gebhart/patrepeval huggingface dataset:
Granzyme M and K release in human experimental endotoxemia (2016)

Granzymes are serine proteases involved in killing of tumor cells and virally infected cells. However, granzymes are also upregulated in blood under inflammatory conditions and contribute to cytokine release and processing. Here, we show that granzyme M (GrM) and to a lesser extent GrK are transiently elevated in the circulation following LPS administration in humans. GrM is released upon stimulation of whole blood with LPS or the gram-negative bacteria Escherichia coli BL21, Pseudomonas aeruginosa, and Neisseria meningitidis. GrK is only released upon stimulation with P. aeruginosa. Thus, GrM and GrK are differentially released in response to LPS and gram-negative bacteria.
Novel Synthesis of Stagonolide-F, Putaminoxin and Aspinolide-A (2011)

Novel synthesis of putaminoxin, stagonolide-F and aspinolide-A have been achieved by utilizing (S) and (R)- malic acid. The key feature of the synthetic strategy includes Horner-Wittig olefination, double bond reduction and Steglich esterification. Olefinic acid for putaminoxin and stagonolide-F was prepared from (S)-malic acid whereas olefinic acid for aspinolide-A was prepared from (R)-malic acid and olefinic alcohols for putaminoxin, stagonolide-F and aspinolide-A were prepared by using Browns asymmetric allylboration. Keywords: Decanolides, (S) and (R) malic acid, Horner-Wittig olefination, Steglich esterification, Brown's asymmetric allylboration, Ring closing metathesis (R.C.M.), microcarpalide, Stagonolide-F, putaminoxin, butyraldehyde
Fiber laser generating switchable radially and azimuthally polarized beams with 140 mW output power at 1.6 μm wavelength (2009)

We report a fiber laser design that is capable of producing switchable radially and azimuthally polarized beams at 1.6 μm. A c-cut calcite crystal within a three-lens telescope is inserted in the cavity of an erbium doped fiber laser design. Due to the axially symmetric birefringence of the calcite crystal, radially, and azimuthally polarized modes have spatially separated foci in the cavity. Switching between the radially and azimuthally polarized outputs can be achieved by simply translating one of the lenses of the telescope. Output power more than 135 mW for both polarizations has been obtained.
Propagation of trust and distrust (2004)

A (directed) network of people connected by ratings or trust scores, and a model for propagating those trust scores, is a fundamental building block in many of today's most successful e-commerce and recommendation systems. We develop a framework of trust propagation schemes, each of which may be appropriate in certain circumstances, and evaluate the schemes on a large trust network consisting of 800K trust scores expressed among 130K people. We show that a small number of expressed trusts/distrust per individual allows us to predict trust between any two people in the system with high accuracy. Our work appears to be the first to incorporate distrust in a computational trust propagation setting.
Synthesis of stimuli-responsive double hydrophilic block copolymers by ATRP and RAFT and their use as nanostructure-directing agents of mesoporous silica materials (2017)

International audience
Modeling Human Glioblastoma Subtypes in vitro using Stem Cell Culture Conditions (2013)

This thesis is focused on neural stem cell (NSC) and glioma biology. I discuss how NSCs interact with extracellular matrix (ECM) proteins in the stem cell niche, and investigate the consequences of deregulated Platelet-derived growth factor (PDGF) signaling for embryonic NSCs in transgenic mice. Furthermore I present cell cultures of human glioblastoma multiforme (GBM) that models human disease, taking into account the heterogeneity of GBM. Finally, interactions between brain tumors and mast cells are studied using the glioma cultures.In paper I, the importance of NSC interactions with the ECM in the stem cell niche during development is discussed. Contacts between NSCs and the ECM in the subventricular zone (SVZ) are emerging as important regulatory mechanisms. We show that early postnatal neural stem and progenitor cells (NSPC) attach to collagen I, and that the adhesion is explained by higher expression of collagen receptor integrins compared to adult NSPC. Further, blood vessels in the SVZ express collagen I, indicating a possible functional relationship.Growth factors, e.g. PDGF, regulate NSC proliferation and differentiation. Aberrant activation of growth factor signaling pathways also plays a role in brain tumor formation. Paper II demonstrates that transgenic mice expressing PDGF-B at high levels in embryonic NSCs displayed mild neurological defects but no hyperplasia or brain tumors. This suggests that a high level of PDGF is not sufficient to induce brain tumors from NSCs without further mutations.Paper III presents a novel panel of human glioma stem cell (GSC) lines from GBM that display NSC markers in vitro and form secondary orthotopic tumors in vivo. GBM has recently been categorized in molecular subclasses and we demonstrate, for the first time, that these subclasses can be retained in vitro by stem cell culture conditions. We have thus generated models for research and drug development aiming at a focused treatment depending on GBM subtype.Interactions with the immune system are integral parts of tumorigenesis. Mast cells are found in glioma and in paper IV we demonstrate that the grade-dependent infiltration of mast cells is in part mediated by macrophage migration inhibitory factor and phosphorylation of STAT5.
Illustrating Ensemble Predictability across Scales Associated with the 13–15 February 2019 Atmospheric River Event (2022)

The “Valentine’s Day” atmospheric river (AR) event that affected a majority of California during 13–15 February 2019 ranked as an AR3 (Ralph et al. 2019) along most of the California coast and reached AR4 intensity in Southern California. The strong onshore flow and dynamically favorable characteristics of the Valentine’s Day AR produced both an intense and long-duration precipitation event resulting in widespread hydrometeorological impacts across California. Palomar Observatory in northern San Diego County observed >10 in. (>254 mm) of precipitation in 24 h, the highest 24-h accumulation since record keeping began in 1943 (Hatchet et al. 2020
Figure S7 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis (2023)

&lt;p&gt;Knockdown of SKP2 inhibits breast cancer cell proliferation and tumor formation.&lt;/p&gt;
ChemInform Abstract: High Oxidation State Multiple Metal—Carbon Bonds (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
SIGIRR Downregulation and Interleukin-1 Signaling Intrinsic to Renal Cell Carcinoma (2022)

Renal cell carcinoma is highly inflamed, and tumor cells are embedded into a microenvironment enriched with IL1. While inflammatory pathways are well characterized in the immune system, less is known about these same pathways in epithelial cells; it is unclear if and how innate immune signals directly impact on cancer cells, and if we could we manipulate these for therapeutic purposes. To address these questions, we first focused on the inflammatory receptors belonging to the IL1- and Toll-like receptor family including negative regulators in a small cohort of 12 clear cell RCC (ccRCC) patients' samples as compared to their coupled adjacent normal tissues. Our data demonstrated that renal epithelial cancer cells showed a specific and distinctive pattern of inflammatory receptor expression marked by a consistent downregulation of the inhibitory receptor SIGIRR mRNA. This repression was confirmed at the protein level in both cancer cell lines and primary tissues. When we analyzed <i>in silico</i> data of different kidney cancer histotypes, we identified the clear cell subtype as the one where SIGIRR was mostly downregulated; nonetheless, papillary and chromophobe tumor types also showed low levels as compared to their normal counterpart. RNA-sequencing analysis demonstrated that IL1 stimulation of the ccRCC cell line A498 triggered an intrinsic signature of inflammatory pathway activation characterized by the induction of distinct "pro-tumor" genes including several chemokines, the autocrine growth factor IL6, the atypical co-transcription factor NFKBIZ, and the checkpoint inhibitor PD-L1. When we looked for the macroareas most represented among the differentially expressed genes, additional clusters emerged including pathways involved in cell differentiation, angiogenesis, and wound healing. To note, SIGIRR overexpression in A498 cells dampened IL1 signaling as assessed by a reduced induction of NFKBIZ. Our results suggest that SIGIRR downregulation unleashes IL1 signaling intrinsic to tumor cells and that manipulating this pathway may be beneficial in ccRCC.
Contextualizing Algebraic Word Problems through Story Using Technology (2014)

Using stories in mathematics helps students situate mathematics within a context. This chapter presents an activity for the integration of stories and word problems into an algebra course designed for pre-service teachers. The pre-service teachers designed and created stories using technology (digital cameras and PowerPoint) to support algebraic explorations at the elementary and secondary levels based on the Common Core Standards. A balance of technology, language arts, and mathematics content is possible with these stories. The activity can be extended beyond the university classroom by guiding secondary students in creating their own algebraic stories in the classroom.
Supramolecular design in 2D covalent organic frameworks (2020)

2D covalent organic frameworks (COFs) are a class of porous polymers with highly crystalline structures and tunable function. The structure of a 2D-COF consists of two dimensional sheets held together through covalent bonds which are then stacked together through non-covalent forces. Since their first report, the synthesis of new COFs has relied mostly on imparting functionality to the monomer structures through covalent modification, or through the use of new thermodynamically controlled covalent bond forming methods. This tutorial review will discuss recent efforts to use supramolecular design to leverage the non-covalent forces between COF monomers and sheets to improve their properties and function. The importance of supramolecular interactions in COFs to their mechanisms of formation and overall structure will also be covered.
Epitaxially grown GaAsN random laser (2003)

We have studied the photoluminescence properties of as-grown GaAs1−xNx epitaxial layers grown on GaAs containing 0.6%, 1.77%, and 2.8% nitrogen. We found laser emission from thick (d&amp;gt;200 nm) GaAs0.972N0.028 layers exhibiting the characteristic lasing properties of random lasers. This is unusual because random lasers have so far only been associated with highly disordered or random media. We believe that high gain in combination with structural inhomogeneities that are evident in these GaAs0.972N0.028 layers, can explain the random lasing in such epitaxial layers.
Carotenoids: Nature’s unique pigments for light and energy processing (1994)

Abstract
Plasmodium vivax DBP Binding to Aotus nancymaae Erythrocytes Is Duffy Antigen Dependent (2010)

Plasmodium vivax is the second leading cause of malaria worldwide. Invasion of human erythrocytes by P. vivax merozoites is dependent upon the interaction between the parasite Duffy binding protein (PvDBP) and the erythrocyte Duffy antigen receptor. Therefore, disruption of this vital interaction is an attractive target for therapeutic intervention. Although Aotus nancymaae is a commonly used primate model for human P. vivax infections, it has not been confirmed that the interaction between Ao. nancymaae erythrocytes and P. vivax is Duffy antigen dependent. Our results indicate that normal Ao. nancymaae erythrocytes readily bind to PvDBPII and that this binding is completely abolished with chymotrypsin treatment of the erythrocytes. Furthermore, the results of our inhibition assays show a dose-dependent decrease in binding with increasing amounts of anti-PvDBPII polyclonal rabbit sera or anti-Fy6 monoclonal antibody. These data indicate that the interaction between Ao. nancymaae erythrocytes and P. vivax DBPII is Duffy antigen dependent, validating this model system for in vivo studies of anti-PvDBP inhibition.
Cumulation of High-Temperature Low-Cycle Fatigue Damage in Two-Temperature Tests (1982)

The cumulation of damage in high-temperature low-cycle fatigue is investigated for a cast cobalt-base superalloy MarM509, by using two-temperature testing. The two temperature levels [600 and 900°C (873 and 1173 K)] are taken as representative of low and high temperature behavior. At low temperatures crack initiation is crystallographic, while at high temperatures MC carbides are preferentially oxidized, giving rise to early initiation. Testing is conducted at a constant plastic strain range (Δεp/2 = 0.2 percent), and the remaining fatigue life is determined at one temperature after cycling at the other temperature for a definite amount of the expected life. The fatigue lives so obtained exhibit a large deviation from Miner's rule, particularly when the first cycling is carried out at the higher temperature. A detailed metallographic study using a replication technique shows that this deviation was related to the differences in the microcracking process at each temperature. More quantitatively, an estimate of the life to initiation is defined using a potential drop technique, which has shown that conservative predictions can be made from the application of Miner's rule to the initiation period.
Growth factor and Bcl-2 mediated survival during abortive proliferation of hybridoma cell line (1998)

Cultures of the CRL-1606 hybridoma (ATCC) have been reported to undergo continuous proliferation with simultaneous death during nutrient limited fed-batch fermentations. The bcl-2 proto-oncogene has been shown to prevent cell death under a variety of otherwise death inducing conditions. We were interested in elucidating the nature of the massive death observed in cultures of CRL-1606, specifically with respect to the possible environmental causes, and the ability of overexpressed human bcl-2 (hbcl-2) to mitigate cell death. Abortive proliferation, or continuous proliferation in the presence of continuous death, could be induced in serum free cultures of CRL-1606 through the withdrawal of insulin provided the culture was competent for cell proliferation. Culture competency for proliferation was found to be solely determined by the presence of cell culture nutrients. Abortive proliferation was defective in cultures transfected with hbcl-2 and the enhanced viability observed resulted from an increased viable cell population and at the expense of the nonviable cell population normally found in untransfected cultures. Abortive proliferation was also observed in serum containing cultures upon serum shiftdowns. Like the insulin-supplemented serum free culture system, hbcl-2 transfected cultures exhibited defects in the abortive proliferation process. These results suggest that the massive death observed during nutrient-limited fed-batch fermentation originate, in part, from growth or survival factor limitations. Hence, approaches to design cell culture media that account for the cell's proliferation requirements without accounting for the cell's survival requirements may represent a cell death sentence. Given the transformed nature of the hybridomas, we conclude that the abortive proliferation of CRL-1606 is a consequence of inappropriate cell cycle entry in a survival factor limited environment.
A New Network Traffic Classification Method Based on Classifier Integration (2015)

With development of scale, diversity and complexity of network traffic, the drawbacks of traditional machine learning methods on traffic classification is gradually exposed, especially the false positive problem in large-scale real network traffic classification is particularly serious. In this paper, aiming at reducing the false positive rate of network traffic classification, an effective network traffic classification method ---CMM method. CMM method contains three steps, including dividing the training set into clusters, forming sub-classifiers, and classifier integration in accordance with the principle of minimization and maximization. In this paper, we firstly demonstrate the effectiveness of this method in reducing the false positive rate. Secondly, we conduct experiments in large-scale national backbone network, such as the SSL protocol classification and experimental results verify the effectiveness of this method in large-scale the actual network traffic classification.
The All Particle Monte Carlo method: Atomic data files (1990)

Development of the All Particle Method, a project to simulate the transport of particles via the Monte Carlo method, has proceeded on two fronts: data collection and algorithm development. In this paper we report on the status of the data libraries. The data collection is nearly complete with the addition of electron, photon, and atomic data libraries to the existing neutron, gamma ray, and charged particle libraries. The contents of these libraries are summarized.
A phase II and pharmacodynamic study of sunitinib in relapsed/refractory oesophageal and gastro-oesophageal cancers (2015)

Sunitinib is well tolerated but only a select subgroup of patients benefited. Serum VEGF-A and -C may be early predictors of benefit. On this study, patients with clinical benefit from sunitinib had higher tumour CFB expression, and thus has identified CFB as a potential predictor for efficacy of anti-angiogenic therapy. These findings need validation from future prospective trials.
Automatic cardiac evaluations using a deep video object segmentation network (2022)

This study has achieved excellent performance on the left and right ventricle segmentation, leading to more accurate estimations of vital cardiac parameters such as ejection fraction and fractional area change parameters in the left and right ventricle functionalities, respectively. The results represent that our method can predict an assured, accurate, and reliable cardiac function diagnosis in clinical screenings.
Improving Atmospheric River Forecasts With Machine Learning (2019)

Abstract This study tests the utility of convolutional neural networks as a postprocessing framework for improving the National Center for Environmental Prediction's Global Forecast System's integrated vapor transport forecast field in the Eastern Pacific and western United States. Integrated vapor transport is the characteristic field of atmospheric rivers, which provide over 65% of yearly precipitation at some western U.S. locations. The method reduces full‐field root‐mean‐square error (RMSE) at forecast leads from 3 hr to seven days (9–17% reduction), while increasing correlation between observations and predictions (0.5–12% increase). This represents an approximately one‐ to two‐day lead time improvement in RMSE. Decomposing RMSE shows that random error and conditional biases are predominantly reduced. Systematic error is reduced up to five‐day forecast lead, but accounts for a smaller portion of RMSE. This work demonstrates convolutional neural networks potential to improve forecast skill out to seven days for precipitation events affecting the western United States.
Mast Cell Derived Histamine Negatively Regulates Hematopoiesis (2022)

ABSTRACT Hematopoietic stem cells (HSCs) are essential for generating all blood cell types and maintaining immune function and oxygen transport. This requires tight regulation of self-renewal, differentiation, and quiescence, driven by intrinsic and extrinsic signals. While the influence of many HSC progeny on HSC decisions are recognized, the role of mast cells (MCs) remain understudied. MCs are known for their immunomodulatory functions through the secretion of factors such as histamine and could offer new insights into HSC regulation. In this study, we describe a novel role for MC-derived histamine in modulating HSC behavior. We observed that genetically MC-deficient “SASH” mice exhibit increased hematopoietic output and bone marrow (BM) HSCs, characterized by an enhanced quiescent signature that increases resistance to myeloablative chemotherapy. The SASH microenvironment also contained increased frequencies of HSC-supportive cell types and expression of genes conducive to HSC maintenance, which together accelerated HSC engraftment when wild-type BM was transplanted into SASH recipients. Moreover, we found lower serum histamine levels in SASH mice, and that the enhanced hematopoietic phenotype observed in these mice could be reversed by administering exogenous histamine. Subsequent experiments with FDA-approved antihistamines in wild-type mice revealed that cetirizine, an H1R inverse agonist, notably increased HSC frequency in the BM. Overall, our findings implicate MCs are negative regulators of HSC function. This lays the groundwork for future studies to elucidate the underlying mechanisms and explore the therapeutic potential of modulating histamine signaling to promote hematopoiesis.
Vestibular compensation in a patient with a cerebellar infarction (1997)

We report the case of a 67-year-old man who suffered a traumatic unilateral peripheral vestibular injury subsequent to an unrelated prior cerebellar infarction that occurred at least 2 years earlier. The patient's clinical course was marked by poor compensation for his peripheral vestibular loss. Four months after his vestibular injury, his symptoms of dizziness had not resolved. He had a spontaneous vestibular nystagmus, and laboratory testing indicated an asymmetric semicircular canal-ocular reflex. The otolith-ocular reflex, tested using off-vertical axis rotation, also was asymmetric but had a preserved modulation component. Visual-vestibular interaction and semicircular canal-otolith interaction were normal. An MRI indicated preservation of the flocculo-nodular lobe but infarction of the pyramis and uvula. Taken together, the findings in this case suggest that despite structural and functional preservation of the flocculo-nodular lobe, an anatomic region often labeled the "vestibulo-cerebellum", a lesion of the cerebellum that can impair CNS compensation for a unilateral peripheral lesion in humans.
The mass spectra of some corticosteroid boronates (1971)

Abstract The mass spectra of methyl, n‐butyl, t‐butyl, phenyl and cyclohexyl boronates of various classes of steroid are reported and discussed. Steroid types represented are 17α, 21‐dihydroxy‐20‐ketones, 17α, 20, 21‐triols, 17α, 20‐diols, 20, 21‐ketols. Each gives rise to characteristic fragmentation modes, although derivatives of the 20α‐ and 20β‐hydroxy compounds have similar spectra.
Health Evaluation of Experimental Laboratory Mice (2012)

Good science and good animal care go hand in hand. A sick or distressed animal does not produce the reliable results that a healthy and unstressed animal produces. This unit describes the essentials of assessing mouse health, colony health surveillance, common conditions, and determination of appropriate endpoints. Understanding the health and well-being of the mice used in research enables the investigator to optimize research results and animal care.