gebhart/patrepeval huggingface dataset:
Extracellular Electron Transfer by Shewanella oneidensis Controls Pd Nanoparticle Phenotype (2018)

Abstarct Biological production of inorganic materials is impeded by relatively few organisms possessing genetic and metabolic linkage to material properties. The physiology of electroactive bacteria is intimately tied to inorganic transformations, which makes genetically tractable and well-studied electrogens, such as Shewanella oneidensis , attractive hosts for material synthesis. Notably, this species is capable of reducing a variety of transition-metal ions into functional nanoparticles, but exact mechanisms of nanoparticle biosynthesis remain ill-defined. We report two key factors of extracellular electron transfer by S. oneidensis , the outer membrane cytochrome, MtrC, and soluble redox shuttles (flavins), that affect Pd nanoparticle formation. Changes in the expression and availability of these electron transfer components drastically modulated particle phenotype, including particle synthesis rate, structure, and cellular localization. These relationships may serve as the basis for biologically tailoring Pd nanoparticle catalysts and could potentially be used to direct the biogenesis of other metal nanomaterials.
Competition Between Tumor and Mononuclear Phagocyte System Causing the Low Tumor Distribution of Nanoparticles and Strategies to Improve Tumor Accumulation (2016)

In the past few decades, nanoparticles have shown their advantages in anti-cancer therapy. After intravenous injection, they could preferentially arrive at tumor tissue either by extravasation from tumor vasculature or targeting vascular endothelial cells. But at the same time, their quantity in mononuclear phagocyte system (MPS) is far more than that in tumor. In this review, we discuss the advantages of MPS in spleen and liver over tumor on competing nanoparticles. The biophysical causes of spleen and liver help the MPS to capture nanoparticles, such as sufficient flux of blood stream, capillary network with fenestrations in liver and venous sinuses in spleen. Meanwhile, liver and spleen are the two major organs that contain MPS. Various properties of nanoparticles may affect their biodistribution. It is suggested that nanoparticles with proper size and shape, suitable charge, polyethyleneglycol and ligands will minimize the clearance by MPS. Several novel and promising approaches for cancer therapy are introduced in this review. This review seeks to provide guidelines for improving nanoparticles accumulation in tumor through both optimizing nanoparticles design and novel ways to design nanodelivery system for cancer therapy.
Raman imaging of rat nonalcoholic fatty liver tissues reveals distinct biomolecular states (2023)

An essential challenge in diagnosing states of nonalcoholic fatty liver disease (NAFLD) is the early prediction of progression from nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH) before the disease progresses. Histological diagnoses of NAFLD rely on the appearance of anomalous tissue morphologies, and it is difficult to segment the biomolecular environment of the tissue through a conventional histopathological approach. Here, we show that hyperspectral Raman imaging provides diagnostic information on NAFLD in rats, as spectral changes among disease states can be detected before histological characteristics emerge. Our results demonstrate that Raman imaging of NAFLD can be a useful tool for histopathologists, offering biomolecular distinctions among tissue states that cannot be observed through standard histopathological means.
Retreatment with Hyaluronic Acid Viscosupplementation in Knee Osteoarthritis: Agreement between EUROVISCO Guidelines and Current Medical Practice (2021)

In current practice, physicians tended to reinject their patients less than recommended, although EUROVISCO guidelines for viscosupplementation retreatment consider decision criteria that clearly correspond to those of practitioners in real life. These include the patients' willingness to be treated or the patients' perception of the effectiveness of the treatment.
Skeletal progenitors preserve proliferation and self-renewal upon inhibition of mitochondrial respiration by rerouting the TCA cycle (2022)

A functional electron transport chain (ETC) is crucial for supporting bioenergetics and biosynthesis. Accordingly, ETC inhibition decreases proliferation in cancer cells but does not seem to impair stem cell proliferation. However, it remains unclear how stem cells metabolically adapt. In this study, we show that pharmacological inhibition of complex III of the ETC in skeletal stem and progenitor cells induces glycolysis side pathways and reroutes the tricarboxylic acid (TCA) cycle to regenerate NAD<sup>+</sup> and preserve cell proliferation. These metabolic changes also culminate in increased succinate and 2-hydroxyglutarate levels that inhibit Ten-eleven translocation (TET) DNA demethylase activity, thereby preserving self-renewal and multilineage potential. Mechanistically, mitochondrial malate dehydrogenase and reverse succinate dehydrogenase activity proved to be essential for the metabolic rewiring in response to ETC inhibition. Together, these data show that the metabolic plasticity of skeletal stem and progenitor cells allows them to bypass ETC blockade and preserve their self-renewal.
Circulating and cell-bound antibodies increase coxsackievirus B4-induced production of IFN-α by peripheral blood mononuclear cells from patients with type 1 diabetes (2002)

Increased levels of IFN-alpha have been found in patients with type 1 diabetes who have detectable levels of coxsackievirus B4 (CVB4) RNA in their blood. The IFN-alpha-inducing activity of CVB4 in vitro is weak but can be enhanced by human IgGs. Therefore, it was investigated in vitro whether a preferential IFN-alpha response of peripheral blood mononuclear cells (PBMCs) to CVB4 exists in patients with type 1 diabetes (n=56) compared with healthy subjects (n=20) and whether antibodies play a role. In patients, the levels of IFN-alpha obtained after stimulation by PBMCs with CVB4 were higher (P=0.008), an individual IFN-alpha response by PBMCs to CVB4 was more frequent (P=0.0004) and increased levels of IFN-alpha were observed in CVB4-infected whole blood cultures. The IFN-alpha-inducing activity of patients plasma and IgGs mixed with CVB4 and then added to PBMCs was high in comparison with healthy subjects (P<0.001) and was inhibited by preincubating the cells with anti-FcgammaRII, anti-FcgammaRIII and anti-CAR (coxsackievirus and adenovirus receptor) antibodies. The strong IFN-alpha responsiveness of PBMCs to CVB4 suggested that IgGs bound to the cell surface might play a role. A short 56 degrees C incubation of PBMCs from patients responsive to CVB4 generated supernatants, which, when added to cells, exhibited IFN-alpha-enhancing activity in combination with CVB4, whereas those of controls did not. Specific antibodies for FcgammaRI, FcgammaRII and CAR inhibited this activity. These studies demonstrate that CVB4, through interactions with circulating and/or cell-bound IgGs, can strongly induce the production of IFN-alpha by PBMCs from patients with type 1 diabetes.
Neoadjuvant Immune-Checkpoint Blockade in Triple-Negative Breast Cancer: Current Evidence and Literature-Based Meta-Analysis of Randomized Trials (2020)

Chemotherapy based on the sequential use of anthracyclines and taxanes has long represented the most efficacious approach in the management of early-stage, triple-negative breast cancer, whose aggressive behavior is widely renowned. This standard chemotherapy backbone was subsequently enriched by the use of carboplatin, based on its association with increased pathologic complete response and efficacy in the metastatic setting. Following the results from the IMpassion130 trial, the recent approval of the immunotherapic agent atezolizumab in combination with chemotherapy as first-line treatment for programmed-death ligand 1-positive, unresectable locally advanced, or metastatic triple-negative breast cancer increasingly fueled the flourishing of trials of immune-checkpoint inhibitors in the early setting. In this work, we review the most recent inherent literature in light of key methodological issues and provide a quantitative summary of the results from phase II-III randomized trials of immunotherapic agents combined with chemotherapy in the setting of interest. Hints regarding future directions are also discussed.
Structure of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus in Complex with a Protective Monoclonal Antibody (2015)

M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2.
Attractiveness and Confidence in Walking Style of Male and Female Virtual Characters (2020)

Animated virtual characters are essential to many applications. Little is known so far about biological and personality inferences made from a virtual character’s body shape and motion. Here, we investigated how sex-specific differences in walking style relate to the perceived attractiveness and confidence of male and female virtual characters. The characters were generated by reconstructing body shape and walking motion from optical motion capture data. The results suggest that sexual dimorphism in walking style plays a different role in attributing biological and personality traits to male and female virtual characters. This finding has important implications for virtual character animation.
The impact of underwater acoustic channel structure and dynamics on the performance of adaptive coherent equalizers (2004)

Channel estimate based equalizers are those for which observations of the received signal are used to estimate the channel impulse response and possibly the statistics of the interfering noise field, and these estimates are used to calculate the equalizer filter coefficients. Channel estimate based decision feedback equalizers (CE‐DFE), linear MMSE equalizers (L‐MMSE), and Passive Time‐Reversal equalizers (P‐TR) are all examples of coherent channel estimate based equalizers. Equations are derived for analyzing the performance of these channel estimated based equalizers. The performance is characterized in terms of the mean squared soft decision error (σs2) of each equalizer. This error is decomposed into two components. These are the minimum achievable error (σo2) and the excess error (σε2). The former is the soft decision error that would be realized by the equalizer if the filter coefficient calculation were based upon perfect knowledge of the channel impulse response and statistics of the interfering noise field. The latter is the additional soft decision error that is realized due to errors in the estimates of these channel parameters. Here, the impact of errors in the channel impulse estimation errors on σε2 is considered (i.e., the equalizer is assumed to have accurate knowledge of the statistics of the interfering noise field.). The error equations allow for a direct comparison of the performance characteristics of these equalizers as well as an evaluation of the impact of the characteristics of the acoustic channel on equalizer performance.
Discovery of Highly Potent and Selective Pan-Aurora Kinase Inhibitors with Enhanced in Vivo Antitumor Therapeutic Index (2012)

Serine/threonine protein kinases Aurora A, B, and C play essential roles in cell mitosis and cytokinesis. Currently a number of Aurora kinase inhibitors with different isoform selectivities are being evaluated in the clinic. Herein we report the discovery and characterization of 21c (AC014) and 21i (AC081), two structurally novel, potent, kinome-selective pan-Aurora inhibitors. In the human colon cancer cell line HCT-116, both compounds potently inhibit histone H3 phosphorylation and cell proliferation while inducing 8N polyploidy. Both compounds administered intravenously on intermittent schedules displayed potent and durable antitumor activity in a nude rat HCT-116 tumor xenograft model and exhibited good in vivo tolerability. Taken together, these data support further development of both 21c and 21i as potential therapeutic agents for the treatment of solid tumors and hematological malignancies.
New telechelic polymers and sequential copolymers by polyfunctional initiator–transfer agents (inifers). XLI. Kinetic and reactivity studies on sterically hindered inifers (1984)

Abstract The kinetics of chain transfer to the bifunctional initiating and transfer agents (binifers) 1,4‐di(2‐chloro‐2‐propyl)benzene ( p ‐DCC), 1,3‐di(2‐chloro‐2‐propyl)‐5‐tert‐butylbenzene ( m ‐tBuDCC), and 1,3‐di(2‐chloro‐2‐propyl)‐4,6‐dimethylbenzene ( m ‐DMeDCC) in the polymerization of isobutylene has been investigated. Chain transfer to monomer was shown to be absent up to −20°C in CH 3 Cl/ n ‐hexane and CH 2 Cl 2 / n ‐hexane mixtures using the m ‐tBuDCC/BCl 3 binifer system. Chain transfer constants ( C i ) to m ‐tBuDCC and k t / k p ratios determined in the range from −30°C to −80°C in CH 3 Cl/ n ‐hexane mixtures and pure CH 3 Cl solvent are reported, and the activation energy differences E tr,l − E p and E t − E p were calculated. Chain transfer constants to p ‐DCC and m ‐DMeDCC were determined by the use of pure CH 3 Cl diluent at −50°C. The chain transfer reactivity of five different inifers is discussed and compared based on C I values obtained under identical conditions, with special regard to the new, sterically hindered binifer m‐DMeDCC of extraordinary reactivity.
Channel prediction for link adaptation in fast fading environments (2007)

We present a channel predictor based on a basis function approach formulation of a Kalman filter channel estimator. The estimator models chan- nel variations via truncated discrete cosine transform (DCT), which is robust to the shape of the channel Doppler spectrum. We show that the DCT can be ap- proximated by a set of linear narrow passband filters that can be formulated as Kalman filters that track a set of decoupled parameters. Because the variation of these parameters is much slower than the channel fading, and the modeling accuracy provided by the fil- ter bank is much better than with traditional models, good prediction performance is achieved by extrapo- lation in time. Because Doppler frequencies of interest are much lower than the signal bandwidth, a broader prediction horizon is obtained by decimating the es- timated channel samples and scaling up in frequency the filter bank accordingly. The derived predictor at- tains less than 10% power prediction error with a pre- diction horizon of 1 Doppler wavelength (more than one data frame for typical prediction horizons in cel- lular systems).
Extracting and querying network attack scenarios knowledge in IDS using PCTCG and alert semantic networks (2005)

The increasing use of intrusion detection system gives rise to a huge volume of alert logs, making it hard for security administrators to uncover hidden attack scenarios. In this paper, we propose a four-layer semantic scheme designed to allow inferring attack scenarios and enabling attack semantic queries. The modified case grammar, PCTCG, is used to convert the raw alerts into machine-understandable uniform alert streams. The 2-atom alert semantic network, 2-AASN are used to generate attack scenario classes. Afterwards, based on the alert context, attack scenario instances are extracted and attack semantic query results on attack scenario instances using spreading activation technique are forwarded to the security administrator.
Epidemiology of basal-like breast cancer (2019)

Risk factors for the newly identified “intrinsic” breast cancer subtypes (luminal A, luminal B, basal-like and human epidermal growth factor receptor 2-positive/estrogen receptor-negative) were determined in the Carolina Breast Cancer Study, a population-based, case–control study of African-American and white women. Immunohistochemical markers were used to subtype 1,424 cases of invasive and in situ breast cancer, and case subtypes were compared to 2,022 controls. Luminal A, the most common subtype, exhibited risk factors typically reported for breast cancer in previous studies, including inverse associations for increased parity and younger age at first full-term pregnancy. Basal-like cases exhibited several associations that were opposite to those observed for luminal A, including increased risk for parity and younger age at first term full-term pregnancy. Longer duration breastfeeding, increasing number of children breastfed, and increasing number of months breastfeeding per child were each associated with reduced risk of basal-like breast cancer, but not luminal A. Women with multiple live births who did not breastfeed and women who used medications to suppress lactation were at increased risk of basal-like, but not luminal A, breast cancer. Elevated waist-hip ratio was associated with increased risk of luminal A in postmenopausal women, and increased risk of basal-like breast cancer in pre- and postmenopausal women. The prevalence of basal-like breast cancer was highest among premenopausal African-American women, who also showed the highest prevalence of basal-like risk factors. Among younger African-American women, we estimate that up to 68% of basal-like breast cancer could be prevented by promoting breastfeeding and reducing abdominal adiposity.
Direct thermo-optical tuning of silicon photonic devices (Conference Presentation) (2019)

Thanks to its high Kerr non-linearity and its low linear absorption, silicon is a material of choice for optical devices in the mid-infrared (from 3 to 5 microns) such as microresonators. In this wavelength range, the available optical sources such as quantum cascade lasers have a limited tunability. Tuning the refractive index of silicon can be achieved by a temperature change of the chip and has been previously demonstrated on ring resonators using integrated heaters or thermo-electric elements. We present a new method for thermo-optical tuning of silicon devices by directly using the light from a laser diode operating at 450 nm. The blue light focused on the silicon induces a local elevation of temperature and thus the refractive index locally increases. When applying this method on silicon ring resonator, the elevation of temperature leads to a decreasing free-spectral range and thus shift the resonances to lower frequencies. At 4.5 µm we measured a tuning efficiency of 200 MHz per mW of incident light. Numerical simulations of the thermo-optical effect show the locality of this tuning method, and confirm the experimental results. Finally a frequency study of the response of this method is performed and a time constant of the order of the micro-second is measured. In conclusion, we propose a fast, local, and non-invasive method for tuning silicon resonators operating in the mid-infrared that can be extended to any silicon-based device.
Year in review 2005: critical care--nephrology. (2006)

We summarize original research in the field of critical care nephrology accepted or published in 2005 in Critical Care and, when considered relevant or directly linked to this research, in other journals. The articles have been grouped into four categories to facilitate a rapid overview. First, physiopathology, epidemiology and prognosis of acute renal failure (ARF): an extensive review and some observational studies have been performed with the aim of describing aspects of ARF physiopathology, precise epidemiology and long-term outcomes. Second, several authors have performed clinical trials utilizing a potential nephro-protective drug, fenoldopam, with different results. Third, the issue of continuous renal replacement therapies dose has been addressed in a small prospective study and a large observational trial. And fourth, alternative indications to extracorporeal treatment of ARF and systemic inflammatory response syndrome have been explored by three original clinical studies.
Physiological Effects Of Extracellular Nucleotides In The Inner Ear (2000)

1. Electrochemical homeostasis, sound transduction and auditory neurotransmission in the cochlea are influenced by extracellular purines and pyrimidines. 2. Evidence that ATP and related nucleotides influence inner ear function arises from a considerable number of cellular, molecular and physiological studies in vitro and in vivo. 3. With a full understanding of these processes, which include ionotropic (P2X receptor) and metabotropic (P2Y receptor) signal transduction pathways, signal termination involving ecto-nucleotidases and recycling via nucleoside transporters, exciting possibilities emerge for treating hearing disorders, such as Meniere's disease, tinnitus and sensorineural deafness.
Synthesis and Hydrodesulfurization properties of fullerene-like (CO,Ni)/MoS2 Catalysts (2012)

International @ RAFFINAGE+GBE:RZN:PAF
Superconducting Bi-Ca-Sr-Cu-O Fibers Grown by the Laser-Heated Pedestal Growth Method (1988)

Superconducting fibers of several compositions including the nominal composition Bi(2)CaSrCu(2)O(8) have been grown by means of the laser-heated pedestal growth method. The influence of starting composition and growth conditions on structure and superconducting properties is discussed. The a-b planes of the material are parallel to the fiber axis (along the growth direction), providing the ideal condition for conduction along the copper-oxygen planes.
Tetrel and Pnictogen Bonds Complement Hydrogen and Halogen Bonds in Framing the Interactional Landscape of Barbituric Acids (2020)

Experimental and theoretical studies of fluoro-, chloro-, and bromo-substituted derivatives of barbituric acid and indandione show that imide protons form short hydrogen bonds and bromine or, to a lesser extent, chlorine atoms form halogen bonds. The imide nitrogen atoms act as effective pnictogen bond donors, while C(sp2) and C(sp3) atoms act as tetrel bond donors; the resulting N···O and C···O close interactions are a distinctive feature of crystal lattices in all compounds. Importantly, halogen atoms promote the electrophilicity of C(sp3) sites and favor the formation of C(sp3)···O close contacts. Oxygen atoms of carbonyl groups of barbituric and indandione units or of water molecules function as the interaction acceptor sites: namely, they donate electron density to hydrogen, halogen, nitrogen, and carbon atoms. Modeling of various barbituric acid derivatives indicates that the positive electrostatic potentials of π-holes orthogonal to the C(sp2) carbons and σ-holes on the elongation of quasi-axial F/Cl/Br-C(sp3) bonds merge to produce a single well-defined point of the most positive electrostatic potential on one face of the barbituric acids. This single local maximum of the potential on the molecular face is close to the site occupied by the oxygen forming the C(sp3)···O, and C(sp2)···O, short contacts observed in crystals.