gebhart/patrepeval huggingface dataset:
Triple-optical autocorrelation for direct optical pulse-shape measurement (2002)

Triple optical autocorrelation of femtosecond optical pulses was realized simply with third-harmonic-generation technique. This optical technique provides complete knowledge of transient pulse intensity variation directly in time domain. Only analytic calculation is needed to obtain the pulse-shape from data without direction-of-time ambiguity. Combined with a spectral measurement and the Gerchberg–Saxton algorithm, except for pulses with complete temporal and spectral symmetry that will cause a twofold ambiguity, exact phase variation in time can also be retrieved through an iterative calculation with an O(n) complexity.
HIPPOCRATE: an intrinsically safe robot for medical applications (2002)

We have developed a robotic system to assist doctors when they are moving ultrasonic probes on the patient's skin while exerting a given effort. The probes are used to monitor arteries for cardiovascular disease prevention, namely to reconstruct the 3D profile of arteries. A preliminary feasibility study making use of an industrial robot has been made to validate the force control scheme. It has proven the interest of the robotized approach for such a medical application. In order to comply with safety constraints, a dedicated robotic system HIPPOCRATE has been designed. The paper describes the arm and the controller architectures, with emphasis on design strategies selected to meet safety requirements.
Rapid hepatic fate specification of adipose‐derived stem cells and their therapeutic potential for liver failure (2008)

Our data highlight the properties of ASC as having a special affinity for hepatocyte differentiation in vitro and liver regeneration in vivo. Thus, ASC may be a superior choice for the establishment of a therapy for injured liver.
Rabies virus glycoprotein pseudotyping of lentiviral vectors enables retrograde axonal transport and access to the nervous system after peripheral delivery (2001)

In this report it is demonstrated for the first time that rabies-G envelope of the rabies virus is sufficient to confer retrograde axonal transport to a heterologous virus/vector. After delivery of rabies-G pseudotyped equine infectious anaemia virus (EIAV) based vectors encoding a marker gene to the rat striatum, neurons in regions distal from but projecting to the injection site, such as the dopaminergic neurons of the substantia nigra pars compacta, become transduced. This retrograde transport to appropriate distal neurons was also demonstrated after delivery to substantia nigra, hippocampus and spinal cord and did not occur when vesicular stomatitis virus glycoprotein (VSV-G) pseudotyped vectors were delivered to these sites. In addition, peripheral administration of rabies-G pseudotyped vectors to the rat gastrocnemius muscle leads to gene transfer in motoneurons of lumbar spinal cord. In contrast the same vector pseudotyped with VSV-G transduced muscle cells surrounding the injection site, but did not result in expression in any cells in the spinal cord. Long-term expression was observed after gene transfer in the nervous system and a minimal immune response which, together with the possibility of non-invasive administration, greatly extends the utility of lentiviral vectors for gene therapy of human neurological disease.
MACC1 – a novel target for solid cancers (2013)

MACC1 has been identified as a prognostic biomarker in a variety of solid cancers. MACC1 correlated with tumor formation and progression, development of metastases and patient survival representing a decisive driver for tumorigenesis and metastasis. MACC1 was also demonstrated to be of predictive value for therapy response. MACC1 is a promising therapeutic target for anti-tumor and anti-metastatic intervention strategies of solid cancers. Its clinical utility, however, must be demonstrated in clinical trials.
Distributed Spectrum Sensing for Cognitive Radio Networks by Exploiting Sparsity (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A cooperative approach to the sensing task of wireless cognitive radio (CR) networks is introduced based on a basis expansion model of the power spectral density (PSD) map in space and frequency. Joint estimation of the model parameters enables identification of the (un)used frequency bands at arbitrary locations, and thus facilitates spatial frequency reuse. The novel scheme capitalizes on two forms of sparsity: the first one introduced by the narrow-band nature of transmit-PSDs relative to the broad swaths of usable spectrum; and the second one emerging from sparsely located active radios in the operational space. An estimator of the model coefficients is developed based on the Lasso algorithm to exploit these forms of sparsity and reveal the unknown positions of transmitting CRs. The resultant scheme can be implemented via distributed online iterations, which solve quadratic programs locally (one per radio), and are adaptive to changes in the system. Simulations corroborate that exploiting sparsity in CR sensing reduces spatial and frequency spectrum leakage by 15 dB relative to least-squares (LS) alternatives. </para>
Understanding Binding Affinity:  A Combined Isothermal Titration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin (2003)

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.
Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio (2008)

The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol(-1), i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80-85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10-15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol(-1), i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40-45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic Archaea accounted for 10% of the total microbial community.
Oxidants, Antioxidants, and Free Radicals (2017)

Redox, radicals and antioxidants analysis of free radicals their products and antioxidants vitamin E - vitamin E and polyunsturated fats antioxidants and pro-oxidant relationship alpha-tocopheral, beta- Carotene and oxidative modification of human, low-density lipoprotein response of antioxidant system to physical and chemical stress zinc as a cardioprotective antioxidant ascorbic acid, melatonin and the adrenal gland - a commentary antioxidant properties of Glutathione and its role in tissue protection antioxidant effects of hypotaurine and taurine antioxidative activity of ergothionine and ovothiol the toxicology of antioxidants toxicity of oxygen and ozone peroxidation of lipids and liver damage role of free radicals in alcohol-induced tissue injury oxidant injury from inhaled particle matter edmagenic gases cause lung toxicity by generating reactive intermediates species RIS lipid peroxidation and antioxidant depletion induced by blast overpressure food antioxidants - their dual role in carcinogenesis anticarcinogenic effects of synthetic phenolic antioxidants.
Clinical core of the Alzheimer's disease neuroimaging initiative: Progress and plans (2010)

The Clinical Core of the Alzheimer's Disease Neuroimaging Initiative (ADNI) has provided clinical, operational, and data management support to ADNI since its inception. This article reviews the activities and accomplishments of the core in support of ADNI aims. These include the enrollment and follow-up of more than 800 subjects in the three original cohorts: healthy controls, amnestic mild cognitive impairment (now referred to as late MCI, or LMCI), and mild Alzheimer's disease (AD) in the first phase of ADNI (ADNI 1), with baseline longitudinal, clinical, and cognitive assessments. These data, when combined with genetic, neuroimaging, and cerebrospinal fluid measures, have provided important insights into the neurobiology of the AD spectrum. Furthermore, these data have facilitated the development of novel clinical trial designs. ADNI has recently been extended with funding from an NIH Grand Opportunities (GO) award, and the new ADNI GO phase has been launched; this includes the enrollment of a new cohort, called early MCI, with milder episodic memory impairment than the LMCI group. An application for a further 5 years of ADNI funding (ADNI 2) was recently submitted. This funding would support ongoing follow-up of the original ADNI 1 and ADNI GO cohorts, as well as additional recruitment into all categories. The resulting data would provide valuable data on the earliest stages of AD, and support the development of interventions in these critically important populations.
Epidermal stem cells: markers, patterning and the control of stem cell fate (1998)

Within the epidermis, proliferation takes place in the basal layer of keratinocytes that are attached to an underlying basement membrane. Cells that leave the basal layer undergo terminal differentiation as they move towards the tissue surface. The basal layer contains two types of proliferative keratinocyte: stem cells, which have unlimited self-renewal capacity, and transit amplifying cells, those daughters of stem cells that are destined to withdraw from the cell cycle and terminally differentiate after a few rounds of division. Stem cells express higher levels of the beta 1-integrin family of extracellular matrix receptors than transit amplifying cells and this can be used to isolate each subpopulation of keratinocyte and to determine its location within the epidermis. Variation in the levels of E-cadherin, beta-catenin and plakoglobin within the basal layer suggests that stem cells may also differ from transit amplifying cells in intercellular adhesiveness. Stem cells have a patterned distribution within the epidermal basal layer and patterning is subject to autoregulation. Constitutive expression of the transcription factor c-Myc promotes terminal differentiation by driving keratinocytes from the stem cell compartment into the transit amplifying compartment.
Anticonvulsant effects of aerial parts of Passiflora incarnata extract in mice: involvement of benzodiazepine and opioid receptors (2007)

It seems that Pasipay could be useful for treatment absence seizure and these effects may be related to effect of it on GABAergic and opioid systems. More studies are needed in order to investigate its exact mechanism.
Immune Response of Healthy Women to 2 Different Group B Streptococcal Type V Capsular Polysaccharide–Protein Conjugate Vaccines (2004)

GBS type V conjugate vaccines are safe and immunogenic and would be appropriate for inclusion in a candidate multivalent GBS vaccine.
Molecular Mechanisms of Multiple Drug Resistance in Clinical Isolates of Mycobacterium tuberculosis (1995)

The molecular mechanisms of resistance to streptomycin, rifampin, and isoniazid in 53 Mycobacterium tuberculosis clinical isolates were examined. Twenty-five of 44 streptomycin-resistant strains had mutations in the rpsL gene and 5 of these had rrs gene perturbations. The region of the rpoB gene that is associated with resistance to rifampin was altered in 28 of 29 rifampin-resistant strains. Mutations in known genetic markers of isoniazid resistance were detected in 25 of 42 isoniazid-resistant isolates: 20 strains had katG gene alterations and 5 had perturbations in the inhA operon. Of the 20 multiply resistant strains with reduced sensitivity to streptomycin, rifampin, and isoniazid, 11 had mutations in genetic markers associated with resistance to each of these three drugs. These studies suggest that the primary mechanism of multiple drug resistance in tuberculosis is the accumulation of mutations in individual drug target genes.
Yield effects on bale density and time required for commercial harvesting and baling of switchgrass (1996)

The objective of this study was to obtain mowing, raking and baling data for switchgrass yields to determine whether economic projections for harvesting and baling are valid for switchgrass as an energy crop. The study demonstrated that data for haymaking cannot be extrapolated to switchgrass.
Autonomous multi-floor indoor navigation with a computationally constrained MAV (2011)

In this paper, we consider the problem of autonomous navigation with a micro aerial vehicle (MAV) in indoor environments. In particular, we are interested in autonomous navigation in buildings with multiple floors. To ensure that the robot is fully autonomous, we require all computation to occur on the robot without need for external infrastructure, communication, or human interaction beyond high-level commands. Therefore, we pursue a system design and methodology that enables autonomous navigation with real time performance on a mobile processor using only onboard sensors. Specifically, we address multi-floor mapping with loop closure, localization, planning, and autonomous control, including adaptation to aerodynamic effects during traversal through spaces with low vertical clearance or strong external disturbances. We present experimental results with ground truth comparisons and performance analysis.
Transient accumulation of human mature thymocytes and regulatory T cells with CD28 superagonist in “human immune system” Rag2-/-γc-/- mice (2006)

Efficient and quick reconstitution of T-cell compartments in lymphopenic patients is of great importance to prevent opportunistic infections, but remains difficult to achieve. Human T-cell proliferation in a T-cell-receptor (TCR)-independent manner is possible in vitro with superagonist anti-CD28 antibodies, and such molecules are therefore promising therapeutic tools. Here, we investigated the in vivo effects of superagonist anti-CD28 treatment on human developing and mature T cells, in the recently developed model of "human immune system" BALB/c Rag2(-/-)gammac(-/-) mice. Our results show that superagonist anti-CD28 treatment transiently induces a 7-fold increase in thymocyte numbers and up to 18-fold accumulation of mature thymocytes. The increased thymic production lead to transient accumulation of mature T cells in the periphery at the peak of treatment effect (day 6). In addition, long-term peripheral T-cell depletion was induced. Furthermore, the concomitant selective expansion and accumulation of suppressive CD4+CD25+FoxP3+ T cells was induced in a transient manner. Superagonist anti-CD28 therapy could therefore be of clinical interest in humans, both for beneficial effect on thymic T-cell production as well as regulatory T-cell accumulation.
A developmental pathway involving four phenotypically and functionally distinct subsets of CD3-CD4-CD8- triple-negative adult mouse thymocytes defined by CD44 and CD25 expression (1993)

We have subdivided mouse CD4-CD8-CD3- triple-negative (TN) thymocytes into four subsets based upon expression of CD44 and CD25, including CD44+CD25-, CD44+CD25+, CD44-CD25+ and CD44-CD25-. Characterization of these cells revealed several features distinct to each subset, in particular the expression of high levels of c-kit (the receptor for stem cell factor) by CD44+CD25-TN and CD44+CD25+TN but not by CD44-CD25+TN and CD44-CD25-TN. The CD44+CD25+TN subset also included the IL-7 and stem cell factor-responsive cells, whereas only minimal responsiveness was observed by the CD44- populations. These subsets also showed differential cytokine production potential (CD44+CD25- > CD44+CD25+ > CD44-CD25+ > CD44-CD25-) after stimulation with calcium ionophore, PMA and IL-1. The repopulation potential of these subsets in 2-deoxyguanosine-treated fetal thymic lobes supports the following maturation sequence: CD44+CD25- -->CD44+CD25+ -->CD44-CD25+ -->CD44-CD25-. Furthermore, the sequence of progression from CD44+CD25+ to CD44-CD25+ cells was confirmed by their TCR beta-chain gene configuration. The former population exhibits germ-line TCR beta-chain configuration, whereas the latter subset shows a rearranged pattern.
An Emerging Adeno-Associated Viral Vector Pipeline for Cardiac Gene Therapy (2013)

The naturally occurring adeno-associated virus (AAV) isolates display diverse tissue tropisms in different hosts. Robust cardiac transduction in particular has been reported for certain AAV strains. Successful applications of these AAV strains in preclinical and clinical settings with a focus on treating cardiovascular disease continue to be reported. At the same time, these studies have highlighted challenges such as cross-species variability in AAV tropism, transduction efficiency, and immunity. Continued progress in our understanding of AAV capsid structure and biology has provided the rationale for designing improved vectors that can possibly address these concerns. The current report provides an overview of cardiotropic AAV, existing gaps in our knowledge, and newly engineered AAV strains that are viable candidates for the cardiac gene therapy clinic.
Temperature-insensitive UV-induced Bragg gratingsin silica-based planar lightwavecircuits on Si (1999)

A novel technique is proposed to realise temperature-insensitive Bragg gratings in silica-based lightwave circuits on Si using a bimetal plate. A wavelength shift &lt; 0.15 nm is successfully demonstrated between –40 and 80°C in the Bragg gratings written in a Mach-Zehnder interferometer.
Calcitonin precursors are reliable markers of sepsis in a medical intensive care unit (2000)

In a medical ICU, serum calcitonin precursor concentrations are more sensitive and are specific markers of sepsis as compared with serum C-reactive protein, interleukin-6, and lactate levels.
A comparison of peptide and folate receptor targeting of cancer cells: from single agent to nanoparticle (2011)

Chemical conjugation to peptides reduces colloidal stability, which is a limiting factor in the development of targeting nanoparticles. Mechanistic studies are needed in order to develop peptide targeting for nanoparticles to rival the selectivity that has been achieved with the small molecule folate. Although most of the work so far has been done using gold nanoparticles, biological and polymer nanoparticles are more colloidally stable and present enormous opportunities for coupling to peptides.
Thermostable aminopeptidase from Pyrococcus horikoshii (1999)

From the genome sequence data of the thermophilic archaeon Pyrococcus horikoshii, an open reading frame was found which encodes a protein (332 amino acids) homologous with an endoglucanase from Clostridium thermocellum (42% identity), deblocking aminopeptidase from Pyrococcus furiosus (42% identity) and an aminopeptidase from Aeromonas proteolytica (18% identity). This gene was cloned and expressed in Escherichia coli, and the characteristics of the expressed protein were examined. Although endoglucanase activity was not detected, this protein was found to have aminopeptidase activity to cleave the N-terminal amino acid from a variety of substrates including both N-blocked and non-blocked peptides. The enzyme was stable at 90 degrees C, with the optimum temperature over 90 degrees C. The metal ion bound to this enzyme was calcium, but it was not essential for the aminopeptidase activity. Instead, this enzyme required the cobalt ion for activity. This enzyme is expected to be useful for the removal of N(alpha)-acylated residues in short peptide sequence analysis at high temperatures.
The Natural Alliance Between Type I Interferon and Dendritic Cells and Its Role in Linking Innate and Adaptive Immunity (2002)

Dendritic cells (DCs) are the most potent antigen-presenting cells (APCs) and thus play a pivotal role in induction of the immune response. Recent studies in both human and mouse models have shown that type I IFN, cytokines originally characterized for their antiviral activity and exerting multiple biologic effects, efficiently promote the differentiation and activation of DCs. These observations, together with the findings that DCs can express biologically relevant levels of type I interferon (IFN) and, in particular, that high amounts of these cytokines are released by specialized DC precursors (i.e., plasmacytoid DCs) in response to viral infections, strongly suggest the existence of a natural alliance between type I IFN and DCs, which is instrumental in ensuring an efficient immune response to both infectious agents and tumors. Further recent knowledge on the interactions between type I IFN and DCs emphasizes the importance of these cytokines in linking innate and adaptive immunity and may lead to new perspectives in their use as vaccine adjuvants as well as in strategies for the development of DC-based vaccines.