gebhart/patrepeval huggingface dataset:
Characterization of the mitochondrial function and genetics in the pathogenesis of collagen VI related disorders (958.1) (2014)

Background: Alteration in the collagen VI protein causes Bethlem Myopathy and Ullrich Congenital Muscular Dystrophy. Mitochondrial dysfunction, ultrastructural defects, increased apoptosis and autophagy impairment are associated to muscle of young Col6a1‐/‐ mice and patients. Results: To clarify the pathophysiology of this disorder we are characterizing Col6a1‐/‐ mice at different ages. Preliminary studies show reduced cell growth, decreased respiratory capacity, increased ROS production and increased mitochondrial mass on myoblasts isolated from old Col6a1‐/‐ mice. Mutant cells show altered cytoskeleton structure that could explain why dysfunctional mitochondria accumulate and are not removed by autophagy. We are also determining if the progression of this myopathy is related to the accumulation of mtDNA mutations. Methods: We study: cell growth capacity, mitochondrial membrane potential and mass, oxygen consumption capacity, ROS production, mitochondrial dynamics and cytoskeleton structure in primary muscle cells; and skeletal muscle tissue properties with histological methods. To assess mtDNA mutations levels, we had developed a next generation sequencing protocol that avoids any PCR step in preparing the DNA prior to sequencing. This innovative approach is now being applied to various tissues, with particular reference to the diaphragm the most affected muscle.
ChemInform Abstract: Direct Acting, Highly Mutagenic, α‐Hydroxy N‐Nitrosamines from 4‐Chloroindoles. (1986)

Abstract The indole derivative (I), a constituent of fava beans, produces on nitrosation under simulated gastric conditions the oxime (II).
Regional assessment of in vivo myocardial stiffness using 3D magnetic resonance elastography in a porcine model of myocardial infarction (2017)

These results demonstrate the feasibility of assessing in vivo regional myocardial stiffness with high-frequency 3D cardiac MRE. Magn Reson Med 79:361-369, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Genetic Circuit Dynamics: Hazard and Glitch Analysis (2020)

Multiple input changes can cause unwanted switching variations, or <i>glitches</i>, in the output of genetic combinational circuits. These glitches can have drastic effects if the output of the circuit causes irreversible changes within or with other cells such as a cascade of responses, apoptosis, or the release of a pharmaceutical in an off-target tissue. Therefore, avoiding unwanted variation of a circuit's output can be crucial for the safe operation of a genetic circuit. This paper investigates what causes unwanted switching variations in combinational genetic circuits using hazard analysis and a new dynamic model generator. The analysis is done in previously built and modeled genetic circuits with known glitching behavior. The dynamic models generated not only predict the same steady states as previous models but can also predict the unwanted switching variations that have been observed experimentally. Multiple input changes may cause glitches due to propagation delays within the circuit. Modifying the circuit's layout to alter these delays may change the likelihood of certain glitches, but it cannot eliminate the possibility that the glitch may occur. In other words, function hazards cannot be eliminated. Instead, they must be avoided by restricting the allowed input changes to the system. Logic hazards, on the other hand, can be avoided using hazard-free logic synthesis. This paper demonstrates this by showing how a circuit designed using a popular genetic design automation tool can be redesigned to eliminate logic hazards.
Single exposure contacts are dead. Long live single exposure contacts! (2011)

The paper describes a process/design co-optimization effort based on an SRAM design to enable a single exposure contact process for the 28nm technology half node. As a start, a change to the wiring concept of the standard SRAM design was implemented. The resulting individual contact layer elements may seem even more resolution critical to the casual observer. But in reality, the flexibility for source-mask optimization had been significantly improved. In a second step, wafer targets and mask dimension options (using various kinds of OPC methods and SRAF strategies) were run through several optimization iterations. This included interlevel considerations due to stringent overlap requirements. Several promising SRAM design as well as mask options were identified and experimentally verified to finally converge to an optimum mask and wafer target layout. Said optimum solution still supports an automated OPC approach using standard EDA tools and off the shelf OPC strategies. In a last step, a 1Mbit electrically testable SRAM was designed and manufactured together with alternative SRAM designs and process options. After explaining the changes to the wiring of the SRAM design, the paper discusses in great detail various mask optimization solutions and their consequences on wafer target and printability. Simulation and experimental results are compared and the concluding optimized solution is explained. Furthermore, some key lithography and etch process elements that became the single exposure process enabler are explained in more detail. Finally, the paper will take a look at electrical results of the 1Mbit electrically testable SRAM as the ultimate proof of concept.
Intracranial Meningiomas in the Aged: Surgical Outcome in the Era of Computed Tomography (1989)

Seventy-five patients older than 60 years of age underwent surgical resection of intracranial meningiomas during a 10-year period at a single institution. All patients had a computed tomographic scan preoperatively, and all were followed for at least 3 months postoperatively. There were 50 patients 61 to 70 years of age (Group A), and 25 patients older than 70 years (Group B). Sixteen patients (21%) were asymptomatic, and no patient was severely disabled preoperatively. Operative morbidity and mortality and outcome at 3 months were assessed and correlated with age, preoperative neurological status, and tumor size and location. Operative mortality was 6.6% (6% in Group A; 8% in Group B). Perioperative morbidity (including medical and surgical complications and worsening in neurological status) was 48% (46% in Group A; 52% in Group B). Neurological status 3 months after surgery was improved by at least one grade as compared to before surgery in 40% of patients (38% in Group A; 44% in Group B), unchanged in 29% (34% in Group A; 20% in Group B), and worsened in 31% (28% in Group A; 36% in Group B). While nearly half of the patients were asymptomatic 3 months after surgery, 11 patients (15%) had died or remained seriously disabled. Outcome at 3 months correlated significantly with low neurological grade preoperatively and with a tumor location over the cortical convexity. There was no significant correlation with age or tumor size. We conclude that resection of intracranial meningiomas is associated with significant morbidity and mortality in the elderly.(ABSTRACT TRUNCATED AT 250 WORDS)
ChemInform Abstract: Synthesis of Casein‐Related Peptides and Phosphopeptides. Part 7. The Efficient Synthesis of Ser(P)‐Containing Peptides by the Use of Boc‐ Ser(PO3R2)‐OH Derivatives (1991)

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.
The MRI Eigencoil: 2N-Channel SNR with N-Receivers (2003)

= ss which is just a SoS operation in the new basis. Due to some basic symmetry existing between the n-elements of an array and therefore N, there may be some degeneracy between the eigenmodes. The number of degenerate eigenmodes (d) means the n-element phased array has degree m = n - d < n. Degenerate eigenmodes can be linearly mixed (preserving there eigenvalue) to produce new eigenmodes with most of the SNR concentrated in one of the two modes, leaving almost all the SNR contained in m-channels. This, of course, is the principle of Quad/Antiquad pairs now extended to higher degrees. Images were collected on a Siemens 1.5T Symphony 8 channel scanner using the Siemens 8-Channel Head Array (3), with elements equally separated by π/4 around the head. The Eigencoil TM was formed by inserting an m-degree K' -1 hardware combiner inline between the output of the Head Array and the system interface.
Accelerating-particle-deposition method for quickly evaluating long-term performance of fin-and-tube heat exchangers. (2018)

Fin-and-tube heat exchanger is the most commonly used heat exchanger type in air-conditioning systems. In the actual operation of air-conditioning systems, the dust particles involved in the air may partly deposit and form particulate fouling on fins and tubes when the dusty air flows through the heat exchangers. The deposited particles may gradually block the passageway of air flow and occupy the heat transfer area, which results in the continuous increase of air side thermal resistance and the significant deterioration of the heat transfer capacity of heat exchangers during the long-term operation. In order to quickly evaluate the long-term performance of fin-and-tube heat exchangers, an accelerating-particle-deposition method, which is capable of implementing the particle deposition process on the long-running heat exchangers in a short time, is proposed in this study. The idea of the accelerating-particle-deposition method is to employ high concentration dusty air flow through heat exchangers in the accelerated test, and to quickly form the particulate fouling with the same weight as that on long-running heat exchangers under the actual operating environment with low particle concentration. The accelerating factor, which is defined as the ratio of the actual running time to the accelerated testing time, is calculated based on the deposition weight of dust particles. The deposition weight is calculated by the relationship of the impact frequency and deposition probability of dust particles with the particle concentration of dusty air. An experimental apparatus for accelerating the particle deposition process and testing the heat transfer capacity of fin-and-tube heat exchangers is designed. The predicted long-term performances of heat exchangers based on the proposed accelerating-particle-deposition method are compared with the actual performance data of heat exchangers after 5-8 years’ operation published by China Quality Certification Center. The comparison results show that, the predicted results agree well with the actual operation data, and the mean deviation of the heat transfer capacity is within 10%.
A novel role of sphingosine 1-phosphate receptor S1pr1 in mouse thrombopoiesis (2012)

Millions of platelets are produced each hour by bone marrow (BM) megakaryocytes (MKs). MKs extend transendothelial proplatelet (PP) extensions into BM sinusoids and shed new platelets into the blood. The mechanisms that control platelet generation remain incompletely understood. Using conditional mutants and intravital multiphoton microscopy, we show here that the lipid mediator sphingosine 1-phosphate (S1P) serves as a critical directional cue guiding the elongation of megakaryocytic PP extensions from the interstitium into BM sinusoids and triggering the subsequent shedding of PPs into the blood. Correspondingly, mice lacking the S1P receptor S1pr1 develop severe thrombocytopenia caused by both formation of aberrant extravascular PPs and defective intravascular PP shedding. In contrast, activation of S1pr1 signaling leads to the prompt release of new platelets into the circulating blood. Collectively, our findings uncover a novel function of the S1P-S1pr1 axis as master regulator of efficient thrombopoiesis and might raise new therapeutic options for patients with thrombocytopenia.
Comparison of pattern recognition methods for computer-assisted classification of spectra of heart sounds in patients with a porcine bioprosthetic valve implanted in the mitral position (1990)

The diagnostic performance of two pattern recognition methods (or classifiers) to detect valvular degeneration was evaluated in 48 patients with a porcine bioprosthetic heart valve inserted in the mitral position. Twenty patients had a normal porcine bioprosthetic valve and 28 patients had a degenerated bioprosthetic valve. One method was based on the Gaussian-Bayes model and the second on the "nearest neighbor" algorithm using three distance measurements. Eighteen diagnostic features were extracted from the sound spectrum of each patient and, for each method, a two-class supervised learning approach was used to determine the most discriminant diagnostic patterns composed of 6 features or less. The probability of error of the classifiers was estimated with the leave-one-out approach. The performance of each method to discriminate between normal and degenerated bioprosthetic valves was verified by clinical evaluation of the valves. The best performance in evaluation of the sound spectrum (98% correct classifications) was obtained with the Bayes classifier and two patterns of six features each. The percentage of false positive classifications of valve degeneration was 0% and the percentage of false negative classifications was 4%. Sensitivity for the detection of valve degeneration was 96%, specificity was 100%, positive predictive value was 100%, and negative predictive value was 95%. The best performance of the nearest neighbor method (94% correct classifications) was obtained by using the Mahalanobis distance and five patterns composed of three, four, five, or six diagnostic features. Using a pattern composed of only three features, the percentage of false positive classifications for degeneration was 10% and the percentage of false negative classifications was 4%.(ABSTRACT TRUNCATED AT 250 WORDS)
Transdermal Administration of Aqueous Pregabalin Solution as a Potential Treatment Option for Patients with Neuropathic Pain to Avoid Central Nervous System-Mediated Side Effects (2014)

Pregabalin, (S)-3-isobutyl-γ-aminobutyric acid (GABA), is a widely used adjuvant therapy for patients with neuropathic pain, which is defined as chronic pain caused by lesions or diseases of the somatosensory nervous system. However, dizziness and somnolence (sleepiness) are common dose-limiting side effects, probably due to excessive sedative effects on higher centers of the central nervous system (CNS) which are involved in the anticonvulsant and analgesic actions of pregabalin. We speculated that transdermal delivery would minimize centrally mediated side effects. To test this idea, we evaluated the analgesic effects of pregabalin delivered through the transdermal route in animal models of neuropathic pain. Transdermally administered pregabalin increased the pain thresholds in response to mechanical stimuli in a partial sciatic nerve ligation model in rats and a spinal nerve ligation model in mice, and surprisingly also in normal animals. It is noteworthy that simple transdermal application of an aqueous solution of pregabalin is effective. This could be a useful treatment option to avoid or minimize the CNS-mediated side effects of orally administered pregabalin.
Work Function Engineering of Molybdenum Gate Electrodes by Nitrogen Implantation (2001)

The continued scaling of complementary metal oxide semiconductor (CMOS) devices into the sub-70 nm regime will require a fundamental change in transistor gate stack materials. Refractory metals and their metallic derivatives are among the few materials other than poly-silicon suitable for use as metal oxide semiconductor field effect transistor gate electrodes. In this paper we report the dependence of the Mo gate work function on nitrogen implant dose and energy. By implanting nitrogen into stacks, the interfacial Mo work function can be controllably lowered from an initial (unimplanted) value of The ability to engineer the Mo gate work function over the range of the Si energy bandgap makes it an attractive candidate for future bulk-Si and ultrathin body silicon-on-insulator-CMOS gate electrodes. © 2001 The Electrochemical Society. All rights reserved.
ShadowReplica (2013)

Dynamic data flow tracking (DFT) is a technique broadly used in a variety of security applications that, unfortunately, exhibits poor performance, preventing its adoption in production systems. We present ShadowReplica, a new and efficient approach for accelerating DFT and other shadow memory-based analyses, by decoupling analysis from execution and utilizing spare CPU cores to run them in parallel. Our approach enables us to run a heavyweight technique, like dynamic taint analysis (DTA), twice as fast, while concurrently consuming fewer CPU cycles than when applying it in-line. DFT is run in parallel by a second shadow thread that is spawned for each application thread, and the two communicate using a shared data structure. We avoid the problems suffered by previous approaches, by introducing an off-line application analysis phase that utilizes both static and dynamic analysis methodologies to generate optimized code for decoupling execution and implementing DFT, while it also minimizes the amount of information that needs to be communicated between the two threads. Furthermore, we use a lock-free ring buffer structure and an N-way buffering scheme to efficiently exchange data between threads and maintain high cache-hit rates on multi-core CPUs. Our evaluation shows that ShadowReplica is on average ~2.3× faster than in-line DFT (~2.75× slowdown over native execution) when running the SPEC CPU2006 benchmark, while similar speed ups were observed with command-line utilities and popular server software. Astoundingly, ShadowReplica also reduces the CPU cycles used up to 30%.
Prediction of Passive Intermodulation From Coaxial Connectors in Microwave Networks (2008)

Coaxial connectors are frequently the dominant contributors to passive intermodulation (PIM) distortion in high-frequency networks. This paper reports on a circuit model enabling estimation of PIM distortion by coaxial connectors in the design of high-frequency networks. A method of modeling the effect of multiple point sources of PIM is applied to coaxial connectors, allowing the prediction of the PIM of networks with several connectors. Typical ranges of PIM produced by common connectors in a two-tone test are reported. The stability and repeatability of PIM produced by a single connector is examined. Nonlinear current-voltage curves for coaxial connectors are given that predict the PIM distortion output by coaxial connectors over a broad range of input powers. An experimental verification is given showing that PIM of a system can be predicted if the characteristics of the individual components are known.
Defective Innate Immunity and Hyperinflammation in Newborn Cystic Fibrosis Transmembrane Conductance Regulator–Knockout Ferret Lungs (2014)

Mucociliary clearance (MCC) and submucosal glands are major components of airway innate immunity that have impaired function in cystic fibrosis (CF). Although both of these defense systems develop postnatally in the ferret, the lungs of newborn ferrets remain sterile in the presence of a functioning cystic fibrosis transmembrane conductance regulator gene. We evaluated several components of airway innate immunity and inflammation in the early CF ferret lung. At birth, the rates of MCC did not differ between CF and non-CF animals, but the height of the airway surface liquid was significantly reduced in CF newborn ferrets. CF ferrets had impaired MCC after 7 days of age, despite normal rates of ciliogenesis. Only non-CF ferrets eradicated Pseudomonas directly introduced into the lung after birth, whereas both genotypes could eradicate Staphylococcus. CF bronchoalveolar lavage fluid (BALF) had significantly lower antimicrobial activity selectively against Pseudomonas than non-CF BALF, which was insensitive to changes in pH and bicarbonate. Liquid chromatography-tandem mass spectrometry and cytokine analysis of BALF from sterile Caesarean-sectioned and nonsterile naturally born animals demonstrated CF-associated disturbances in IL-8, TNF-α, and IL-β, and pathways that control immunity and inflammation, including the complement system, macrophage functions, mammalian target of rapamycin signaling, and eukaryotic initiation factor 2 signaling. Interestingly, during the birth transition, IL-8 was selectively induced in CF BALF, despite no genotypic difference in bacterial load shortly after birth. These results suggest that newborn CF ferrets have defects in both innate immunity and inflammatory signaling that may be important in the early onset and progression of lung disease in these animals.
Fabrication of SiC nanopillars by inductively coupled SF6/O2 plasma (2011)

International audience
Effect of nanocoating with rhamnogalacturonan‐I on surface properties and osteoblasts response (2011)

Long-term stability of titanium implants are dependent on a variety of factors. Nanocoating with organic molecules is one of the methods used to improve osseointegration. Therefore, the aim of this study is to evaluate the in vitro effect of nanocoating with pectic rhamnogalacturonan-I (RG-I) on surface properties and osteoblasts response. Three different RG-Is from apple and lupin pectins were modified and coated on amino-functionalized tissue culture polystyrene plates (aminated TCPS). Surface properties were evaluated by scanning electron microscopy, contact angle measurement, atomic force microscopy, and X-ray photoelectron spectroscopy. The effects of nanocoating on proliferation, matrix formation and mineralization, and expression of genes (real-time PCR) related to osteoblast differentiation and activity were tested using human osteoblast-like SaOS-2 cells. It was shown that RG-I coatings affected the surface properties. All three RG-I induced bone matrix formation and mineralization, which was also supported by the finding that gene expression levels of alkaline phosphatase, osteocalcin, and collagen type-1 were increased in cells cultured on the RG-I coated surface, indicating a more differentiated osteoblastic phenotype. This makes RG-I coating a promising and novel candidate for nanocoatings of implants.
Effect of Monomers on the Basal Spacing of Sodium Montmorillonite and the Structures of Polymer−Clay Nanocomposites (2004)

The basal spacings of sodium montmorillonite (MMT) dispersed in various solvents and monomers were measured via X-ray diffraction. Some liquids with strong hydrogen-bonding groups (δh) showed little suspended MMT, but liquids with moderate or poor hydrogen-bonding groups precipitated MMT completely, this indicates that δh is an important factor for the dispersion state of natural MMT in a liquid. The basal spacing expansion also depends on polar components (δp) and hydrogen-bonding components (δh) of organic liquids. Liquids with high δh values showed expansion in the order of methyl alcohol > ethyl alcohol > 2-propyl alcohol > n-hexane > toluene > benzene, and monomers with high δp values exhibited expansion in the order of n-butyl acrylate > acrylonitrile > methyl methacrylate > styrene. Because dipole−dipole interactions involved both δh and δp, liquid dipole moments were adopted to explain the expansion of MMT in polymer−MMT nanocomposites. Monomers with high dipole moments showed large basal spacings before polymerization and produced exfoliated polymer−MMT nanocomposites, whereas those with low dipole moments showed smaller basal spacings and produced intercalated polymer−MMT nanocomposites.