gebhart/patrepeval huggingface dataset:
Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability ofSaccharomyces cerevisiaeS288C Strains (2009)

The mitochondrial genome (mtDNA) is required for normal cellular function; inherited and somatic mutations in mtDNA lead to a variety of diseases. Saccharomyces cerevisiae has served as a model to study mtDNA integrity, in part because it can survive without mtDNA. A measure of defective mtDNA in S. cerevisiae is the formation of petite colonies. The frequency at which spontaneous petite colonies arise varies by approximately 100-fold between laboratory and natural isolate strains. To determine the genetic basis of this difference, we applied quantitative trait locus (QTL) mapping to two strains at the opposite extremes of the phenotypic spectrum: the widely studied laboratory strain S288C and the vineyard isolate RM11-1a. Four main genetic determinants explained the phenotypic difference. Alleles of SAL1, CAT5, and MIP1 contributed to the high petite frequency of S288C and its derivatives by increasing the formation of petite colonies. By contrast, the S288C allele of MKT1 reduced the formation of petite colonies and compromised the growth of petite cells. The former three alleles were found in the EM93 strain, the founder that contributed approximately 88% of the S288C genome. Nearly all of the phenotypic difference between S288C and RM11-1a was reconstituted by introducing the common alleles of these four genes into the S288C background. In addition to the nuclear gene contribution, the source of the mtDNA influenced its stability. These results demonstrate that a few rare genetic variants with individually small effects can have a profound phenotypic effect in combination. Moreover, the polymorphisms identified in this study open new lines of investigation into mtDNA maintenance.
Role of Oxidative Stress in Calcific Aortic Valve Disease: From Bench to Bedside - The Role of a Stem Cell Niche (2013)

Role of Oxidative Stress in Calcific Aortic Valve Disease: From Bench to Bedside - The Role of a Stem Cell Niche
Coupled-Circuit Modeling of 3, 6, and 9-Phase Induction Machine Drive Systems (2006)

This paper describes a coupled-circuit physical-variable modeling of multiphase induction motors. The presented modeling interface makes it straightforward to implement an induction machine with arbitrary number of phases and/or phase groups on the stator and the rotor. The 3-, 6-, and 9-phase motors are simulated and compared. It is shown that machines with higher number of phases have less severe torque pulsation and the stator current increase following a loss of one phase. For the 9-phase machine, several studies involving loss of multiple phases are also presented, wherein the relative location of the faulted phases is shown to have a significant impact on redistribution of currents and resulting electromagnetic torque. The proposed models can be used to represent induction motors and generators for transient studies involving multiple faults, system-level reconfiguration, and survivability.
Lower Urinary Tract Symptoms in Prostate Cancer Patients Treated With Radiation Therapy: Past and Present (2021)

The incidence of prostate cancer (PCa) is increasing concomitantly with population aging. Accordingly, interest in radiation therapy (RT) and the frequency of RT are also increasing. The types of RT can be broadly divided into external beam RT (EBRT), brachytherapy (BT), and combination therapy (EBRT+BT). Lower urinary tract symptoms (LUTS) after RT for the treatment of PCa are common; however, there are few reviews on the relationship between RT and LUTS. Herein, we review the causes and incidence of LUTS, as well as the evaluation and treatment options. Because of the reported risks of RT, patients undergoing RT should be counseled regarding the challenges of treatment and informed that they may have higher failure rates than nonirradiated patients. Moreover, thorough evaluation and treatment strategies are needed to support treatment recommendations. With a review of the existing literature, this narrative article provides an overview to aid urologists in treating patients presenting with complications associated with RT for the treatment of PCa. Further research is required to provide evidence of the effectiveness and feasibility of the management approach to the care of patients with LUTS after RT for the treatment of PCa.
A Modal-Based Real-Time Piano Synthesizer (2010)

This paper presents a real-time piano synthesizer where both the transverse and longitudinal motion of the string is modeled by modal synthesis, resulting in a coherent and highly parallel model structure. The paper applies recent developments in piano modeling and focuses on the issues related to practical implementation (e.g., numerical stability, aliasing, and efficiency). A strong emphasis is given to modeling nonlinear string vibrations, and a new variation of earlier synthesis techniques is proposed which is particularly well suited for modal synthesis. For soundboard modeling, the possibilities of using fast Fourier transform-based fast convolution and parallel second-order filters are discussed. Additionally, the paper describes the details of the software implementation and discusses the computational complexity of each model block. The piano model runs on current computer hardware with full polyphony in real time.
Light-induced reversible conductivity changes in silicon-on-insulator nanowires (2004)

Silicon-on-insulator (SOI) samples are preferred for extention of the metal-oxide-silicon technology. Here, we report a reversible change in electrical conductivity in dark conditions of a 20-nm-thick SOI layer, induced by illumination. In spite of some similarities with the Staebler–Wronski effect in hydrogenated amorphous silicon, we point out important differences such as the crystalline nature of our silicon film, the lack of hydrogen and a much shorter relaxation time at ambient temperature. This time can even be reduced by application of a vertical electric field. We suggest that interface traps play a major role in this mechanism. Finally, we noticed a conductivity change between ambient light and dark conditions.
3PT207 Acute Modulation of Synaptic Plasticity of Pyramidal Neurons by Activin in Adult Hippocampus(The 50th Annual Meeting of the Biophysical Society of Japan) (2012)

TheBiophysicalSociety of Japan General IncorporatedAssociation examined whetherthe inositol 1.4,5-trisphosphate (IP3)-induced Ca2' release {IICR) is involved in the regutation ofthe synaptic clustering of GABAARs.In hippocampa] neurons from mice ]acking intraeellular Ca!' releasing channel IP3 receptor type 1 (IPiR1), clusters of GABAAR and those of its scaffbtd protein gephyrin were significantly srna]ler than in wild type neurons, In wild type neurons, the inhibition ofIICR by specific inhibitors resutted in the decrease in GABAAR and gephyrin cluster size, without reducing the amount of GABAAR on the cell surface, Single particle tracking with quantum dot (QD-SPT) revealed that the ]oss of tP3Rl and inhibition of ItCR enhanced the ]atera] difTlision of GABAARs.The incTease of GABAAR tatera] mobility resulting from the loss ofIICR was completely prevented by an inhibitor ofca]cineurin.Our resu]ts suggest that IP3tCa2' signaling contributes lo the stabilization of synaptic GABAA R clusters thTough the regulation of GABAA R laterat diffusion, possibly through phosphory]ation.
Гетерологическая экспрессия лимфотоксинов мыши в клетках Escherichia coli и получение антител к ним (1999)

В клетках Е. coli экспрессированы гены, кодирующие фрагменты полипептидных цепей лимфоток-синов (LT) мыши: укороченный с N-конца LTα и внеклеточный домен LTβ, с гепта- и гексагистиди-новыми эпитопами на N-конце соответственно. Очищенные металлохелатной хроматографией рекомбинантные белки использованы для получения поликлональных антител, специфически распознающих LT мыши.
Validity and reliability of the Assessment of Spondyloarthritis International Society Health Index in English‐speaking patients with axial spondyloarthritis in Singapore (2019)

This study supports the ASAS HI as a valid and reliable measure of health status for use in patients with axSpA in Singapore.
ChemInform Abstract: Metallomacrocycles: Supramolecular Chemistry with Hard and Soft Metal Cations in Action (1994)

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.
Metal–Organic‐Framework‐Derived Hollow N‐Doped Porous Carbon with Ultrahigh Concentrations of Single Zn Atoms for Efficient Carbon Dioxide Conversion (2018)

The development of efficient and low energy-consumption catalysts for CO<sub>2</sub> conversion is desired, yet remains a great challenge. Herein, a class of novel hollow porous carbons (HPC), featuring well dispersed dopants of nitrogen and single Zn atoms, have been fabricated, based on the templated growth of a hollow metal-organic framework precursor, followed by pyrolysis. The optimized HPC-800 achieves efficient catalytic CO<sub>2</sub> cycloaddition with epoxides, under light irradiation, at ambient temperature, by taking advantage of an ultrahigh loading of (11.3 wt %) single-atom Zn and uniform N active sites, high-efficiency photothermal conversion as well as the hierarchical pores in the carbon shell. As far as we know, this is the first report on the integration of the photothermal effect of carbon-based materials with single metal atoms for catalytic CO<sub>2</sub> fixation.
Supplementary Figures 1-5 from Src and Caveolin-1 Reciprocally Regulate Metastasis via a Common Downstream Signaling Pathway in Bladder Cancer (2023)

Supplementary Figures 1-5 from Src and Caveolin-1 Reciprocally Regulate Metastasis via a Common Downstream Signaling Pathway in Bladder Cancer
VAscular Lesions DetectiOn (2020)

This is the challenge design document for the "VAscular Lesions DetectiOn" Challenge, accepted for MICCAI 2021. Appropriate blood supply is essential to the healthy maintenance of brain tissue. With age, vascular changes are observed in the smallest vessels resulting in impaired function. Changes to the surrounding tissue can be observed using magnetic resonance imaging. White matter hyperintensities are one such prominent marker of cerebral small vessel disease and their automated segmentation has been the focus of a large body of research as well as of segmentation challenges. Other markers of CSVD exist and their quantification along with WMH is essential to grasp the overall picture of the vascular burden related to CSVD. They include notably lacunes, enlarged perivascular spaces and cerebral microbleeds. Manual annotations are extremely time-consuming and suffer greatly from inter- and intra-rater variability, due to their small size and the difficulty of distinguishing these markers from each other and similarly appearing structures as well as the lack of a way to uncover the "real" ground truth. However, many studies have hinted at their potential to become essential biomarkers. Automated methods are therefore required to make their quantification not only robust and reliable, but simply feasible. So far development of such methods has been impeded by the methodological issues related to their very small size and the sparsity in the data but also the absence of sufficient gold standard/and or evaluation of the labeling noise. This challenge aims at promoting the development of new solutions for the automated detection, differentiation and segmentation of such very sparse and small objects while leveraging the presence of weak and noisy labels. The challenge will have a technical impact in the following fields: use of weak labels, assessment of prediction uncertainty, object detection, class imbalance, multi-scale object detection. The biomedical impact will not only directly impact the field of cerebral small vessel disease research but also other brain pathologies such as multiple sclerosis where similar objects have recently been shown renewed interest. More broadly translation of developed techniques to other fields where sparse object detection is essential will be impacted (mammography, lung nodule detection...).
Composition and Oxidative Stability of a Structured Lipid from Amaranth Oil in a Milk‐Based Infant Formula (2009)

Amaranth oil can be enzymatically modified to match breast milk fat analog requirements. We have developed a structured lipid (SL) from amaranth oil that, in combination with milk fat, delivers recommended amounts of docosahexaenoic acid (DHA) with palmitic acid specifically esterified at the sn-2 position of the triacylglycerol (TAG) backbone. The aim of this study was to study the final fatty acid (FA) contribution and oxidation stability of an infant formula prepared using the structured lipid DCAO (DHA-containing customized amaranth oil). DCAO was included as complementary fat in a "prototype" infant formula, and prepared in parallel with a "control" infant formula under the same processing conditions. The same ingredients but different complementary fat sources were used. A blend of the most commonly used vegetable oils (palm olein, soybean, coconut, and high-oleic sunflower oils) for infant formula was used instead of DCAO in the "control" formula. Additionally, "prototype" and "control" infant formulas were compared to a "commercial" product in terms of FA composition. The oxidative stability index (OSI) of the extracted fats from "prototype,""control," and "commercial" infant formulas were evaluated and compared to the OSI of the substrate fat replacers used. DCAO was the least stable compared to other fat analogs. The use of commercial antioxidants in DCAO containing products should prevent oxidation and therefore increase their stability.
Crosstalk compensation for a rapid, higher-resolution impedance spectrum measurement (2012)

Crosstalk Compensation is an approach that enables rapid, higher-resolution impedance spectra measurements of energy storage devices. The input signal consists of a sum-of-sines excitation current that has a known frequency spread. The advantage of Crosstalk Compensation is that high resolution spectra can be acquired within one period of the lowest frequency while also including non-harmonic frequencies. The crosstalk interference at a given frequency can be pre-determined and assigned to an error matrix. The real and imaginary impedance can then be calculated based on the inverse of the error matrix and captured response. Analytical validation of Crosstalk Compensation was performed using a battery equivalent circuit model. Two different frequency ranges were simulated, and both indicated that a minimum step factor between frequencies should be 1.25 to reduce the error in compensating the captured response signal. For a frequency range of 1638.4–0.1 Hz, for example, a maximum of 45 frequencies should be included within the excitation signal to accurately acquire the impedance spectra at high resolution. A simplified derivation of Crosstalk Compensation and its corresponding analytical validation studies are discussed.
Odours and incontinence: What does the nose know? (2018)

The fear of producing malodours that can be detected by others is a daily cause of anxiety for millions of people with incontinence. For many, the risk-whether real or imagined-that leaked waste products will be detectable by odour is sufficiently concerning to result in limitations on many types of activities. However, worry about personal odours can sensitise our olfactory system and cause us to be more aware of odours that may otherwise not be perceptible. In addition, heightened olfactory attention can often lead to odour misattributions, such as when we erroneously identify our body as the source of an odour that may simply be present in the environment. Odours produced by our bodies (endogenous odours) do enjoy a greater access to emotional brain centers and are processed faster than general odours. Here we provide examples from both everyday life and laboratory studies to explain how and why the olfactory system is unique among our sensory systems and how this knowledge can provide insights to our concerns about smell and incontinence and inform the development of products and solutions for incontinence.
Characterization of DcsC, a PLP-independent racemase involved in the biosynthesis of d-cycloserine (2012)

The biosynthetic gene cluster responsible for the generation of the antibiotic D-cycloserine (DCS) has recently been disclosed. One of the putative enzymes described was DcsC, which showed a high degree of homology to diaminopimelate epimerase (DapF). Based on this homology, the activity of DcsC was presumed to be the racemization of O-ureido-L-serine, a proposed intermediate in DCS biosynthesis. Here we describe the cloning, overexpression and characterization of this enzyme. Using synthetic standards we show that DcsC is a racemase that operates on both O-ureido-L- and D-serine, and that it employs a two-base mechanism, with a thiolate-thiol pair in the active site. The activity of this enzyme was shown to be optimal at pH ~ 7.8, with a similar k(cat)/K(M) ratio in both the L→D direction and D→L direction. Activity was abolished with thiol-inactivating reagents such as iodoacetamide and Hg(2+) ions. Further evidence for a thiolate in the active site was obtained through the use of an epoxide-containing substrate analogue (6), which became covalently attached to the enzyme.
Direct excitation of xenon by ballistic electrons emitted from nanocrystalline‐silicon planar cathode and vacuum‐ultraviolet light emission (2010)

Abstract— To verify the possible use of energetic electrons for direct excitation of inert gas molecules, a nanocrystalline‐silicon (nc‐Si) planar ballistic emitter is operated in a high‐pressure xenon gas ambience. Under the pulse drive, vacuum‐ultraviolet (VUV) light emission is detected without any signs of discharge. The transient behavior of the VUV light emission properly corresponds to that of the nc‐Si emitter. In accordance with quantitative analyses of electron‐emission characteristics and the VUV output, the electron‐to‐photon conversion efficiency reaches 81% in the relatively efficient emitter case. The VUV output power is mainly determined from the number of electrons with energies compatible the with internal excitation of xenon. The emission spectrum observed at a pressure of 10 kPa shows peaks at 152 and 172 nm, which are thought to be originated from metastable Xe 2 * states. In contrast to the case of conventional impact ionization, no near‐infrared (NIR) peaks are seen in the spectrum. These results strongly suggest that the incidence of energetic electrons causes direct excitation of xenon molecules followed by radiative relaxation through intermediate states. The generated VUV light can be easily converted to visible light using a phosphor screen. As a discharge‐free VUV light emission, this phenomenon is potentially applicable to mercury‐free, high‐efficacy, and high‐stability flat‐panel light‐emitting device.
Column‐Profile Measurements Using Fiber‐Optic Spectroscopy (1988)

Abstract Fiber‐optic spectroscopy was used to measure the flow of a fluorescent dye in a column packed with glass beads. Optical fibers inserted between the packed beads served as light pipes to transmit excitation light to the measurement zone at their distal end and to return fluorescent emission to a spectrometer. In this way, the dye concentration at the point of measurement was monitored. Data are presented demonstrating that flow can be monitored at several points in the column by multiplexing more than one fiber into a single spectrometer. This technique provides a tool to make fundamental flow measurements that have to date been experimentally impossible.
Efficacy and safety of mitoxantrone in multiple sclerosis: a retrospective analysis of 105 patients (2005)

Background: Several controlled trials have shown mitoxantrone (MIX) to be effective in relapsing-remitting and secondary progressive multiple sclerosis (RRMS, SPMS). The MS therapy consensus group has recommended the use of MIX for treatment escalation in patients with progressive RRMS and SPMS refractory to immunomodulatory drugs. In clinical practice it is often difficult to decide which patients will be likely to benefit from initiating MIX therapy. Objective: To assess safety and efficacy of MIX in the Regensburg cohort of MS patients.
Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi (2018)

Trichothecenes are a family of terpenoid toxins produced by multiple genera of fungi, including plant and insect pathogens. Some trichothecenes produced by the fungus Fusarium are among the mycotoxins of greatest concern to food and feed safety because of their toxicity and frequent occurrence in cereal crops, and trichothecene production contributes to pathogenesis of some Fusarium species on plants. Collectively, fungi produce over 150 trichothecene analogs: i.e., molecules that share the same core structure but differ in patterns of substituents attached to the core structure. Here, we carried out genomic, phylogenetic, gene-function, and analytical chemistry studies of strains from nine fungal genera to identify genetic variation responsible for trichothecene structural diversity and to gain insight into evolutionary processes that have contributed to the variation. The results indicate that structural diversity has resulted from gain, loss, and functional changes of trichothecene biosynthetic (TRI) genes. The results also indicate that the presence of some substituents has arisen independently in different fungi by gain of different genes with the same function. Variation in TRI gene duplication and number of TRI loci was also observed among the fungi examined, but there was no evidence that such genetic differences have contributed to trichothecene structural variation. We also inferred ancestral states of the TRI cluster and trichothecene biosynthetic pathway, and proposed scenarios for changes in trichothecene structures during divergence of TRI cluster homologs. Together, our findings provide insight into evolutionary processes responsible for structural diversification of toxins produced by pathogenic fungi.