Miracle-dz/UniFAR-FTUs huggingface dataset:
Burkholderia pseudomallei Triggers Altered Inflammatory Profiles in a Whole-Blood Model of Type 2 Diabetes-Melioidosis Comorbidity

ABSTRACT Melioidosis is a potentially fatal disease caused by the bacterium Burkholderia pseudomallei. Type 2 diabetes (T2D) is the most common comorbidity associated with melioidosis. B. pseudomallei isolates from melioidosis patients with T2D are less virulent in animal models than those from patients with melioidosis and no identifiable risk factors. We developed an ex vivo whole-blood assay as a tool for comparison of early inflammatory profiles generated by T2D and nondiabetic (ND) individuals in response to a B. pseudomallei strain of low virulence. Peripheral blood from individuals with T2D, with either poorly controlled glycemia (PC-T2D [n = 6]) or well-controlled glycemia (WC-T2D [n = 8]), and healthy ND (n = 13) individuals was stimulated with B. pseudomallei. Oxidative burst, myeloperoxidase (MPO) release, expression of pathogen recognition receptors (TLR2, TLR4, and CD14), and activation markers (CD11b and HLA-DR) were measured on polymorphonuclear (PMN) leukocytes and monocytes. Concentrations of plasma inflammatory cytokine (interleukin-6 [IL-6], IL-12p70, tumor necrosis factor alpha [TNF-α], monocyte chemoattractant protein 1 [MCP-1], IL-8, IL-1β, and IL-10) were also determined. Following stimulation, oxidative burst and MPO levels were significantly elevated in blood from PC-T2D subjects compared to controls. Differences were also observed in expression of Toll-like receptor 2 (TLR2), CD14, and CD11b on phagocytes from T2D and ND individuals. Levels of IL-12p70, MCP-1, and IL-8 were significantly elevated in blood from PC-T2D subjects compared to ND individuals. Notably, differential inflammatory responses of PC-T2D, WC-T2D, and ND individuals to B. pseudomallei occur independently of bacterial load and confirm the efficacy of this model of T2D-melioidosis comorbidity as a tool for investigation of dysregulated PMN and monocyte responses to B. pseudomallei underlying susceptibility of T2D individuals to melioidosis.
Review of land flow accounting methods and recommendations for further development

Robust land footprint indicators can potentially extend the consumption-based resource use indicator of the German sustainability strategy, which focuses on abiotic resources including fossil fuels, metals, and construction and industrial minerals and decidedly excludes biotic resources. Various approaches exist for quantifying the land embodied in international trade flows and consumption, i.e. the land footprint. These can be classified into a) environmental-economic accounting approaches, applying input-output analysis and tracking supply chains in monetary values, b) physical accounting approaches, using an accounting framework based on data for production, trade and utilization of agricultural and forestry commodities and tracking supply chains in physical units, and c) hybrid accounting, combining elements from both environmental-economic and physical accounting. The results of recent studies vary widely, indicating a lack of robustness and thus hampering their application in policy making. This report provides an in-depth review of the current state of the art in measuring land footprints. We identify differences in available accounting methods and indicate their shortcomings, which are mainly attributable to the product and supply chain coverage and detail, and biases introduced by the use of monetary flows as a proxy for actual physical flows. We offer options and give clear recommendations for the further development of actual and virtual global biomass and land flow ac-counting methods, particularly highlighting the advantages of hybrid accounting approaches as a framework for the robust and transparent assessment of land footprints associated with global bio-mass flows. German Title: Kritische Betrachtung von Methoden zur Berechnung von Flachenfusabdrucksindikatoren und Empfehlungen fur deren Weiterentwicklung
The Maximum Principles for Stochastic Recursive Optimal Control Problems Under Partial Information

A maximum principle for partially observed stochastic recursive optimal control problems is obtained under the assumption that control domains are not necessarily convex and forward diffusion coefficients do not contain control variables. Such kind of recursive optimal control problems have wide applications in finance and economics such as recursive utility optimization and principal-agent problems. By virtue of a classical spike variational approach and a filtering technique, the maximum principle is obtained, and the related adjoint processes are characterized by the solutions of forward-backward stochastic differential equations in finite-dimensional spaces. Then our theoretical results are applied to study a partially observed linear-quadratic recursive optimal control problem. In addition, for the case with initial and terminal state constraints, the corresponding maximum principle is also obtained by using Ekeland's variational principle.
The succession dynamics of a macroalgal community after a flood disturbance in a tropical stream from São Paulo State, southeastern Brazil

A dinâmica sucessional de uma comunidade de macroalgas em um riacho tropical (20o58' S e 49o25' W) foi investigada apos a ocorrencia de um disturbio promovido pela sequencia de chuvas intensas. Altos niveis de precipitacao pluviometrica causaram quase completa perda da comunidade de macroalgas presas ao substrato e provocaram uma forte pressao contra o seu imediato reestabelecimento. Apos este disturbio, um programa de amostragens semanais, conduzido durante o periodo de maio/1999 a janeiro/2000, foi estabelecido para investigar a recolonizacao da comunidade de macroalgas. A comunidade sofreu forte alteracao durante o processo de sucessao. O numero de especies variou de um a sete por amostragem. A abundância global da comunidade de macroalgas nao revelou nenhum padrao de variacao temporal consistente. Nos estagios sucessionais iniciais foi verificada uma forte predominância de tufos, seguido por filamentos nao ramificados. Estagios sucessionais tardios mostraram ocorrencia quase que exclusiva de formas gelatinosas, incluindo filamentos e colonias. A trajetoria sucessional foi mediada pela disponibilidade de fosforo e a composicao da comunidade seguiu um esquema de alteracoes segundo as formas de crescimento das especies. Entretanto, acredita-se que tanto processos deterministicos quanto estocasticos ocorrem em ecossistemas loticos, porem sendo dependentes da escala de tempo considerada na analise sucessional.
Distributed Intrusion Detection System Using Clustering approach And Genetic Algorithm

Data mining is the method of determining interesting patterns or knowledge from huge quantity of data. Intrusion detection systems (IDSs) are typically diffuse along with other preventive security mechanisms. Certain DM techniques exploited for ID can be categorize into two classes: misuse intrusion detection and anomaly intrusion detection. For providing security against attacks, we introduced hybrid approach for detecting anomaly intrusion which is the combination of clustering techniques and optimization. In hybrid approach, DBSCAN and K-MEANS clustering approach of data mining is combined with genetic algorithm. The approach is implemented on KDD99 dataset. In this paper results are also presented and comparisons between their base values and proposed results are also given. Keywords—data mining;IDS;multi agent;
Left atrial function in cats with left-sided cardiac disease and pleural effusion or pulmonary edema.

BACKGROUND Congestive heart failure (CHF) in cats with left-sided heart disease is sometimes manifest as pleural effusion, in other cases as pulmonary edema. HYPOTHESIS Those cats with pleural effusion have more severe left atrial (LA) dysfunction than cats with pulmonary edema. ANIMALS 30 healthy cats, 22 cats with pleural effusion, and 12 cats with pulmonary edema. All cats were client owned. METHODS Retrospective study. Measurements of LA size and function were made using commercial software on archived echocardiograms. Cases were identified through searches of medical records and of archived echocardiograms for cats with these conditions. RESULTS There was no difference (P = .3) in LA size between cats with pleural effusion and cats with pulmonary edema. Cats with pleural effusion had poorer (P = .04) LA active emptying and increased (P = .006) right ventricular (RV) diameter when compared with cats with pulmonary edema and healthy cats. Cats that exhibited LA active emptying of <7.9%, total emptying of <13.6% (diameter) or <19.4% (area), or RV diameter of >3.6 mm were significantly (P < .001) more likely to manifest pleural effusion. CONCLUSIONS AND CLINICAL IMPORTANCE Poorer LA function and increased RV dimensions are associated with pleural effusion in cats with left-sided heart disease.
The Effects of Insulin and Strontium Ranelate on Guided Bone Regeneration in Diabetic Rats

ALEXANDRU NEMTOI1, VLAD DANILA2*, ELIZA DRAGAN2, SORIN PASCA3, ANA NEMTOI2, MIHAI CONSTANTIN2, ANCA SAVA1, DANISIA HABA2 1 Gr. T. Popa University of Medicine and Pharmacy, Department of Anatomy, 16 Universitatii Str. , 700115, Iasi, Romania 2 Gr. T. Popa University of Medicine and Pharmacy, Department of Oral and Maxillofacial Surgey, 16 Universitatii Str. , 700115, Iasi, Romania 3 Ion Ionescu de la Brad University of Agricultural Sciences and Veterinary Medicine, Department of Pathological Anatomy and Forensic Medicine, 3 Mihail Sadoveanu Alley, 700490, Iasi, Romania
Large-scale structured sparse image reconstruction with correlated multiple-measurement vectors using Bayesian learning

This paper proposes a Bayesian learning approach to structured sparse image reconstruction. In contrast to conventional paradigms which convert images into high-dimensional vectors and thus are impractical for recovering large-scale images, we formulate columns of image matrices into a multiple-measurement-vector (MMV) model to reduce the problem dimension. Besides, we simultaneously exploit the tree structure of image wavelet coefficients and the column correlations of image matrices in wavelet domain as two prior structured constraints to improve reconstruction accuracy. Experimental results reveal that our method significantly outperforms other MMV-based strategies in terms of reconstruction error and provides a practical and efficient alternative to large-scale structured sparse image reconstruction.
YOUNG GALAXY CANDIDATES IN THE HUBBLE FRONTIER FIELDS. I. A2744

We report the discovery of 24 Lyman-break candidates at 7 ≲ z ≲ 10.5, in the Hubble Frontier Fields (HFF) imaging data of A2744 (z = 0.308), plus Spitzer/IRAC data and archival ACS data. The sample includes a triple image system with a photometric redshift of z ≃ 7.4. This high redshift is geometrically confirmed by our lens model corresponding to deflection angles that are 12% larger than the lower-redshift systems used to calibrate the lens model at z = 2.019. The majority of our high-redshift candidates are not expected to be multiply lensed given their locations in the image plane and the brightness of foreground galaxies, but are magnified by factors of ∼1.3–15, so that we are seeing further down the luminosity function than comparable deep-field imaging. It is apparent that the redshift distribution of these sources does not smoothly extend over the full redshift range accessible at z < 12, but appears to break above z = 9. Nine candidates are clustered within a small region of 20″ across, representing a potentially unprecedented concentration. Given the poor statistics, however, we must await similar constraints from the additional HFF clusters to properly examine this trend. The physical properties of our candidates are examined using the range of lens models developed for the HFF program by various groups including our own, for a better estimate of underlying systematics. Our spectral-energy-distribution fits for the brightest objects suggest stellar masses of ≃ 109 M☉, star formation rates of ≃ 4 M☉ yr−1, and a typical formation redshift of z ≲ 19.
STAT6-Deficient Mice Exhibit Normal Induction of Murine AIDS and Expression of Immunoglobulin E following Infection with LP-BM5 Murine Leukemia Viruses

ABSTRACT The unique Gag polyprotein of the replication-defective virus responsible for murine AIDS (MAIDS) induces B-cell activation, proliferation, and differentiation, including immunoglobulin class switch-recombination to immunoglobulin E (IgE). Secretion of IgE normally requires the serial induction of interleukin 4 (IL-4), engagement of the IL-4 receptor, activation of signal transducer and activator of transcription (STAT) 6, and induction of Iɛ germline transcripts as a prelude to switching. Remarkably, expression of IgE is equivalent in normal and IL-4-deficient mice with MAIDS (Morawetz et al., J. Exp. Med. 184:1651–1661, 1996). To understand this anomaly, we studied mice with a null mutation of STAT6. Lymphoproliferation and immunodeficiency, the hallmarks of MAIDS, developed with comparable kinetics and degree in normal and mutant mice. In addition, serum IgE levels were indistinguishable in mice of either genotype. We conclude that B cells from mice with MAIDS activate unique IL-4- and STAT6-independent signaling pathways for B-cell activation and differentiation.
Tissue Distribution of Calcineurin and its Sensitivity to Inhibition by Cyclosporine

The immunosuppressive activity of cyclosporine is mediated by inhibiting calcineurin phosphatase. However, calcineurin is widely distributed in other tissues. We examined the degree of calcineurin inhibition by cyclosporine in various tissues. In vitro, the cyclosporine concentration inhibiting 50% (IC50) of calcineurin was ∼ 10 ng/mL in human and mouse leukocytes suspensions. In vitro and in vivo IC50s of cyclosporine in homogenates of mouse kidney, heart, liver, testis, and spleen were also comparable (9–48 ng/mL). The maximum calcineurin inhibition by cyclosporine varied, from 83 to 95% of calcineurin activity in spleen, kidney, liver, and testis to 60% in heart and only 10% in brain. Maximum calcineurin inhibition was increased by the addition of cyclophilin A, indicating that cyclophilin concentrations were limiting in some tissues, at least in this assay. Western analysis of mouse tissues showed significantly less cyclophilin in heart than other tissues. cyclosporine concentrations per weight of tissue protein were highest in kidney and liver and lowest in brain and testis after oral dosing, with intermediate levels in spleen, heart, and whole blood. Thus each cyclosporine dose produces rapid and widespread inhibition of calcineurin in tissues, with differences in total susceptibility of each tissue.
Cognitive Neural Dynamics in Inferior Temporal Cortex during a Visual Working Memory Task

Intelligent organisms are capable of tracking objects even when they temporarily disappear from sight, a cognitive capacity commonly referred to as visual working memory (VWM). The neural basis of VWM has been the subject of significant scientific debate, with recent work focusing on the relative roles of posterior visual areas, such as the inferior temporal cortex (ITC), and the prefrontal cortex. Here we reexamined the contribution of ITC to VWM by recording from highly selective individual ITC neurons as monkeys engaged in multiple versions of an occlusion-based memory task. As expected, we found strong evidence for a role of ITC in stimulus encoding. We also found that almost half of these selective cells showed stimulus-selective delay period modulation, with a small but significant fraction exhibiting differential responses even in the presence of simultaneously visible interfering information. When we combined the informational content of multiple neurons, we found that the accuracy with which we could decode memory content increased drastically. The memory epoch analyses suggest that behaviorally relevant visual memories were reinstated in ITC. Furthermore, we observed a population-wide enhancement of neuronal response to a match stimulus compared with the same stimulus presented as a nonmatch. The single-cell enhancement preceded any match effects identified in the local field potential, leading us to speculate that enhancement is the result of neural processing local to ITC. Moreover, match enhancement was only later followed by the more commonly observed match suppression. Altogether, the data support the hypothesis that, when a stimulus is held in memory, ITC neurons are actively biased in favor of task-relevant visual representations and that this bias can immediately impact subsequent recognition events.
Spin-correlations and magnetic structure in an Fe monolayer on 5d transition metal surfaces

We present a detailed first principles study on the magnetic structure of an Fe monolayer on different surfaces of 5d transition metals. We use the spin-cluster expansion technique to obtain parameters of a spin model, and predict the possible magnetic ground state of the studied systems by employing the mean field approach and, in certain cases, by spin dynamics calculations. We point out that the number of shells considered for the isotropic exchange interactions plays a crucial role in the determination of the magnetic ground state. In the case of Ta substrate we demonstrate that the out-of-plane relaxation of the Fe monolayer causes a transition from ferromagnetic to antiferromagnetic ground state. We examine the relative magnitude of nearest neighbour Dzyaloshinskii–Moriya (D) and isotropic (J) exchange interactions in order to get insight into the nature of magnetic pattern formations. For the Fe/Os(0 0 0 1) system we calculate a very large D/J ratio, correspondingly, a spin spiral ground state. We find that, mainly through the leading isotropic exchange and Dzyaloshinskii–Moriya interactions, the inward layer relaxation substantially influences the magnetic ordering of the Fe monolayer. For the Fe/Re(0 0 0 1) system characterized by large antiferromagnetic interactions we also determine the chirality of the 120° Néel-type ground state.
The Effect of Habitat Exposure and Ontogeny on the Survival Skills of Hatchery Red Drum

Abstract We examined the influence of prerelease exposure to natural vegetation on the survival skills of a marine finfish, the red drum Sciaenops ocellatus. Red drum larvae at 18 d posthatch (10–12 mm standard length [SL]) were collected from a Texas Parks and Wildlife Department hatchery and reared with and without smooth cordgrass Spartina alterniflora, for either 10 or 20 d. High-speed video was then used to quantify a suite of prey capture and antipredator performance variables at days 28 (∼23 mm SL) and 38 (∼32 mm SL). Repeated-measures analysis of variance indicated that the timing and distance of key variables (e.g., maximum gape, time to maximum gape, gape cycle duration) increased significantly in older fish, while reaction distance and time to maximum velocity decreased with age. The time to reach maximum velocity was less for individuals reared in vegetation, yet these fish also had a shorter reaction distance to predatory stimuli and took longer to capture prey. Additionally, interindividual .
The Number of Lymph Node Metastases in Gastric Cancer Correlates with the Angiotensin I–Converting Enzyme Gene Insertion/Deletion Polymorphism

Purpose: In the present study, we aimed to substantiate the putative significance of angiotensin I–converting enzyme (ACE) on gastric cancer biology by investigating the influence of its gene polymorphism on gastric cancer progression. Experimental Design: Genomic DNA was purified from peripheral blood mononuclear cells or tissue specimens. Amplified ACE gene fragments were separated on agarose gels. D or I alleles were identified by the presence of 190- or 490-bp fragments, respectively. Local expression of ACE was investigated by immunohistochemistry. Results: Twenty-four of 113 (21%) gastric cancer patients had the II, 57 (51%) the ID, and 32 (28%) the DD genotype. The distribution of the ACE genotypes did not differ significantly from the control group of 189 patients without gastric cancer. However, the ACE genotypes correlated with the number of lymph node metastases and the Unio Internationale Contra Cancrum (UICC) tumor stage. Patients with the II genotype had a highly significantly smaller number of lymph node metastases (P < 0.001) and a significantly lower UICC tumor stage (P = 0.01) than patients with the DD genotype. No correlation was found between tumor type, tumor location, local tumor growth, distant metastases, and the ACE genotype. The expression of ACE in gastric cancer was investigated by immunohistochemistry in 100 of 113 patients. ACE was expressed by endothelial cells in all (100%) specimens and by tumor cells in 56 (56%) specimens. Conclusions: Our study shows that ACE is expressed locally in gastric cancer and that the gene polymorphism influences metastatic behavior.
Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

Human metabolism involves thousands of reactions and metabolites. To interpret this complexity, computational modeling becomes an essential experimental tool. One of the most popular techniques to study human metabolism as a whole is genome scale modeling. A key challenge to applying genome scale modeling is identifying critical metabolic reactions across diverse human tissues. Here we introduce a novel algorithm called Cost Optimization Reaction Dependency Assessment (CORDA) to build genome scale models in a tissue-specific manner. CORDA performs more efficiently computationally, shows better agreement to experimental data, and displays better model functionality and capacity when compared to previous algorithms. CORDA also returns reaction associations that can greatly assist in any manual curation to be performed following the automated reconstruction process. Using CORDA, we developed a library of 76 healthy and 20 cancer tissue-specific reconstructions. These reconstructions identified which metabolic pathways are shared across diverse human tissues. Moreover, we identified changes in reactions and pathways that are differentially included and present different capacity profiles in cancer compared to healthy tissues, including up-regulation of folate metabolism, the down-regulation of thiamine metabolism, and tight regulation of oxidative phosphorylation.
Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources

ABSTRACT We report the draft genomes of four Salmonella enterica isolates evaluated for the contribution of plasmids to virulence. Strains SE163A, SE696A, and SE710A carry plasmids demonstrated to facilitate plasmid-associated virulence, while SE819 is less virulent and has been used as a recipient for conjugation experiments to assess plasmid-encoded virulence mechanisms.