in the southern Sydney Basin, Australia. This succession accumulated in several depositional environments and sub‐environments that range from non‐marine (fluvial) to marine (outer shelf), representing the fill of a sedimentary basin that resembles a fault‐bounded, rift basin. The stratigraphic analysis indicates a deepening‐upward trend, and the sequence stratigraphic approach has established that these sediments can be attributed to the lowstand, transgressive, and highstand systems tracts. Lowstand sediments can be defined by fluvial facies that are located between the subaerial unconformity and the maximum regressive surface. Transgressive facies correspond to estuarine, upper and lower shoreface, and inner and outer shelf depositional environments and are located between the maximum regressive and the maximum flooding surfaces. Highstand bottomset sediments are accumulated above the maximum flooding surface and are represented by outer shelf facies. The stratigraphic architecture indicates the development of an almost complete depositional sequence, mainly developed under the control of tectonically induced subsidence, but also influenced by the high sedimentation rates and the high gradient of the inherited topography. Eustatic sea‐level fluctuations were of minor importance during the deposition of the examined sediments.
Adversarial Uncertainty in Multi-Robot Patrol

We study the problem of multi-robot perimeter patrol in adversarial environments, under uncertainty of adversarial behavior. The robots patrol around a closed area using a nondeterministic patrol algorithm. The adversary's choice of penetration point depends on the knowledge it obtained on the patrolling algorithm and its weakness points. Previous work investigated full knowledge and zero knowledge adversaries, and the impact of their knowledge on the optimal algorithm for the robots. However, realistically the knowledge obtained by the adversary is neither zero nor full, and therefore it will have uncertainty in its choice of penetration points. This paper considers these cases, and offers several approaches to bounding the level of uncertainty of the adversary, and its influence on the optimal patrol algorithm. We provide theoretical results that justify these approaches, and empirical results that show the performance of the derived algorithms used by simulated robots working against humans playing the role of the adversary is several different settings.
ArchiveSpark: Efficient Web archive access, extraction and derivation

Web archives are a valuable resource for researchers of various disciplines. However, to use them as a scholarly source, researchers require a tool that provides efficient access to Web archive data for extraction and derivation of smaller datasets. Besides efficient access we identify five other objectives based on practical researcher needs such as ease of use, extensibility and reusability. Towards these objectives we propose ArchiveSpark, a framework for efficient, distributed Web archive processing that builds a research corpus by working on existing and standardized data formats commonly held by Web archiving institutions. Performance optimizations in ArchiveSpark, facilitated by the use of a widely available metadata index, result in significant speed-ups of data processing. Our benchmarks show that ArchiveSpark is faster than alternative approaches without depending on any additional data stores while improving usability by seamlessly integrating queries and derivations with external tools.
Citrobacter rodentium of mice and man

The major classes of enteric bacteria harbour a conserved core genomic structure, common to both commensal and pathogenic strains, that is most likely optimized to a life style involving colonization of the host intestine and transmission via the environment. In pathogenic bacteria this core genome framework is decorated with novel genetic islands that are often associated with adaptive phenotypes such as virulence. This classical genome organization is well illustrated by a group of extracellular enteric pathogens, which includes enteropathogenic Escherichia coli (EPEC), enterohaemorrhagic E. coli (EHEC) and Citrobacter rodentium, all of which use attaching and effacing (A/E) lesion formation as a major mechanism of tissue targeting and infection. Both EHEC and EPEC are poorly pathogenic in mice but infect humans and domestic animals. In contrast, C. rodentium is a natural mouse pathogen that is related to E. coli, hence providing an excellent in vivo model for A/E lesion forming pathogens. C. rodentium also provides a model of infections that are mainly restricted to the lumen of the intestine. The mechanism's by which the immune system deals with such infections has become a topic of great interest in recent years. Here we review the literature of C. rodentium from its emergence in the mid‐1960s to the most contemporary reports of colonization, pathogenesis, transmission and immunity.
Particle-Induced Pulmonary Acute Phase Response Correlates with Neutrophil Influx Linking Inhaled Particles and Cardiovascular Risk

Background Particulate air pollution is associated with cardiovascular disease. Acute phase response is causally linked to cardiovascular disease. Here, we propose that particle-induced pulmonary acute phase response provides an underlying mechanism for particle-induced cardiovascular risk. Methods We analysed the mRNA expression of Serum Amyloid A (Saa3) in lung tissue from female C57BL/6J mice exposed to different particles including nanomaterials (carbon black and titanium dioxide nanoparticles, multi- and single walled carbon nanotubes), diesel exhaust particles and airborne dust collected at a biofuel plant. Mice were exposed to single or multiple doses of particles by inhalation or intratracheal instillation and pulmonary mRNA expression of Saa3 was determined at different time points of up to 4 weeks after exposure. Also hepatic mRNA expression of Saa3, SAA3 protein levels in broncheoalveolar lavage fluid and in plasma and high density lipoprotein levels in plasma were determined in mice exposed to multiwalled carbon nanotubes. Results Pulmonary exposure to particles strongly increased Saa3 mRNA levels in lung tissue and elevated SAA3 protein levels in broncheoalveolar lavage fluid and plasma, whereas hepatic Saa3 levels were much less affected. Pulmonary Saa3 expression correlated with the number of neutrophils in BAL across different dosing regimens, doses and time points. Conclusions Pulmonary acute phase response may constitute a direct link between particle inhalation and risk of cardiovascular disease. We propose that the particle-induced pulmonary acute phase response may predict risk for cardiovascular disease.
Arachidonoyl-phosphatidylcholine oscillates during the cell cycle and counteracts proliferation by suppressing Akt membrane binding

The activity of protein kinase B (Akt)—a major kinase promoting cell proliferation and survival—oscillates during the cell cycle. To investigate whether membrane phospholipids may regulate Akt phosphorylation and thus activity, we monitored the lipid profile of nocodazole-synchronized mouse NIH 3T3 fibroblasts during the cell cycle by liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS/MS). The proportion of sn-2-arachidonoyl-phosphatidylcholine (20:4-PC) inversely correlated with Akt activity. Increasing the cellular ratio of 20:4-PC by supplementation of 20:4-PC to the cell culture medium diminished Akt [serine (Ser)473] phosphorylation. Saturated and monounsaturated phosphatidylcholines, used as control had no effect; 20:4-PC reduced cell proliferation relative to controls, interfered with S-phase transition, and suppressed Akt downstream signaling and cyclin expression like LY294002, which is a specific inhibitor of the phosphatidylinositol-3-kinase/Akt pathway. Additive effects of 20:4-PC and LY294002 were not observed, underlining the critical role of Akt for 20:4-PC signaling; 20:4-PC suppressed Akt membrane translocation as shown by immunofluorescence microscopy but left the concentration of the anchor lipid phosphatidylinositol-3,4,5-trisphosphate unchanged. An in vitro binding assay suggests that 20:4-PC attenuates the interaction of Akt with its membrane binding site. We conclude that 20:4-PC oscillates during the cell cycle and delays cell cycle progression by inhibiting Akt membrane binding.
Overweight prevalence and trends for children and adolescents. The National Health and Nutrition Examination Surveys, 1963 to 1991.

OBJECTIVE To examine prevalence of overweight and trends in overweight for children and adolescents in the US population. DESIGN Nationally representative cross-sectional surveys with an in-person interview and a medical examination, including measurement of height and weight. PARTICIPANTS Between 3000 and 14,000 youths aged 6 through 17 years examined in each of five separate national surveys during 1963 to 1965, 1966 to 1970, 1971 to 1974, 1976 to 1980, and 1988 to 1991 (Cycles II and III of the National Health Examination Survey, and the first, second, and third National Health and Nutrition Examination Surveys, respectively). MAIN OUTCOME MEASURES Prevalence of overweight based on body mass index and 85th or 95th percentile cutoff points from Cycles II and III of the National Health Examination Survey. RESULTS From 1988 to 1991, the prevalence of overweight was 10.9% based on the 95th percentile and 22% based on the 85th percentile. Overweight prevalence increased during the period examined among all sex and age groups. The increase was greatest since 1976 to 1980, similar to findings previously reported for adults in the United States. CONCLUSIONS Increasing overweight among youths implies a need to focus on primary prevention. Attempts to increase physical activity may provide a means to address this important public health problem.
Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.

RATIONALE Coronary artery disease (CAD) is a critical determinant of morbidity and mortality. Previous studies have identified several cardiovascular disease risk factors, which may partly arise from a shared genetic basis with CAD, and thus be useful for discovery of CAD genes. OBJECTIVE We aimed to improve discovery of CAD genes and inform the pathogenic relationship between CAD and several cardiovascular disease risk factors using a shared polygenic signal-informed statistical framework. METHODS AND RESULTS Using genome-wide association studies summary statistics and shared polygenic pleiotropy-informed conditional and conjunctional false discovery rate methodology, we systematically investigated genetic overlap between CAD and 8 traits related to cardiovascular disease risk factors: low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, type 2 diabetes mellitus, C-reactive protein, body mass index, systolic blood pressure, and type 1 diabetes mellitus. We found significant enrichment of single-nucleotide polymorphisms associated with CAD as a function of their association with low-density lipoprotein, high-density lipoprotein, triglycerides, type 2 diabetes mellitus, C-reactive protein, body mass index, systolic blood pressure, and type 1 diabetes mellitus. Applying the conditional false discovery rate method to the enriched phenotypes, we identified 67 novel loci associated with CAD (overall conditional false discovery rate <0.01). Furthermore, we identified 53 loci with significant effects in both CAD and at least 1 of low-density lipoprotein, high-density lipoprotein, triglycerides, type 2 diabetes mellitus, C-reactive protein, systolic blood pressure, and type 1 diabetes mellitus. CONCLUSIONS The observed polygenic overlap between CAD and cardiometabolic risk factors indicates a pathogenic relation that warrants further investigation. The new gene loci identified implicate novel genetic mechanisms related to CAD.
Oral administration of 17beta-estradiol over 3 months without progestin co-administration does not improve coronary flow reserve in post-menopausal women: a randomized placebo-controlled cross-over CMR study.

BACKGROUND Several large epidemiological outcome studies did not demonstrate a benefit of combined estrogen-progestin replacement treatment (HRT) on cardiovascular events in elderly postmenopausal women. Whether progestin antagonism is responsible for these negative results or the natural estrogen 17ss-estradial (E2) itself is not effective in the coronary circulation is unknown. AIM To assess the effect of 3 months of E2 treatment on the coronary circulation, i.e., on coronary flow reserve (CFR), in postmenopausal women without established coronary artery disease (CAD). METHODS In a double-blind placebo-controlled cross-over design postmenopausal women (60 +/- 5 years, n = 14) were randomized to either start with placebo or E2 (Estrofem, Novo Nordisk, Copenhagen, Denmark) 2 mg/d given orally over 3 months and to switch thereafter for another 3 months of therapy. At baseline, a stress echocardiography was performed to exclude CAD. CFR was determined by coronary sinus CMR flow measurements (with motion-adapted gating and interactive acquisition window control; spatial/temporal resolution of 0.8 x 0.9 mm2/25-30 ms) which were performed at rest and during vasodilation (dipyridamole 0.56 mg/kg over 4 minutes IV) at baseline, and after 3 and 6 months of therapy, respectively. RESULTS Hemodynamics such as heart rate and systolic and diastolic blood pressure were not different for the control and E2 group. For CFR and for resting and hyperemic coronary sinus blood flow, no differences between the placebo and E2 group were found (2-way ANOVA for repeated measurements). Reproducibility of phase-contrast CMR measurements of CFR was -1.1 +/- 4.9%. CONCLUSIONS In elderly postmenopausal women without significant CAD, oral administration of E2 over 3 months without a progestin co-administration does not improve CFR. This finding yields partly explanation for some large epidemiological trials which could not demonstrate a clinical cardiovascular benefit of HRT in elderly women.
Endomucin, a CD34-like sialomucin, marks hematopoietic stem cells throughout development

To detect as yet unidentified cell-surface molecules specific to hematopoietic stem cells (HSCs), a modified signal sequence trap was successfully applied to mouse bone marrow (BM) CD34−c-Kit+Sca-1+Lin− (CD34−KSL) HSCs. One of the identified molecules, Endomucin, is an endothelial sialomucin closely related to CD34. High-level expression of Endomucin was confined to the BM KSL HSCs and progenitor cells, and, importantly, long-term repopulating (LTR)–HSCs were exclusively present in the Endomucin+CD34−KSL population. Notably, in the yolk sac, Endomucin expression separated multipotential hematopoietic cells from committed erythroid progenitors in the cell fraction positive for CD41, an early embryonic hematopoietic marker. Furthermore, developing HSCs in the intraembryonic aorta-gonad-mesonephros (AGM) region were highly enriched in the CD45−CD41+Endomucin+ fraction at day 10.5 of gestation (E10.5) and in the CD45+CD41+Endomucin+ fraction at E11.5. Detailed analyses of these fractions uncovered drastic changes in their BM repopulating capacities as well as in vitro cytokine responsiveness within this narrow time frame. Our findings establish Endomucin as a novel cell-surface marker for LTR-HSCs throughout development and provide a powerful tool in understanding HSC ontogeny.
Is Our Monetary Structure a Systemic Cause for Financial Instability? Evidence and Remedies from Nature

Fundamental laws govern all complex flow systems, including natural ecosystems, economic and financial systems. Natural ecosystems are practical exemplars of sustainability: enduring, vital, adaptive. The sustainability of any complex flow system can be measured with a single metric as an emergent property of its structural diversity and interconnectivity; it requires a balance in emphasis between efficiency and resilience. The urgent message for economics from nature is that the monoculture of national currencies, justified on the basis of market efficiency, generates structural instability in our global financial system. Economic sustainability therefore requires diversification in types of currencies, specifically through complementary currencies.
Essentializing Differences Between Women and Men

People represent many social categories, including gender categories, in essentialist terms: They see category members as sharing deep, nonobvious properties that make them the kinds of things they are. The present research explored the consequences of this mode of representation for social inferences. In two sets of studies, participants learned (a) that they were similar to a member of the other gender on a novel attribute, (b) that they were different from a member of the other gender on a novel attribute, or (c) just their own standing on a novel attribute. Results showed that participants made stronger inductive inferences about the attribute in question when they learned that it distinguished them from a member of the other gender than in the other conditions. We consider the implications of these results for the representation of social categories and for everyday social inference processes.
Simultaneous Embedding of Planar Graphs

Simultaneous embedding is concerned with simultaneously representing a series of graphs sharing some or all vertices. This forms the basis for the visualization of dynamic graphs and thus is an important field of research. Recently there has been a great deal of work investigating simultaneous embedding problems both from a theoretical and a practical point of view. We survey recent work on this topic.
Effects of High Thoracic Epidural Analgesia on Myocardial Blood Flow in Patients With Ischemic Heart Disease

Background—In patients with ischemic heart disease, high thoracic epidural analgesia (TEA) has been proposed to improve abnormalities of coronary function by inhibiting cardiac sympathetic tone. We evaluated the effect of TEA on myocardial blood flow in patients with ischemic heart disease. Methods and Results—Twenty male patients with multivessel ischemic heart disease were studied. An epidural catheter was inserted between the second and third thoracic vertebral interspace (Th2 to Th3). Analgesia was induced by epidural injection of bupivacaine 0.5%, and a sensory block from the sixth cervical (C6 to C7) to Th10 (Th8 to Th11) vertebral interspace was achieved. Myocardial blood flow was measured with dynamic 13N-ammonia PET with and without TEA at rest, during pharmacological vasodilation with dipyridamole, and during sympathetic stimulation with the cold pressor test. Myocardial blood flow during dipyridamole increased similarly, regardless of TEA, in all regions except in myocardium subtended by collateral arteries in which blood flow increased more with than without TEA (P<0.05). Without TEA, myocardial blood flow during the cold pressor test remained unchanged compared with myocardial blood flow at rest. In contrast, with TEA, myocardial blood flow increased in all vascular territories. Coronary vascular resistance increased during the cold pressor test without TEA, whereas with TEA, coronary resistance decreased in myocardium subtended by nonstenotic and stenotic coronary vessels and remained unchanged in myocardium subtended by occluded vessels. Conclusions—In patients with multivessel ischemic heart disease, TEA partly normalizes the myocardial blood flow response to sympathetic stimulation.
Prevalence of Chronic Atrophic Gastritis in Different Parts of the World

Chronic atrophic gastritis (CAG) is a well-established precursor of intestinal gastric cancer, but epidemiologic data about its occurrence are sparse. We provide an overview on studies that examined the prevalence of CAG in different parts of the world. Articles containing data about the prevalence of chronic atrophic gastritis in unselected population samples and published until November 2005 were identified by searching the MEDLINE database. Furthermore, the references in the identified publications were screened for additional suitable studies. Studies comprising at least 50 subjects were included. Forty-one studies providing data on the prevalence of CAG in unselected population samples could be identified. CAG was determined by gastroscopy in 15 studies and by pepsinogen serum levels in 26 studies. Although results are difficult to compare due to the various definitions of CAG used, a strong increase with age, the lack of major gender differences, and strong variations between populations and population groups (in particular, relatively high rates in certain Asian populations) could be observed quite consistently. We conclude that CAG is relatively common among older adults in different parts of the world, but large variations exist. Large-scale international comparative studies with standardized methodology to determine CAG are needed to provide a coherent picture of the epidemiology of CAG in various populations. Noninvasive measurements of CAG by pepsinogen levels may be particularly suited for that purpose. (Cancer Epidemiol Biomarkers Prev 2006;15(6):1083–94)
Preferential Use of an Anode as an Electron Acceptor by an Acidophilic Bacterium in the Presence of Oxygen

ABSTRACT Several anaerobic metal-reducing bacteria have been shown to be able to donate electrons directly to an electrode. This property is of great interest for microbial fuel cell development. To date, microbial fuel cell design requires avoiding O2 diffusion from the cathodic compartment to the sensitive anodic compartment. Here, we show that Acidiphilium sp. strain 3.2 Sup 5 cells that were isolated from an extreme acidic environment are able to colonize graphite felt electrodes. These bacterial electrodes were able to produce high-density electrocatalytic currents, up to 3 A/m2 at a poised potential of +0.15 V (compared to the value for the reference standard calomel electrode) in the absence of redox mediators, by oxidizing glucose even at saturating air concentrations and very low pHs.
Rational pharmacotherapy in early psychosis

Background An increased focus in research specific to first-episode schizophrenia has provided a rapidly growing body of evidence that can be directly translated to clinical practice. Aims To provide clinical recommendations specific to effective pharmacotherapy of first-episode schizophrenia. Method Evidence from clinical trials focused on the first-episode population is combined with data from other areas of investigation. Results In first-episode psychosis, when to initiate treatment is not always clear, being intimately linked to challenges regarding early detection and diagnosis. There may be differences in antipsychotic dosing, patterns of response and sensitivity to side-effects. Adherence appears to be even more problematic at this stage. Conclusions Clinicians currently treating early psychosis have considerably more information to guide their decision-making. However, the speed at which the field is growing is a reminder totreatthis knowledge as a work in progress.