gebhart/patrepeval huggingface dataset:
Transcriptome Analysis of Infected and Bystander Type 2 Alveolar Epithelial Cells during Influenza A Virus Infection Reveals In Vivo Wnt Pathway Downregulation (2018)

Influenza virus outbreaks remain a serious threat to public health. A greater understanding of how cells targeted by the virus respond to the infection can provide insight into the pathogenesis of disease. Here we examined the transcriptional profile of <i>in vivo</i>-infected and uninfected type 2 alveolar epithelial cells (AEC) in the lungs of influenza virus-infected mice. We show for the first time the unique gene expression profiles induced by the <i>in vivo</i> infection of AEC as well as the transcriptional response of uninfected bystander cells. This work allows us to distinguish the direct and indirect effects of infection at the cellular level. Transcriptome analysis revealed that although directly infected and bystander AEC from infected animals shared many transcriptome changes compared to AEC from uninfected animals, directly infected cells produce more interferon and express lower levels of Wnt signaling-associated transcripts, while concurrently expressing more transcripts associated with cell death pathways, than bystander uninfected AEC. The Wnt signaling pathway was downregulated in both <i>in vivo</i>-infected AEC and <i>in vitro</i>-infected human lung epithelial A549 cells. Wnt signaling did not affect type I and III interferon production by infected A549 cells. Our results reveal unique transcriptional changes that occur within infected AEC and show that influenza virus downregulates Wnt signaling. In light of recent findings that Wnt signaling is essential for lung epithelial stem cells, our findings reveal a mechanism by which influenza virus may affect host lung repair.<b>IMPORTANCE</b> Influenza virus infection remains a major public health problem. Utilizing a recombinant green fluorescent protein-expressing influenza virus, we compared the <i>in vivo</i> transcriptomes of directly infected and uninfected bystander cells from infected mouse lungs and discovered many pathways uniquely regulated in each population. The Wnt signaling pathway was downregulated in directly infected cells and was shown to affect virus but not interferon production. Our study is the first to discern the <i>in vivo</i> transcriptome changes induced by direct viral infection compared to mere exposure to the lung inflammatory milieu and highlight the downregulation of Wnt signaling. This downregulation has important implications for understanding influenza virus pathogenesis, as Wnt signaling is critical for lung epithelial stem cells and lung epithelial cell differentiation. Our findings reveal a mechanism by which influenza virus may affect host lung repair and suggest interventions that prevent damage or accelerate recovery of the lung.
The effects of an unstable shoe on energy expenditure and knee and ankle joint moments during walking in women (2013)

"The effects of an unstable shoe on energy expenditure and knee and ankle joint moments during walking in women." Footwear Science, 5(sup1), pp. S95–S96
Engagement of the external domains of CD45 tyrosine phosphatase can regulate the differentiation of immature CD4+CD8+ thymocytes into mature T cells. (1994)

Immature precursor cells are induced in the thymus to express clonotypic T-cell antigen receptors (TCRs) and to differentiate into mature T cells. Perhaps the least understood event which occurs during intrathymic development is the positive selection of immature CD4+CD8+ thymocytes for differentiation into mature CD4+ and CD8+ T cells based on the TCR specificity individual thymocytes express. TCR expression by CD4+CD8+ thymocytes is quantitatively regulated by CD4-mediated activation of p56lck protein-tyrosine kinase whose activity can in turn be regulated by the membrane-bound protein-tyrosine-phosphatase CD45. Here we show that antibody engagement of CD45 external domains enhances Lck tyrosine kinase activity in CD4+CD8+ thymocytes, inhibits TCR expression, and inhibits differentiation of immature CD4+CD8+ thymocytes into mature T cells. Thus, engagement of the external domains of CD45 tyrosine phosphatase can regulate the ability of immature CD4+CD8+ thymocytes to undergo positive selection, suggesting an important regulatory role for intrathymic ligands that are capable of engaging CD45 within the thymus.
A Comparative Analysis of Industry Human-AI Interaction Guidelines (2020)

With the recent release of AI interaction guidelines from Apple, Google, and Microsoft, there is clearly interest in understanding the best practices in human-AI interaction. However, industry standards are not determined by a single company, but rather by the synthesis of knowledge from the whole community. We have surveyed all of the design guidelines from each of these major companies and developed a single, unified structure of guidelines, giving developers a centralized reference. We have then used this framework to compare each of the surveyed companies to find differences in areas of emphasis. Finally, we encourage people to contribute additional guidelines from other companies, academia, or individuals, to provide an open and extensible reference of AI design guidelines at https://ai-open-guidelines.readthedocs.io/.
Multidisciplinary design optimization to reduce erosion of blades in a mixed flow fan (2013)

This paper presents an anti-erosion design approach of multidisciplinary design optimization (MDO) for turbomachinery to improve the erosion resistance of the blades, and its application to the design of an industrial mixed flow fan is given. The method is based on a concept for turbomachinery anti-erosion design in the aerodynamic design stage by modifying the geometry of the turbomachinery. The MDO approach replaces the traditional time consuming design method through automatic analyses of the aerodynamic performance, stress distribution and erosion characteristics, controlled by the optimization strategy. In the MDO approach, a multi-objective optimization algorithm non-dominated sorting genetic algorithm-II combined with radial basis function meta-model is used to find the compromise between the conflicting demands of high-efficiency and low average erosion rate with constraints on the pressure ratio and the safety factor for the blade; finite element method is used to analyze the static mechanical responses of the blade; a Navier-Stokes solver is used to predict the aerodynamic performance; solid particle paths in a viscous flow are calculated by Lagrangian method, and then the prediction of erosion is performed based on Tabakoff erosion model. Both the aerodynamic and anti-erosion performances of three selected robust optimal solutions on the Pareto front are compared to those of the baseline. The results show that the main reason for the efficiency improvement of the optimized blades is probably the smaller flow separation region and weaker secondary flows. Further comparative analysis between the baseline blade and the compromise blade for the impinging parameters is presented, and the erosion rate of compromise blade can be considerably decreased due to the lower impact velocity, suitable impact angle and fewer impact times in comparison with that of the baseline blade. As a conclusion, it can be drawn that the proposed approach gives a further opportunity for turbomachinery anti-erosion design in consideration of other disciplines, and the methodology presented can be also applied to other turbomachinery and anti-erosion problem by a minor modification.
Synthesis and Characterization of Stable Cu–Pt Nanoparticles under Reductive and Oxidative Conditions (2023)

We report a synthesis method for highly monodisperse Cu-Pt alloy nanoparticles. Small and large Cu-Pt particles with a Cu/Pt ratio of 1:1 can be obtained through colloidal synthesis at 300 °C. The fresh particles have a Pt-rich surface and a Cu-rich core and can be converted into an intermetallic phase after annealing at 800 °C under H<sub>2</sub>. First, we demonstrated the stability of fresh particles under redox conditions at 400 °C, as the Pt-rich surface prevents substantial oxidation of Cu. Then, a combination of <i>in situ</i> scanning transmission electron microscopy, <i>in situ</i> X-ray absorption spectroscopy, and CO oxidation measurements of the intermetallic CuPt phase before and after redox treatments at 800 °C showed promising activity and stability for CO oxidation. Full oxidation of Cu was prevented after exposure to O<sub>2</sub> at 800 °C. The activity and structure of the particles were only slightly changed after exposure to O<sub>2</sub> at 800 °C and were recovered after re-reduction at 800 °C. Additionally, the intermetallic CuPt phase showed enhanced catalytic properties compared to the fresh particles with a Pt-rich surface or pure Pt particles of the same size. Thus, the incorporation of Pt with Cu does not lead to a rapid deactivation and degradation of the material, as seen with other bimetallic systems. This work provides a synthesis route to control the design of Cu-Pt nanostructures and underlines the promising properties of these alloys (intermetallic and non-intermetallic) for heterogeneous catalysis.
DNAzymes to β1 and β3 mRNA Down-regulate Expression of the Targeted Integrins and Inhibit Endothelial Cell Capillary Tube Formation in Fibrin and Matrigel (2002)

A novel approach based on DNA-cleaving deoxyribozymes (DNAzymes) was developed to control expression of beta(1) and beta(3) integrins in endothelial cells. To engineer a specific cleavage site in mRNA, the flanking domains of DNAzymes were derived from oligodeoxynucleotides complementary to sequences corresponding to 1053-1070 and 1243-1267 in beta(1) and beta(3) mRNA, respectively. Phosphorothioate analogues of these antisense oligodeoxynucleotides, designated beta1-1053 and beta3-1243, significantly inhibited expression of beta(1) and beta(3) integrin subunits in endothelial and K562 cells at the level of mRNA and protein synthesis. They also specifically decreased the cell surface expression of corresponding subunits in endothelial cells and K562 cells, as measured by flow cytometry. In functional tests, beta1-1053 and beta3-1243 markedly reduced adhesion of cells to fibronectin and vitronectin, respectively. We designed DNAzymes to beta(1) and beta(3) mRNAs containing a 15-deoxynucleotide catalytic domain that was flanked by two substrate recognition segments of 8 and 10 deoxynucleotides for beta(1) and beta(3) DNAzymes, respectively. Both DNAzymes in the presence of Mg(2+) specifically cleaved their substrates, synthetic beta(1) and beta(3) mRNA fragments. Although DNAzymes were partially modified with phosphorothioate and with 2'-O-methyl groups at both the 5' and 3' ends indicated similar kinetic parameters, they were significantly more potent than the unmodified DNAzymes because of their much higher resistance to nuclease degradation. Similar to the antisense oligonucleotides, DNAzymes abolished microvascular endothelial cell capillary tube formation in fibrin and Matrigel. In conclusion, DNAzymes to beta(1) and beta(3) mRNAs with 2'-O-methyl modifications are potentially useful as gene-inactivating agents and may ultimately provide a therapeutic means to inhibit angiogenesis in vivo.
Are Co-Culture Approaches Able to Improve Biological Functions of Bioartificial Livers? (2017)

International audience
The Chemokine Receptor CCR3 Is Potentially Involved in the Homing of Prostate Cancer Cells to Bone: Implication of Bone-Marrow Adipocytes (2021)

Bone metastasis remains the most frequent and the deadliest complication of prostate cancer (PCa). Mechanisms leading to the homing of tumor cells to bone remain poorly characterized. Role of chemokines in providing navigational cues to migrating cancer cells bearing specific receptors is well established. Bone is an adipocyte-rich organ since 50 to 70% of the adult bone marrow (BM) volume comprise bone marrow adipocytes (BM-Ads), which are likely to produce chemokines within the bone microenvironment. Using in vitro migration assays, we demonstrated that soluble factors released by <i>human</i> primary BM-Ads are able to support the directed migration of PCa cells in a CCR3-dependent manner. In addition, we showed that CCL7, a chemokine previously involved in the CCR3-dependent migration of PCa cells outside of the prostate gland, is released by <i>human</i> BM-Ads. These effects are amplified by obesity and ageing, two clinical conditions known to promote aggressive and metastatic PCa. In <i>human</i> tumors, we found an enrichment of CCR3 in bone metastasis vs. primary tumors at mRNA levels using Oncomine microarray database. In addition, immunohistochemistry experiments demonstrated overexpression of CCR3 in bone versus visceral metastases. These results underline the potential importance of BM-Ads in the bone metastatic process and imply a CCR3/CCL7 axis whose pharmacological interest needs to be evaluated.
Systems for accumulation, storage and release of hydrogen (2020)

The results of studies on the hydrogen accumulation, storage and release systems differing in the type of hydrogen interaction with the material (medium) used for hydrogen storage are analyzed. Published data on the use of polycyclic hydrocarbons as the basis for hydrogen storage in a chemically bound state are summarized. Substrate-structure-dependent differences between the mechanisms of heterogeneous catalytic hydrogenation reactions of mono- and polycyclic aromatic hydrocarbons with hydrogen storage capacity &gt; 7 mass% and dehydrogenation of corresponding polycyclic naphthenes are discussed. The bibliography includes 188 references.
Towards highly reliable enterprise network services via inference of multi-level dependencies (2007)

Localizing the sources of performance problems in large enterprise networks is extremely challenging. Dependencies are numerous, complex and inherently multi-level , spanning hardware and software components across the network and the computing infrastructure. To exploit these dependencies for fast, accurate problem localization, we introduce an Inference Graph model, which is well-adapted to user-perceptible problems rooted in conditions giving rise to both partial service degradation and hard faults. Further, we introduce the Sherlock system to discover Inference Graphs in the operational enterprise, infer critical attributes, and then leverage the result to automatically detect and localize problems. To illuminate strengths and limitations of the approach, we provide results from a prototype deployment in a large enterprise network, as well as from testbed emulations and simulations. In particular, we find that taking into account multi-level structure leads to a 30% improvement in fault localization, as compared to two-level approaches.
Expression of CXCR3 on Mononuclear Cells and CXCR3 Ligands in Patients With Metastatic Renal Cell Carcinoma in Response to Systemic IL-2 Therapy (2007)

Chemokines play an important role in regulating tumor-mediated immunity, angiogenesis, and tumor cell metastasis. The chemokine receptor, CXCR3, is expressed in various human tumors, including renal cell carcinoma (RCC). CXCR3 is also associated with antiangiogenic effects in multiple tumors, and we hypothesized that interleukin-2 (IL-2) treatment of patients with metastatic clear cell RCC could augment CXCR3 levels on circulating mononuclear cells and correlate to outcome. The kinetics of CXCR3 expression on circulating mononuclear cells and its ligands (CXCL9, CXCL10, and CXCL11) in plasma were evaluated in 20 patients with metastatic clear cell RCC during cycles 1 and 2 of high dose IL-2 therapy. Subpopulations of peripheral blood mononuclear cells (PBMCs) were studied by dual color flow cytometry. Angiogenic ligands were measured and an "angiogenic ratio" was calculated prehigh and posthigh dose IL-2. CXCR3 expression on PBMC at baseline was similar in patients with metastatic RCC and normal controls. PBMC CXCR3 expression increased during treatment, and peaked during cycle 2. Plasma from RCC patients displayed similar baseline levels of CXCR3 ligands to normal controls. However, the angiogenic ratio was significantly increased in patients with metastatic RCC at baseline. Plasma levels of CXCR3 ligands increased during treatment, resulting in a reversal in the angiogenic ratio to favor angiostatic chemokines. The CXCR3/CXCR3 ligand biologic axis and angiogenic ratio may be important biomarkers in clear cell RCC patients who are undergoing high dose IL-2 therapy.
Spatiotemporal Classification with limited labels using Constrained Clustering for large datasets (2023)

Creating separable representations via representation learning and clustering is critical in analyzing large unstructured datasets with only a few labels. Separable representations can lead to supervised models with better classification capabilities and additionally aid in generating new labeled samples. Most unsupervised and semisupervised methods to analyze large datasets do not leverage the existing small amounts of labels to get better representations. In this paper, we propose a spatiotemporal clustering paradigm that uses spatial and temporal features combined with a constrained loss to produce separable representations. We show the working of this method on the newly published dataset ReaLSAT, a dataset of surface water dynamics for over 680,000 lakes across the world, making it an essential dataset in terms of ecology and sustainability. Using this large un- labelled dataset, we first show how a spatiotemporal representation is better compared to just spatial or temporal representation. We then show how we can learn even better representations using a constrained loss with few labels. We conclude by showing how our method, using few labels, can pick out new labeled samples from the unlabeled data, which can be used to augment supervised methods leading to better classification.
Enhanced neuronal death from focal ischemia in AMPA-receptor transgenic mice (1997)

Excitatory amino acid (EAA) receptors play an important role in neuronal cell death in acute cerebral ischemia. Blocking the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) subtype of EAA receptor has been shown to reduce cell death in global cerebral ischemia. However their role in focal stroke, although suggestive, has remained more contentious. To clarify this issue, we generated transgenic mice overexpressing the AMPA receptor (AMPAR) subunit GluR2-flip which would increase AMPAR-mediated currents. Excitatory neurons in these transgenic mice are thus predicted to be more susceptible than wild-type neurons to EAA (glutamate)-induced excitotoxic damage. Consistent with this prediction, cultured neurons from transgenic mice had a lower LD50 for exposure to glutamate (10(-3)-10(-5) M for 5 min) compared to wild-type neurons. Moreover, transgenic mice subjected to permanent focal ischemia of the middle cerebral artery (MCA) using the intralumenal filament model sustained larger infarctions compared to wild-type controls. Hence we have developed a genetic mouse model that demonstrates the crucial role of AMPAR containing GluR2-flip in the pathogenesis of focal hypoxic-ischemic neuronal cell death. This model will be a valuable tool in elucidating molecular mechanisms of glutamate excitotoxicity and evaluating the efficacy of glutamate receptor antagonists in attenuating post-ischemic neuronal cell death.
Emerging viral diseases (2000)

We live in an era of rapidly changing global landscapes and local environments. Viruses with RNA as their genetic material can quickly adapt to and exploit these varying conditions because of the high error rates of the virus enzymes (polymerases) that replicate their genomes. It comes as no surprise, then, that several prominent recent examples of emerging or re-emerging diseases are caused by RNA viruses. However, a complex interplay of factors can influence disease emergence. In addition to virus genetic variation (mutation, recombination, and reassortment), environmental factors (including ecological, social, health care, and behavioral influences) can play important roles. These can include (i) changing weather patterns (e.g., El Nino effects) and damming of rivers, which alters potential virus vector or host abundance and distribution, and (ii) tropical deforestation, which brings humans in close contact with these species-rich (hosts and their parasites) environments. Such factors, coupled with enormous increases in the human population during the last 50 years and urbanization in many developing countries, have greatly expanded the number of sampling events testing the fitness of RNA virus variants in different human cell backgrounds and potential transmission modes. This change, together with the advances in the speed and volume of global transportation, combines to create increased opportunity for emergence and re-emergence of viral diseases. The purpose of this review is to present some prominent recent examples of emerging and re-emerging RNA virus diseases (influenza, hantaviruses, Ebola virus, and Nipah virus) to try to convey a sense of the excitement within this field and the important advances coming about as new technologies are being applied to research the basic question of how new disease outbreaks occur and whether we can gain predictive capability.
A crossed-beam study of the state-resolved integral cross sections for the inelastic scattering of OH(X 2Π) with CO and N2 (1991)

State-resolved cross sections for the inelastic scattering of OH(X 2Π) with CO and N2 have been measured in a crossed molecular beam apparatus over the energy range from 0.5 to 5.5 kcal mol−1. The magnitude and shape of the excitation functions for the same OH final states were virtually independent of the two targets except near threshold. Both spin–orbit conserving and spin–orbit changing transitions have been investigated. Cross sections for spin–orbit changing transitions of large ΔN were approximately the same magnitude as those for spin–orbit conserving transitions. For small ΔN, however, the spin–orbit conserving transitions became more favorable. The Λ-doublet ratio, Π(A′)/Π(A″), in the Π3/2 (F1) manifold differed from unity only for the N2 target for which the ratio became increasingly larger than unity as N′ increased. The observed fine-structure effects were nearly the same as those from the corresponding (reverse) reactive collisions, and a close connection between the inelastic and reactive events has been conjectured.
Supplementary Table 2 from Intrinsic Breast Tumor Subtypes, Race, and Long-Term Survival in the Carolina Breast Cancer Study (2023)

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