gebhart/patrepeval huggingface dataset:
The Lung Immune Prognostic Index (LIPI) stratifies prognostic groups and correlates with gut microbiota (GM) in patients with advanced renal cell carcinoma (RCC). (2023)

719 Background: The LIPI score has been reported as an independent prognostic factor in RCC patients treated with immune checkpoint inhibitors (ICI) or tyrosine kinase inhibitors (TKI). Here, we aimed to correlate LIPI score and GM composition in patients with RCC. Methods: We prospectively collected fecal samples of all comers RCC patients who started a 1 st or beyond line therapy (standard or clinical trial) in the NCT0457446 at Gustave Roussy. Neutrophil to lymphocyte ratio (dNLR) and lactate dehydrogenase (LDH) were obtained from routine blood tests. Shot gun metagenomic sequencing (MGS) data were analyzed by multivariate and pair-wise/fold ratio . Clinical benefit ratio (CBR, complete response + partial response + stable disease, RECIST1.1) and overall survival (OS, from treatment start) were evaluated. Multivariate analysis (MVA) for OS included age, gender, therapy line, IMDC, histology, hypoalbuminemia. Results: From February 2016 to July 2021, 160 patients were screened and 102 were included. Median age was 61 years (22-89), patients were mostly males (75%) and clear cell histology (90%). Patients were treated in 1 st (15%), 2 nd (53%) and beyond (32%) lines. Treated with ICI monotherapy (65%), followed by TKI or mTOR (20%) and ICI combination (19%). IMDC was 32% good (G), 54% intermediate (I) and 14% poor (P) and LIPI was 69% G, 25% I and 6% P. Median OS was 42.9, 17.7 and 8.3 months in patients with LIPI G, I and P, respectively (p&lt;0.0001) . Among IMDC risk groups, IMDC G + LIPI G had better OS compared to other subgroups (p=0.017), and those with IMDC P + LIPI P had the worse OS. Overall, LIPI G had higher rates of CBR than I+P LIPI (74% vs 50%; p=0.0158). At MVA, LIPI was independently associated with OS (HR 6.25, 2.02-24.34; p=0.0187). Overall, Parabacteroides merdae and Veillonella parvula were enriched in LIPI I+P, while LIPI G harbored Faecalibacterium prausnitzii. In patients treated with ICI monotherapy, LIPI I+P were enriched with Bacteroides spp ( P. merdae, Phocaeicola vulgatus), and LIPI G had an overrepresentation of Ruminococcaceae unclass bacterium. Conclusions: We report the first MGS study correlating LIPI score and GM composition in RCC patients. LIPI score correlates with clinical outcomes (OS and CBR) and helped to better-stratified IMDC risk groups. Patients LIPI G harbor health-related commensals, while I and P groups are associated with harmful ones. LIPI score could represent a clinically relevant score to stratify mRCC patients. Clinical trial information: NCT04567446 .
Modulation of P-selectin expression in the postischemic intestinal microvasculature (1997)

The dual radiolabeled monoclonal antibody technique was used to 1) define the magnitude and kinetics of P-selectin expression in murine small intestine exposed to ischemia-reperfusion (I/R), and 2) determine the factor(s) responsible for initiating this response. Within 10 min after release of a 20-min arterial occlusion, intestinal P-selectin expression increased two- to threefold compared with control values. Peak (4-fold) expression of P-selectin was noted at 5 h after reperfusion, returning to the control value at 24 h. The early (10-30 min) I/R-induced upregulation of P-selectin appears to reflect mobilization of a performed pool of the adhesion molecule, whereas the later (5 h) rise appears to be transcription dependent. The early increase in P-selectin expression was not inhibited by pretreatment with either oxypurinol (inhibits xanthine oxidase), diphenhydramine (H1-receptor antagonist), or MK-571 (leukotriene C4/D4 antagonist), nor was it blunted in transgenic mice expressing three times the normal level of copper-zinc superoxide dismutase or in mast cell-deficient mice. However, significant inhibition was noted after treatment with either MK-886 (5-lipoxygenase inhibitor) or a nitric oxide (NO) donor (diethylenetriamine/NO). These findings indicate that the early I/R-induced increase in intestinal P-selectin expression is mediated by a 5-lipoxygenase-dependent NO-inhibitable mechanism.
'How time flies when you's doin' all the talking' (1997)

Since the invention of the typewriter, the keyboard has been king of the human-computer interface, largely because it has been the only one widely available. The search for an alternative method, such as speech, has continued since the 1950s and computers that can be voice controlled have featured in a number of science fiction films, such as the 1968 film ‘2001: A Space Odyssey’. While the conversational skills of the film's master computer HAL have yet to be mastered by today's computers, speech recognition technology has made significant advances from the limited systems that began emerging in the late 1980s. At last speech recognition technology is a viable tool for both business and home computer users
Biophysical Methods for the Study of Microbial Surfaces (2011)

The challenge in studying the surface architecture of different microbial pathogens is to integrate the most current biochemical, spectroscopic, microscopic, and processing techniques. Individually these methods have insufficient sensitivity to reveal complex structures, such as branched, large, viscous polymers with a high structure hydration, size, and complexity. However, when used in combination biophysical techniques are our primary source of information for understanding polydisperse molecules and complex microbial surfaces. Biophysical methods seek to explain biological function in terms of the molecular structures and properties of specific molecules. The sizes of the molecules found in microbial surfaces vary greatly from small fatty acids and sugars to macromolecules like proteins, polysaccharides, and pigments, such as melanin. These molecules, which comprise the building blocks of living organisms, assemble into cells, tissues, and whole organisms by forming complex individual structures with dimensions from 10 to 10,000 nm and larger. Biophysics is directed to determining the structure of specific biological molecules and of the larger structures into which they assemble. Some of this effort involves developing new methods, adapting old methods and building new instruments for viewing these structures. The description of biophysical properties in an experimental model where, properties such as flexibility, hydrodynamic characteristics, and size can be precisely determined is of great relevance to study the affinity of the surfaces with biologically active and inert substrates and the interaction with host molecules. Furthermore, this knowledge could establish the abilities of different molecules and their structures to differentially activate cellular responses. Recent studies in the fungal pathogen Cryptococcus neoformans have demonstrated that the physical properties of its unique polysaccharide capsule correlate with the biological functions associated with the intact capsule and the components comprising the capsule. In this review, we describe the application of biophysical techniques to study and characterize this highly hydrated and fragile fungal surface structure.
Platypus (2016)

Platypus is the first system to localize and identify people by remotely and passively sensing changes in their body electric potential which occur naturally during walking. While it uses three or more electric potential sensors with a maximum range of 2 m, as a tag-free system it does not require the user to carry any special hardware. We describe the physical principles behind body electric potential changes, and a predictive mathematical model of how this affects a passive electric field sensor. By inverting this model and combining data from sensors, we infer a method for localizing people and experimentally demonstrate a median localization error of 0.16 m. We also use the model to remotely infer the change in body electric potential with a mean error of 8.8 % compared to direct contact-based measurements. We show how the reconstructed body electric potential differs from person to person and thereby how to perform identification. Based on short walking sequences of 5 s, we identify four users with an accuracy of 94 %, and 30 users with an accuracy of 75 %. We demonstrate that identification features are valid over multiple days, though change with footwear.
Effect of Resveratrol on the Expression of Autocrine Growth Modulators in Human Breast Cancer Cells (2001)

The effect of resveratrol on the growth of human breast cancer cells was examined. Resveratrol inhibited the growth of estrogen receptor-positive MCF-7 cells cultivated in the presence of estradiol in a dose-dependent fashion. At 10(-5) M, resveratrol maximally inhibited the growth stimulatory effect mediated by 10(-9) M estradiol without affecting cell viability. At the molecular level, resveratrol in a dose-dependent fashion antagonized the stimulation by estradiol of an estrogen response element reporter gene construct and of progesterone receptor gene expression in MCF-7 cells. Resveratrol also inhibited the proliferation of the estrogen-receptor negative human breast carcinoma cell line MDA-MB-468. These later data suggest that resveratrol can also inhibit breast cancer cell proliferation by another mechanism besides estrogen receptor antagonism. We show here that resveratrol altered the expression of several autocrine growth modulators and their receptors in MCF-7 cells. Resveratrol at 10(-5) M inhibited the expression of the autocrine growth stimulators transforming growth factor-alpha (TGF-alpha), PC cell-derived growth factor, and insulin-like growth factor I receptor mRNA. In addition, resveratrol significantly elevated the expression of the growth inhibitor TGF-beta2 mRNA without changes in TGF-beta1 and TGF-beta3 expression. These data suggest that resveratrol inhibits proliferation by altering autocrine growth modulator pathways in breast cancer cells.
An extended Kalman filter (EKF) approach on fuzzy system optimization problem (2004)

Optimizing the membership functions of a fuzzy system can be viewed as a system identification problem for a nonlinear dynamic system. Basically, we can view the optimization of fuzzy membership functions as a weighted least-squares minimization problem, where the error vector is the difference between the fuzzy system outputs and the target values for those outputs. The extended Kalman filter algorithm is a good choice to solve this system identification problem, not only because it is a derivative-based algorithm that is suitable to solve the weighted least-squares minimization problem, but also because of its appealing predictor-corrector feature for nonlinear system model. In this paper, we present an extended Kalman filter approach to optimize the membership functions of the inputs and outputs of the fuzzy controller. The effect of the measurement noise covariance R on the convergence of the fuzzy controller is also investigated. Experimental results show that the optimized fuzzy controller achieves significant improvement on performance. In addition, the smaller the measurement noise covariance R is, the faster the optimized fuzzy controller would converge.
Enhancing Autophagy with Drugs or Lung-directed Gene Therapy Reverses the Pathological Effects of Respiratory Epithelial Cell Proteinopathy (2015)

Recent studies have shown that autophagy mitigates the pathological effects of proteinopathies in the liver, heart, and skeletal muscle but this has not been investigated for proteinopathies that affect the lung. This may be due at least in part to the lack of an animal model robust enough for spontaneous pathological effects from proteinopathies even though several rare proteinopathies, surfactant protein A and C deficiencies, cause severe pulmonary fibrosis. In this report we show that the PiZ mouse, transgenic for the common misfolded variant α1-antitrypsin Z, is a model of respiratory epithelial cell proteinopathy with spontaneous pulmonary fibrosis. Intracellular accumulation of misfolded α1-antitrypsin Z in respiratory epithelial cells of the PiZ model resulted in activation of autophagy, leukocyte infiltration, and spontaneous pulmonary fibrosis severe enough to elicit functional restrictive deficits. Treatment with autophagy enhancer drugs or lung-directed gene transfer of TFEB, a master transcriptional activator of the autophagolysosomal system, reversed these proteotoxic consequences. We conclude that this mouse is an excellent model of respiratory epithelial proteinopathy with spontaneous pulmonary fibrosis and that autophagy is an important endogenous proteostasis mechanism and an attractive target for therapy.
Improvement in Laser Weld Metal Toughness of Low C steel by Refining Microstructure (2009)

This paper deals with the improvement of weld metal toughness by formation of fully acicular ferrite microstructure in laser welding. The addition of 5-20% oxygen into the He shielding gas for laser welding of Ti added base plate formed Ti containing oxide inclusions in weld metal, which acted as the efficient nucleation sites of acicular ferrite. Although coarse grain boundary ferrite was formed along prior austenite grain boundaries, B addition effectively suppressed the formation of grain boundary ferrite. It was shown that the microstructure of laser weld metal was consisted of fully acicular ferrite when Al/O ratio was less than 1.13 and B content was more than 1/2.22(O-0.89Al-0.33Ti). The laser weld metal of fully acicular ferrite exhibited excellent toughness (vTrs<-100°C).
Exosome Production in C2C12 Myoblasts Improves Proliferation and Myogenic Differentiation following Exercise (2020)

Introduction: Mesenchymal stem cells (MSCs) influence tissue regeneration and healing primarily through paracrine secretion of proregenerative factors. Many of these factors are contained within exosomes suggesting that exosome suspensions may be an effective cell-free therapy for tissue regeneration and repair. We have previously shown that mechanical strain (exercise) rescues the myogenic potential of muscle derived stem cells from an aged mouse model (progeria mice). We hypothesized that in vitro “exercise” can improve the regenerative potential of exosomes derived from myoblastic precursors.
HIGH THROUGHPUT ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY - MASS SPECTROMETRIC METHOD FOR DETERMINATION OF ADRENALINE AND CHARACTERIZATION OF ITS STRESS DEGRADATION PRODUCTS: A MECHANISTIC APPROACH (2018)

UPLC-MS analytical procedure has been established for the determination of adrenaline in marketed formulation and in the pure form. The detection of the adrenaline was executed considering positive electrospray ionization (ESI) and selected ion reaction (SIR) modes. Chromatographic separation was achieved using ACQUITY UPLC BEH C 18 column (100 mm 2.1 mm, 1.7 m particles size) using a binary mobile phase mixture of methanol and water (50:50). The mobile phase was set to flow at the rate of 0.3 ml min -1 . The run time time for adrenaline was as short as 1.5 minutes. Linearity was found to be over the concentration range of 1g ml -1 -6g ml -1 . An excellent recovery of 100.18 % -100.68 % was achieved using this procedure. The standard deviation ranged from 0.014 -0.118 in intra-day studies and 0.016 -0.096 in case of inter-day studies. The procedure's quantitation limit was 0.76g ml -1 and detection limit was 0.25 g ml -1 . The method was successfully applied to determine adrenaline in drug formulations. In order to get the information about the stability of adrenaline in various environments forced degradation studies were conducted and the characterization of the stressed samples were performed using mass spectrometry.
Numerical studies for Hall Effect Imaging using linear phased array transducer (2014)

Hall Effect Imaging (HEI) is a method used to image conductivity distribution of a biological body. HEI benefits from the interaction of ultrasound with a static magnetic field to generate velocity current density distribution inside the body. Due to the velocity current density, a resultant voltage is sensed by electrodes attached on surface of the body and used for reconstructing the conductivity distribution. In this study, the feasibility of HEI technique using linear phased array transducer is investigated by numerical studies. A model of 16-element linear phased array transducer is used to benefit from electronic properties of directivity and steerability of linear phased array transducer. In addition, a numerical model of breast and tumor medium is formed to analyze the multiphysics solution which couples acoustics and electromagnetic fields. For image reconstruction, Truncated Singular Value Decomposition method is used with different signal-to-noise ratio values.
Effect of a New Probiotic Saccharomyces cerevisiae Strain on Survival of Escherichia coli O157:H7 in a Dynamic Gastrointestinal Model (2010)

Survival of Escherichia coli O157:H7 was investigated using a dynamic gastrointestinal model. A high bacterial mortality was observed in the stomach and duodenum. In contrast, bacteria grew in the distal parts of the small intestine. The coadministration of Saccharomyces cerevisiae CNCM I-3856 led to a significant reduction of bacterial resumption, maybe through ethanol production.
Polymerization of Lactide Using Achiral Bis(pyrrolidene) Schiff Base Aluminum Complexes (2009)

A series of aluminum ethyls and isopropoxides based on a bis(pyrrolidene) Schiff base ligand framework has been prepared and characterized. NMR studies of the dissolved complexes indicate that they adopt a symmetric structure with a monomeric, five-coordinated aluminum center core. The aluminum ethyls used as catalysts in the presence of 2-propanol as initiator and the aluminum isopropoxides were applied for lactide polymerization in toluene to test their activities and stereoselectivities. All polymerizations are living, as evidenced by the narrow polydispersities and the good fit between calculated and found number-average molecular weights of the isolated polymers. All of these aluminum complexes polymerized (S,S)-lactide to highly isotactic PLA without epimerization of the monomer, furnished isotactic-biased polymer from rac-lactide, and gave atactic polymer from meso-lactide. The study of kinetics indicated that the activity of the bis(pyrrolidene) Schiff base aluminum initiator systems toward lactide polymerization decreases in the following order: (S,S)-lactide > rac-lactide > meso-lactide. The methyl substituents on the diimine bridge or on the pyrrole rings both exert significant influence on the course of the polymerizations, affecting both the stereoselectivity and the polymerization rate. Kinetics using [L2AlEt]/2-propanol (2a/2-propanol) and [L2AlOiPr] (2b) indicated that the polymerizations are both first-order with respect to rac-lactide monomer and catalyst. The higher polymerization rate constant (kp) values for [L2AlOiPr] (2b) compared with those of [L2AlEt]/2-propanol (2a/2-propanol) revealed that in this case the overall polymerization rate was influenced by the relatively slow in situ alcoholysis reaction of aluminum ethyls. Polymerization experiments with [L2AlOiPr] (2b) revealed that with this complex much faster (kp = 13.0 L·mol−1·min−1) lactide polymerizations can be achieved compared with other aluminum complexes.
Simultaneous observation of cavitation bubbles generated in biological tissue by high-speed optical and acoustic imaging methods (2017)

Acoustic cavitation bubbles are useful for enhancing the heating effect in high-intensity focused ultrasound (HIFU) treatment. Many studies were conducted to investigate the behavior of such bubbles in tissue-mimicking materials, such as a transparent gel phantom; however, the detailed behavior in tissue was still unclear owing to the difficulty in optical observation. In this study, a new biological phantom was developed to observe cavitation bubbles generated in an optically shallow area of tissue. Two imaging methods, high-speed photography using light scattering and high-speed ultrasonic imaging, were used for detecting the behavior of the bubbles simultaneously. The results agreed well with each other for the area of bubble formation and the temporal change in the region of bubbles, suggesting that both methods are useful for visualizing the bubbles.
Multiuser MIMO Wideband Joint Communications and Sensing System With Subcarrier Allocation (2023)

In wideband joint communications and sensing (JCAS) systems, the waveforms are often designed and optimized over the entire bandwidth. This significantly limits the degrees of freedom in beamforming and causes severe communications performance loss, especially under a strict radar sensing constraint. In this work, we consider a downlink of a wideband multiuser (MU) multiple-input multiple-output (MIMO) system. We propose a subcarrier allocation strategy incorporated in an efficient JCAS design to improve the communications–sensing performance tradeoff of the system. The main idea is to employ a subset of subcarriers for radar sensing while enabling communications over the entire bandwidth. This creates dedicated subcarriers for communications without any interference from the radar function, whose sensing accuracy can still be guaranteed through strict design constraints. To realize the idea, we formulate the sum rate maximization problem and propose a three-step solution based on successive convex approximation and Riemannian manifold optimization. We further propose efficient initialization methods to reduce complexity and improve the convergence of the employed optimization schemes. Our simulation results for a 32 × 4 MU-MIMO system show that the proposed scheme offers 70% improvement in the system sum rate while guaranteeing the same radar beampattern mean square error and requiring less radio frequency chains compared with the conventional JCAS design over the entire bandwidth.
Real time inverse filter focusing through iterative time reversal (2004)

In order to achieve an optimal focusing through heterogeneous media we need to build the inverse filter of the propagation operator. Time reversal is an easy and robust way to achieve such an inverse filter in nondissipative media. However, as soon as losses appear in the medium, time reversal is not equivalent to the inverse filter anymore. Consequently, it does not produce the optimal focusing and beam degradations may appear. In such cases, we showed in previous works that the optimal focusing can be recovered by using the so-called spatiotemporal inverse filter technique. This process requires the presence of a complete set of receivers inside the medium. It allows one to reach the optimal focusing even in extreme situations such as ultrasonic focusing through human skull or audible sound focusing in strongly reverberant rooms. But, this technique is time consuming and implied fastidious numerical calculations. In this paper we propose a new way to process this inverse filter focusing technique in real time and without any calculation. The new process is based on iterative time reversal process. Contrary to the classical inverse filter technique, this iteration does not require any computation and achieves the inverse filter in an experimental way using wave propagation instead of computational power. The convergence from time reversal to inverse filter during the iterative process is theoretically explained. Finally, the feasibility of this iterative technique is experimentally demonstrated for ultrasound applications.