gebhart/patrepeval huggingface dataset:
Microbial Dynamics in Traditional and Modern Sour Beer Production (2020)

Traditional sour beers are produced by spontaneous fermentations involving numerous yeast and bacterial species. One of the traits that separates sour beers from ales and lagers is the high concentration of organic acids such as lactic acid and acetic acid, which results in reduced pH and increased acidic taste. Several challenges complicate the production of sour beers through traditional methods. These include poor process control, lack of consistency in product quality, and lengthy fermentation times. This review summarizes the methods for traditional sour beer production with a focus on the use of lactobacilli to generate this beverage. In addition, the review describes the use of selected pure cultures of microorganisms with desirable properties in conjunction with careful application of processing steps. Together, this facilitates the production of sour beer with a higher level of process control and more rapid fermentation compared to traditional methods.
Phosphatidylserine-mediated platelet clearance by endothelium decreases platelet aggregates and procoagulant activity in sepsis (2017)

The mechanisms that eliminate activated platelets in inflammation-induced disseminated intravascular coagulation (DIC) in micro-capillary circulation are poorly understood. This study explored an alternate pathway for platelet disposal mediated by endothelial cells (ECs) through phosphatidylserine (PS) and examined the effect of platelet clearance on procoagulant activity (PCA) in sepsis. Platelets in septic patients demonstrated increased levels of surface activation markers and apoptotic vesicle formation, and also formed aggregates with leukocytes. Activated platelets adhered were and ultimately digested by ECs in vivo and in vitro. Blocking PS on platelets or αvβ3 integrin on ECs attenuated platelet clearance resulting in increased platelet count in a mouse model of sepsis. Furthermore, platelet removal by ECs resulted in a corresponding decrease in platelet-leukocyte complex formation and markedly reduced generation of factor Xa and thrombin on platelets. Pretreatment with lactadherin significantly increased phagocytosis of platelets by approximately 2-fold, diminished PCA by 70%, prolonged coagulation time, and attenuated fibrin formation by 50%. Our results suggest that PS-mediated clearance of activated platelets by the endothelium results in an anti-inflammatory, anticoagulant, and antithrombotic effect that contribute to maintaining platelet homeostasis during acute inflammation. These results suggest a new therapeutic target for impeding the development of DIC.
Peroxynitrite Irreversibly Inactivates the Human Xenobioticmetabolizing Enzyme Arylamine N-Acetyltransferase 1 (NAT1) in Human Breast Cancer Cells (2004)

Arylamine N-acetyltransferases (NATs) play an important role in the detoxification and metabolic activation of a variety of aromatic xenobiotics, including numerous carcinogens. Both of the human isoforms, NAT1 and NAT2, display interindividual variations, and associations between NAT genotypes and cancer risk have been established. Contrary to NAT2, NAT1 has a ubiquitous tissue distribution and has been shown to be expressed in cancer cells. Given that the activity of NAT1 depends on a reactive cysteine that can be a target for oxidants, we studied whether peroxynitrite, a highly reactive nitrogen species involved in human carcinogenesis, could inhibit the activity of endogenous NAT1 in MCF7 breast cancer cells. We show here that exposure of MCF7 cells to physiological concentrations of peroxynitrite and to a peroxynitrite generator (3-morpholinosydnonimine N-ethylcarbamide, or SIN1) leads to the irreversible inactivation of NAT1 in cells. Further kinetic and mechanistic analyses using recombinant NAT1 showed that the enzyme is rapidly (k(inact) = 5 x 10(4) m(-1).s(-1)) and irreversibly inactivated by peroxynitrite. This inactivation is due to oxidative modification of the catalytic cysteine. We conclude that the reducing cellular environment of MCF7 cells does not sufficiently protect NAT1 from peroxynitrite-dependent inactivation and that only high concentrations of reduced glutathione could significantly protect NAT1. Thus, cellular generation of peroxynitrite may contribute to carcinogenesis and tumor progression by weakening key cellular defense enzymes such as NAT1.
Deep Contrast Learning for Salient Object Detection (2016)

Salient object detection has recently witnessed substantial progress due to powerful features extracted using deep convolutional neural networks (CNNs). However, existing CNN-based methods operate at the patch level instead of the pixel level. Resulting saliency maps are typically blurry, especially near the boundary of salient objects. Furthermore, image patches are treated as independent samples even when they are overlapping, giving rise to significant redundancy in computation and storage. In this paper, we propose an end-to-end deep contrast network to overcome the aforementioned limitations. Our deep network consists of two complementary components, a pixel-level fully convolutional stream and a segment-wise spatial pooling stream. The first stream directly produces a saliency map with pixel-level accuracy from an input image. The second stream extracts segment-wise features very efficiently, and better models saliency discontinuities along object boundaries. Finally, a fully connected CRF model can be optionally incorporated to improve spatial coherence and contour localization in the fused result from these two streams. Experimental results demonstrate that our deep model significantly improves the state of the art.
Optical coherence elastography: current status and future applications (2011)

Optical coherence tomography (OCT) has several advantages over other imaging modalities, such as angiography and ultrasound, due to its inherently high in vivo resolution, which allows for the identification of morphological tissue structures. Optical coherence elastography (OCE) benefits from the superior spatial resolution of OCT and has promising applications, including cancer diagnosis and the detailed characterization of arterial wall biomechanics, both of which are based on the elastic properties of the tissue under investigation. We present OCE principles based on techniques associated with static and dynamic tissue excitation, and their corresponding elastogram image-reconstruction algorithms are reviewed. OCE techniques, including the development of intravascular- or catheter-based OCE, are in their early stages of development but show great promise for surgical oncology or intravascular cardiology applications.
A Safety Analysis of the ITER Superconducting Magnet System in Case of Loss of Vacuum in the ITER Cryostat (1996)

One of the safety analysis for superconducting magnet system in International Thermonuclear Experimental Reactor (ITER) was carried out. The ITER cryostat will hold many superconducting magnets, such as twenty of toroidal field coils, a central solenoid coil, and seven poloidal coils. Loss of vacuum of the cryostat was considered as the worst assumption and the safety analysis of the magnets was examined when the assumption would be occurred. Accordingly, the loss of vacuum will cause the loss of thermal shield vacuum for the magnets and then a large heat transfer will be generated in the cryostat The magnet pressure and temperature will rise, bringing the magnets to quench. Such behavior was simulated by using a developed computer-aided calculation code. As a result of the calculation, a catastrophic phenomenon doesn't appear in the assumption. It is observed that a quasi-stable state, where the magnet temperature is kept to be less than 7 K, is maintained for more than 600 seconds. Thus, the magnet current can be slowly discharged like as the ordinal operation without magnet quench even in such worst assumption due to a large volume of the cryostat.
Quantum control via encoded dynamical decoupling (2002)

The ideas underlying dynamical decoupling methods are revisited within the framework of quantum-information processing, and their potential for direct implementations in terms of encoded rather than physical degrees of freedom is examined. The usefulness of encoded decoupling schemes as a tool for engineering both closed- and open-system encoded evolutions is investigated based on simple examples.
Introduction to Algebra (2003)

The search for good data-transmission codes has relied, to a large extent, on the powerful and beautiful structures of modern algebra. Many important codes, based on the mathematical structures known as Galois fields, have been discovered. Further, this algebraic framework provides the necessary tools with which to design encoders and decoders. This chapter and Chapter 4 are devoted to developing those topics in algebra that are significant to the theory of data-transmission codes. The treatment is rigorous, but it is limited to material that will be used in later chapters.
Biocontrol of Aspergillus Species on Peanut Kernels by Antifungal Diketopiperazine Producing Bacillus cereus Associated with Entomopathogenic Nematode (2014)

The rhabditid entomopathogenic nematode associated Bacillus cereus and the antifungal compounds produced by this bacterium were evaluated for their activity in reducing postharvest decay of peanut kernels caused by Aspergillus species in in vitro and in vivo tests. The results showed that B. cereus had a significant effect on biocontrol effectiveness in in vitro and in vivo conditions. The antifungal compounds produced by the B. cereus were purified using silica gel column chromatography and their structure was elucidated using extensive spectral analyses. The compounds were identified as diketopiperazines (DKPs) [cyclo-(L-Pro-Gly), cyclo(L-Tyr-L-Tyr), cyclo-(L-Phe-Gly) and cyclo(4-hydroxy-L-Pro-L-Trp)]. The antifungal activities of diketopiperazines were studied against five Aspergillus species and best MIC of 2 µg/ml was recorded against A. flavus by cyclo(4-hydroxy-L-Pro-L-Trp). To investigate the potential application of cyclo(4-hydroxy-L-Pro-L-Trp) to eliminate fungal spoilage in food and feed, peanut kernels was used as a food model system. White mycelia and dark/pale green spores of Aspergillus species were observed in the control peanut kernels after 2 days incubation. However the fungal growth was not observed in peanut kernels treated with cyclo(4-hydroxy-L-Pro-L-Trp). The cyclo(4-hydroxy-L-Pro-L-Trp) was nontoxic to two normal cell lines [fore skin (FS) normal fibroblast and African green monkey kidney (VERO)] up to 200 µg/ml in MTT assay. Thus the cyclo(4-hydroxy-L-Pro-L-Trp) identified in this study may be a promising alternative to chemical preservatives as a potential biopreservative agent which prevent fungal growth in food and feed. To the best of our knowledge, this is the first report demonstrating that the entomopathogenic nematode associated B. cereus and cyclo(4-hydroxy-L-Pro-L-Trp) could be used as a biocontrol agents against postharvest fungal disease caused by Aspergillus species.
Hemophilia B carrier determination based on family-specific mutation detection by DNA single-strand conformation analysis. (1993)

Single-strand conformation (SSC) analysis can distinguish normal from variant DNA fragments containing single point mutations by conformation-induced electrophoretic mobility shifts in non-denaturing polyacrylamide gels. We studied 25 hemophilia B kindreds by using SSC analysis after polymerase chain reaction (PCR) amplification of the eight factor IX exons and their intron boundaries. Variant SSC fragments were unambiguously identified in 24 kindreds, and direct DNA sequencing of variant PCR fragments identified 20 different hemophilia B mutations. This technique was used for rapid and accurate carrier determination in female family members without the need for additional sequencing studies, because carriers have both normal and hemophilia family-specific SSC fragments. Of 25 obligate carriers from 15 kindreds, 24 were confirmed to carry variant fragments. The exception, a patient's daughter homozygous for the normal allele, was demonstrated by subsequent PCR genotyping to be the result of non-paternity. In the additional 32 at-risk females from 16 kindreds studied, 19 were identified as carriers and 13 as non-carriers. Eleven of the unique mutations affected restriction enzyme digestion sites, and carriers could then be identified by appropriate restriction enzyme digestion of amplified DNA. Our study, with hemophilia B as a model system, demonstrates the accuracy and efficiency of SSC analysis in screening and tracking unknown mutations in monogenic inherited disorders with known gene sequences.
Biomimetic actuators using electroactive polymers (EAP) as artificial muscles (2006)

Evolution has resolved many of nature's challenges leading to lasting solutions with maximal performance and effective use of resources. Nature's inventions have always inspired human achievements leading to effective materials, structures, tools, mechanisms, processes, algorithms, methods, systems and many other benefits. The field of mimicking nature is known as Biomimetics and one of its topics includes electroactive polymers that gain the moniker artificial muscles. Integrating EAP with embedded sensors, self-repair and many other capabilities that are used in composite materials can add greatly to the capability of smart biomimetic systems. Such development would enable fascinating possibilities potentially turning science fiction ideas into engineering reality.
Optimization of Organic Molecule Separation and Detection Using Gas Chromatographic Column Based on MEMS Technologies Developed for Planetary and Exobiology Studies (2022)

International audience
A finger-mounted silicon tactile sensor (2002)

Describes the development of a silicon-based force sensor packaged in a flexible polyimide package. Sensitivity to force is realized via the addition of a solid dome over the silicon diaphragm. The dome acts to transmit the applied force to the diaphragm. Torlon and epoxy domes are bench tested. The epoxy dome produces significant hysteresis, while the Torlon dome shows low hysteresis and low nonrepeatability. Output sensitivities of 1.4 mV/V/N are typical. The response is linear for low forces (<10-N) and becomes curvilinear at higher forces when the diaphragm bottoms out. Characterization of the force sensor system and preliminary finger-mounted results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Parallelism to reduce power consumption on FPGA spatiotemporal image processing (2008)

Portable image processing systems require algorithms which reduce the power consumption while maintaining video rate operation. This paper describes how splitting the data stream into multiple processing pipelines can reduce power consumption in contrast to the traditional spatial (pipeline) parallel processing technique. Real-time image processing system functions (Sobel filters and anisotropic diffusion) were implemented to show the principle of the technique. Our results show that partitioning the image into multiple sections gives increasing benefits with shorter processing times, and up to 45% drop in the power consumption.
Profoundly Expanded T-cell Clones in the Inflamed and Uninflamed Intestine of Patients With Crohn’s Disease (2017)

The intestinal T-cell repertoire distribution in Crohn's disease is different from that in the normal gut, containing profoundly expanded T-cell clones that take up a large part of the repertoire. The T-cell repertoire is fairly stable regardless of endoscopic mucosal inflammation or response to therapy.
Selective sorption of gold(iii) by polystyrene-supported α-pyridylamino oligomers (2000)

α-Pyridylamino oligomer was immobilised on a polystyrene support, and the sorption of some metal ions by the polymer was investigated. This polymer was able to preferentially sorb gold(III) from aqueous solutions also containing palladium(II), platinum(IV), ruthenium(III) or copper(II) at pH 1.
Novel Conserved Group A Streptococcal Proteins Identified by the Antigenome Technology as Vaccine Candidates for a Non-M Protein-Based Vaccine (2010)

ABSTRACT Group A streptococci (GAS) can cause a wide variety of human infections ranging from asymptomatic colonization to life-threatening invasive diseases. Although antibiotic treatment is very effective, when left untreated, Streptococcus pyogenes infections can lead to poststreptococcal sequelae and severe disease causing significant morbidity and mortality worldwide. To aid the development of a non-M protein-based prophylactic vaccine for the prevention of group A streptococcal infections, we identified novel immunogenic proteins using genomic surface display libraries and human serum antibodies from donors exposed to or infected by S. pyogenes . Vaccine candidate antigens were further selected based on animal protection in murine lethal-sepsis models with intranasal or intravenous challenge with two different M serotype strains. The nine protective antigens identified are highly conserved; eight of them show more than 97% sequence identity in 13 published genomes as well as in approximately 50 clinical isolates tested. Since the functions of the selected vaccine candidates are largely unknown, we generated deletion mutants for three of the protective antigens and observed that deletion of the gene encoding Spy1536 drastically reduced binding of GAS cells to host extracellular matrix proteins, due to reduced surface expression of GAS proteins such as Spy0269 and M protein. The protective, highly conserved antigens identified in this study are promising candidates for the development of an M-type-independent, protein-based vaccine to prevent infection by S. pyogenes .
Herbicidal Sulfonylamides (1995)

A large number of disparte chemical classes have been shown to inhibit the enzyme acetolactate synthase. The herbicidal activity resulting from the inhibition of this enzyme has resulted in the introduction of novel compounds with low use rates and excellent toxicological and environmental profiles. The design and synthesis of a series of sulfonylamides that inhibit this enzyme are described. Structure activity and herbicidal properties of these compounds are discussed.
It Takes Two to Tango: Endothelial TGFβ/BMP Signaling Crosstalk with Mechanobiology (2020)

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-beta (TGFβ) superfamily of cytokines. While some ligand members are potent inducers of angiogenesis, others promote vascular homeostasis. However, the precise understanding of the molecular mechanisms underlying these functions is still a growing research field. In bone, the tissue in which BMPs were first discovered, crosstalk of TGFβ/BMP signaling with mechanobiology is well understood. Likewise, the endothelium represents a tissue that is constantly exposed to multiple mechanical triggers, such as wall shear stress, elicited by blood flow or strain, and tension from the surrounding cells and to the extracellular matrix. To integrate mechanical stimuli, the cytoskeleton plays a pivotal role in the transduction of these forces in endothelial cells. Importantly, mechanical forces integrate on several levels of the TGFβ/BMP pathway, such as receptors and SMADs, but also global cell-architecture and nuclear chromatin re-organization. Here, we summarize the current literature on crosstalk mechanisms between biochemical cues elicited by TGFβ/BMP growth factors and mechanical cues, as shear stress or matrix stiffness that collectively orchestrate endothelial function. We focus on the different subcellular compartments in which the forces are sensed and integrated into the TGFβ/BMP growth factor signaling.
Cloning and characterization of the Saccharomyces cerevisiae gene encoding NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase. (1993)

Saccharomyces cerevisiae possess a monofunctional, cytoplasmic NAD-dependent 5,10-methylenetetrahydrofolate (THF) dehydrogenase that converts 5,10-methylene-THF to 5,10-methenyl-THF (Barlowe, C. K., and Appling, D.R. (1990) Biochemistry 29, 7089-7094). We have now isolated the gene encoding this enzyme from a yeast genomic library using oligonucleotide probes based on internal peptide sequences from the purified protein. Nucleotide sequence analysis reveals a 320-amino acid open reading frame that contains both of the internal peptide sequences. The predicted molecular weight (36,236) is consistent with the estimated size (33,000-38,000) of the purified protein. Disruption of the chromosomal copy of the gene resulted in loss of NAD-dependent 5,10-methylene-THF dehydrogenase activity and led to a purine requirement in certain genetic backgrounds, confirming a role for this enzyme in the oxidation of cytoplasmic one-carbon units. A single gene was mapped to chromosome XI by hybridization to a yeast chromosomal blot. We propose MTD1 as the name for this gene. Northern analysis of total yeast RNA revealed a single transcript of approximately 1,100 nucleotides. Multiple transcription initiation sites were identified between 58 and 83 base pairs upstream of the start of translation. The amino acid sequences derived from the nucleic acid sequences of seven other methylene-THF dehydrogenases cloned to date have been found to be highly homologous. Although the predicted amino acid sequence of the yeast NAD-dependent enzyme shows slight homology to the other sequences, it appears to be only distantly related to the other 5,10-methylene-THF dehydrogenases.
Statistical modeling for real-time pore pressure prediction from predrill analysis and well logs (2018)

The challenge of pore pressure prediction in an overpressured area near a well is studied. Predrill understanding of pore pressure is available from a 3D geologic model for pressure buildup and release using a basin modeling approach. The pore pressure distribution is updated when well logs are gathered while drilling. Sequential Bayesian methods are used to conduct real-time pore pressure prediction, meaning that every time new well logs are available, the pore pressure distribution is automatically updated ahead of the bit and in every spatial direction (north, east, and depth), with associated uncertainty quantification. Spatial modeling of pore pressure variables means that the data at one well depth location will also be informative of the pore pressure variables at other depths and lateral locations. A workflow is exemplified using real data. The prior model is based on a Gaussian process fitted from geologic modeling of this field, whereas the likelihood model of well-log data is assessed from data in an exploration well in the same area. Results are presented by replaying a drilling situation in this context.
Intelligent Multimedia Presentation in Ubiquitous Multidevice Scenarios (2009)

This intelligent multimedia adaptation and delivery framework tailors to ubiquitous environments, so that users can experience multimedia content using multiple devices in various mobility situations. Multidevice environments offer the potential to enhance the user experience in terms of flexibility and interactivity and will enable novel applications in education, entertainment, collaboration, and communication. We analyzed the different processing steps and defined related framework functionalities such as the generation of the presentation schedule, the computation of the presentation-environment matches, personalization through situation learning, and device(s)-tailored presentation delivery.