gebhart/patrepeval huggingface dataset:
Monoallelic deleterious MUTYH germline variants as a driver for tumorigenesis (2021)

MUTYH encodes a glycosylase involved in the base excision repair of DNA. Biallelic pathogenic germline variants in MUTYH cause an autosomal recessive condition known as MUTYH-associated adenomatous polyposis and consequently increase the risk of colorectal cancer. However, reports of increased cancer risk in individuals carrying only one defective MUTYH allele are controversial and based on studies involving few individuals. Here, we describe a comprehensive investigation of monoallelic pathogenic MUTYH germline variants in 10,389 cancer patients across 33 different tumour types and 117,000 healthy individuals. Our results indicate that monoallelic pathogenic MUTYH germline variants can lead to tumorigenesis through a mechanism of somatic loss of heterozygosity of the functional MUTYH allele in the tumour. We confirmed that the frequency of monoallelic pathogenic MUTYH germline variants is higher in individuals with cancer than in the general population, although this frequency is not homogeneous among tumour types. We also demonstrated that the MUTYH mutational signature is present only in tumours with loss of the functional allele and found that the characteristic MUTYH base substitution (C>A) increases stop-codon generation. We identified key genes that are affected during tumorigenesis. In conclusion, we propose that carriers of the monoallelic pathogenic MUTYH germline variant are at a higher risk of developing tumours, especially those with frequent loss of heterozygosity events, such as adrenal adenocarcinoma, although the overall risk is still low. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A Comprehensive Approach to Mapping the Interacting Surfaces of Murine Amphotropic and Feline Subgroup B Leukemia Viruses with Their Cell Surface Receptors (2000)

Because mutations in envelope glycoproteins of retroviruses or in their cell surface receptors can eliminate function by multiple mechanisms, it has been difficult to unambiguously identify sites for their interactions by site-directed mutagenesis. Recently, we developed a gain-of-function approach to overcome this problem. Our strategy relies on the fact that feline leukemia virus subgroup B (FeLV-B) and amphotropic murine leukemia virus (A-MLV) have closely related gp70 surface envelope glycoproteins and use related Na(+)-dependent phosphate symporters, Pit1 and Pit2, respectively, as their receptors. We previously observed that FeLV-B/A-MLV envelope glycoprotein chimeras spliced between the variable regions VRA and VRB were unable to use Pit1 or Pit2 as a receptor but could efficiently use specific Pit1/Pit2 chimeras. The latter study suggested that the VRA of A-MLV and FeLV-B functionally interact with the presumptive extracellular loops 4 and 5 (ECL4 and -5) of their respective receptors, whereas VRB interacts with ECL2. We also found that FeLV-B gp70 residues F60 and P61 and A-MLV residues Y60 and V61 in the first disulfide-bonded loop of VRA were important for functional interaction with the receptor's ECL4 or -5. We have now extended this approach to identify additional VRA and VRB residues that are involved in receptor recognition. Our studies imply that FeLV-B VRA residues F60 and P61 interact with the Pit1 ECL5 region, whereas VRA residues 66 to 78 interact with Pit1 ECL4. Correspondingly, A-MLV VRA residues Y60 and V61 interact with the Pit2 ECL5 region, whereas residues 66 to 78 interact with Pit2 ECL4. Similar studies that focused on the gp70 VRB implicated residues 129 to 139 as contributing to specific interactions with the receptor ECL2. These results identify three regions of gp70 that interact in a specific manner with distinct portions of their receptors, thereby providing a map of the functionally interacting surfaces.
Vascular Graft with Dynamic Topography Exhibits Reduced Platelet Adhesion Compared with Standard Synthetic Graft (2020)

Afflu, Derek K. MD; Nath, Nandan N. MD; Gonzalez, Kathy MD; Pocivavsek, Luka MD; Pitre, Nandan MS; Velankar, Sachin PhD; Tzeng, Edith MD, FACS Author Information
Quantitative elemental analysis of metal alloys by laser induced breakdown spectroscopy using multivariate calibration (2002)

Laser induced breakdown spectroscopy has enjoyed acceptance as an analytical tool in many areas despite its spectral interferences. We demonstrate here the application of multivariate calibration for quantitative elemental analysis of metal alloys.
Phospho-Regulation of Soma-to-Axon Transcytosis of Neurotrophin Receptors (2018)

The family of neurotrophins provides one of the best-known examples of target-derived instructive cues that regulate distinct aspects of neuronal development. A key mechanism by which target-derived neurotrophins provides trophic support is by the cell biological processes of endocytosis and retrograde trafficking of their Trk receptors from axonal growth cones to cell bodies. Since Trk receptors are being continuously transported back to the cell bodies, a fundamental question is how neurons replenish these receptors in nerve terminals? Here, we report that retrograde signaling by target-derived nerve growth factor (NGF) is necessary for soma-to-axon transcytosis of TrkA receptors in sympathetic neurons. Activated TrkA receptors are retrogradely transported in signaling endosomes from distal axons to cell bodies, where they are inserted on soma surfaces and promote phosphorylation of resident naive receptors, resulting in their internalization. Endocytosed TrkA receptors are then dephosphorylated by PTP1B, an ER-resident protein tyrosine phosphatase, prior to axonal transport. PTP1B inactivation prevents TrkA exit from soma and causes receptor degradation, suggesting a "gatekeeper" mechanism that ensures targeting of inactive receptors to axons to engage with ligand. In mice, PTP1B deletion reduces axonal TrkA levels and attenuates neuron survival and target innervation under limiting NGF (NGF+/-) conditions. These results identify phospho-regulatory mechanisms that underlie a positive feedback loop where target-derived NGF recruits its own receptors to nerve terminals to amplify neuronal responsiveness.
fPoxDB: fungal peroxidase database for comparative genomics (2014)

fPoxDB is a fungi-oriented genomics platform for peroxidases. The sequence-based prediction and diverse analysis toolkits with easy-to-follow web interface offer a useful workbench to study comparative and evolutionary genomics of peroxidases in fungi.
Iron(III)-chelating resins. 3. Synthesis, iron(III)-chelating properties, and in vitro antibacterial activity of compounds containing 3-hydroxy-2-methyl-4(1H)-pyridinone ligands (1993)

The synthesis, iron (III)-chelating properties, and antibacterial activity of several compounds containing the 3-hydroxy-2-methyl-4(1H)-pyridinone (HMP) moiety are described. Using the HMP derivatives iron (III) could be mobilized from iron (III)-binding proteins at physiological pH with a rate order of transferrin > lactoferrin > ferritin. Addition of HMP-containing compounds to a growth medium at a concentration of 20 mM/L resulted in a complete inhibition of the growth of Escherichia coli and about 90% inhibition for Listeria inocua after 7 h of incubation at 37 degrees C. After inhibition of bacteria growth by the HMP derivatives growth started again when ferric ions were added to the medium, which implies that the antibacterial activity is due to a limitation of iron available to the organisms.
Alterations in penicillin-binding proteins in strains ofStreptococcus suispossessing moderate and high levels of resistance to penicillin (1995)

We examined the penicillin-binding proteins (PBPs) of certain field strains of Streptococcus suis, as well as those from laboratory variants having different degrees of resistance to penicillin. Results indicated that (i) S. suis possesses three distinct groups of PBPs, arbitrarily named here PBP 1, PBP 2, and PBP 3, with approximate molecular weights of 97, 82, and 45 kDa respectively; (ii) PBP profiles of field strains of S. suis having different MICs (< or = 0.03) to 16.0 micrograms/ml) were not uniform (PBP 2 being difficult to detect in strains whose MICs exceeded 0.10 micrograms/ml, and PBP 3 which exhibited shifts in molecular weight of approximately 5 kDa); (iii) laboratory variant PBPs 1 and 2 showed decreased affinity for penicillin as compared to the parent strain in antibiotic competition experiments, even though the PBP profiles of both were similar. We suggest that PBP modifications (altered molecular weight and/or decreased affinity for penicillin) are involved in the mechanism of resistance to penicillin by S. suis.
A Low-Power Hardware Accelerator of MFCC Extraction for Keyword Spotting in 22nm FDSOI (2023)

With the development of artificial intelligence, the real-time feature extraction of acoustic signals is required in a wide variety of applications, such as keyword spotting and speech recognition. Feature extraction based on Mel-frequency cepstral coefficients (MFCCs) is one of the most significant methods thereinto. A software implementation of the MFCC extraction results in relatively high power consumption and computational time limitation, often making it unsuitable for tiny battery powered devices. Therefore, an on-chip accelerator of MFCC extraction is of interest in cutting-edge scenarios. This paper presents a fixed-point low-power hardware accelerator of MFCC feature extraction implemented in 22nm FDSOI technology. It consumes an average power of 2.78µW for 1024-sample frame at a clock frequency of 1MHz. For keyword spotting, the quantized accelerator achieves an average accuracy of around 96% working along with different classification networks.
Explorations In Pleated Fabric Garment Structures (2004)

Arashi Shibori, the traditional Japanese process of resist dyeing, is adapted to create pleated fabrics for use in garments. The purpose of this article is to: 1) document the pleating process using sequential photographs that provide enough visual detail to enable replication; 2) summarize the author’s previous experimental research using pleated fabrics; and 3) document the process in the design development of a current endeavor entitled Serendipity.
Measuring the difference in group delays between the cores of a multicore optical fiber by means of time-domain interferometry (2017)

A way of measuring the difference in group delays between the cores of multi-core optical fiber is proposed. The method is based on a low-coherence Mach–Zehnder interferometer and a broadband radiation source. The corresponding experimental setup is constructed and a seven-core optical fiber with identical cores manufactured at the Fiber Optics Research Center, Russian Academy of Sciences, is studied.
Physiological Benefits of Warm-Up (1983)

In brief: Warm-up generates an increase in body temperature that may benefit overall physical performance. Three basic types of warm-up may be used to prepare for strenuous activity: passive, general, and specific. The best of these is specific warm-up, which not only increases the temperature of the body parts involved in the activity but also provides a rehearsal of the event that is to take place.
Influence of Age, Sex, and Hearing Loss on Auditory Brain Stem Response (ABR) Latencies a comment on: E. Stürzebecher, M. Werbs “Effects of age and sex on auditory brain stem response” (Scand Audiol 16, 153, 1987) (1988)

In a previous paper, the hypothesis was established that the shorter auditory brain stem response (ABR) latencies in females, in comparison with males, can be explained solely by the age dependence of the latencies, which is more pronounced in males than in females. According to this concept, ABR latencies in male and female babies are identical but diverge increasingly with increasing age. A multiple regression analysis on considerably enlarged male and female groups has now confirmed the hypothesis as to the differing age dependence in males and females. But the results also show that the male/female ABR latency differences cannot be explained solely by these differences in age dependence. An additional factor has to be taken into account, for which the male/female difference in auditory pathway length is a plausible explanation.
Adenylyl Cyclase Type VI Increases Akt Activity and Phospholamban Phosphorylation in Cardiac Myocytes (2008)

Increased expression of adenylyl cyclase VI has beneficial effects on the heart, but strategies that increase cAMP production in cardiac myocytes usually are harmful. Might adenylyl cyclase VI have beneficial effects unrelated to increased beta-adrenergic receptor-mediated signaling? We previously reported that adenylyl cyclase VI reduces cardiac phospholamban expression. Our focus in the current studies is how adenylyl cyclase VI influences phospholamban phosphorylation. In cultured cardiac myocytes, increased expression of adenylyl cyclase VI activates Akt by phosphorylation at serine 473 and threonine 308 and is associated with increased nuclear phospho-Akt. Activated Akt phosphorylates phospholamban, a process that does not require beta-adrenergic receptor stimulation or protein kinase A activation. These previously unrecognized signaling events would be predicted to promote calcium handling and increase contractile function of the intact heart independently of beta-adrenergic receptor activation. We speculate that phospholamban phosphorylation, through activation of Akt, may be an important mechanism by which adenylyl cyclase VI increases the function of the failing heart.
Logico-Computational Aspects of Rationality (2021)

Taking a historical line, we discuss major aspects of rationality from a logical and computational perspective. Topics include classical notions from the foundations of computability, insights from the de- velopment of computer science and AI, and the picture of rationality emerging in current logical studies of agency. We also discuss two chal- lenges. Distributed computing and evolutionary games replace ’high rationality’ by ’low rationality’ in behavior, so logic may not be neces- sary. Machine learning suggests that logical analysis may not even be possible. Both trigger new logical themes in the study of rationality.
Synchronization of three-phase converters and virtual microgrid implementation utilizing the Power-Hardware-in-the-Loop concept (2010)

This paper addresses the timely issues of synchronization and application of three-phase power converters connected in parallel utilizing the Power-Hardware-in-the-Loop concept. Without proper synchronization, distinguishing the currents circulating between the converters are unclear. The paper centers on control methodology for achieving precise phase synchronization for equal load sharing, with minimum current circulation between the paralleled power converter modules, and robust dynamic system control under different transient conditions. One of the possible applications for the configuration presented in this paper is the conceptual virtual microgrid, which utilizes the reactive power compensation ability of the Static Synchronous Compensator (STATCOM). The microgrid behavior and load dynamics are simulated with a real-time digital simulator which generates appropriate control commands to a power electronics based voltage amplifier interfaced via a cascaded LC-LC type filter to a variable speed drive (VSD). This is necessary as reactive power control is a critical consideration in improving the power quality of power systems. To compensate for reactive power, the STATCOM controller will be developed and integrated into the proposed virtual microgrid system. This concept provides a solution for de-risking these costs as it utilizes the PHIL concept in conjunction with high-fidelity microgrid model and detailed load dynamics. Selected experimental results on two, 25-kVA and 15-kVA, converters in parallel are presented.
Slow pace of life in tropical sedentary birds: a common-garden experiment on four stonechat populations from different latitudes (2003)

It has been hypothesized that organisms living at different latitudes or in different environments adjust their metabolic activity to the prevailing conditions. However, do differences in energy turnover simply represent a phenotypic adaptation to the local environment, or are they genetically based? To test this, we obtained nestling stonechats (Saxicola torquata) from equatorial Kenya (0 degrees N), Ireland (51.5 degrees N), Austria (47.5 degrees N) and Kazakhstan (51.5 degrees N). Birds were hand-raised and kept in Andechs, Germany. We measured their resting metabolic rates (RMR) and locomotor activity at an age of ca. 14 months (July) and 20 months (January), when birds went through postnuptial moult (July), and neither moulted nor exhibited enlarged gonads or migratory activity (January). RMR was generally higher during moult, but differed among populations: RMR was lowest in the resident Kenyan birds, higher in mostly sedentary Irish birds, and highest in migratory Austrian and Kazakhstan birds. Thus our data demonstrate that even in birds kept from early life under common-garden conditions, the 'pace of life', as indicated by metabolic turnover, is lower in sedentary tropical than in north-temperate migratory individuals of the same species. Such intrinsically low energy expenditure in sedentary tropical birds may have important implications for slow development, delayed senescence and high longevity in many tropical organisms.
Advances in excimer laser technology for sub-0.25-μm lithography (2002)

There are several lasers that can provide high-power radiation at deep-UV wavelengths. The only laser that has been successfully used in semiconductor manufacturing as a source for lithography is the excimer laser Excimer lasers provide direct deep-UV light, are scalable in energy and power, and are capable of operating with narrow spectral widths. Also, by providing three wavelengths at 248, 193, and 157 nm, excimer lasers span three generations. They have large beams and a low degree of coherence. Their physics and chemistry are well understood. Thanks to major technical developments, these lasers have kept up with the ever-tightening specifications of the lithography industry. We will discuss what these specifications are and the advances that have been made in laser technology to meet these. We will also identify any possible future limitation in this technology. The success behind the microelectronics explosion is attributed to many factors. The excimer laser is one of them.
Crystal Structure and Physical Properties of Mg6Cu16Si7-type M6Ni16Si7, for M = Mg, Sc, Ti, Nb, and Ta (2007)

Five compounds were investigated for magnetic character and superconductivity, all with non-magnetic nickel and band structures containing flat bands and steep bands. The syntheses and crystal structures, refined by powder X-ray diffraction, are reported for M6Ni16Si7, where M = Mg, Sc, Ti, Nb, and Ta. All compounds form in the Mg6Cu16Si7 structure type. Resistance measurements are also reported on M6Ni16Si7 (M = Mg, Sc, Ti, and Nb) down to 0.3 K, with all four showing metallic conductivity. No superconductivity is observed. Magnetization measurements for all compounds reveal essentially temperature independent paramagnetism, with a tendency toward more enhanced low temperature paramagnetism for the cases of Mg6Ni16Si7 and Sc6Ni16Si7.
Pseudocoloring in Single‐Energy X‐Ray Images (2007)

This chapter contains sections titled: Problem Statement Aspects of the Human Perception of Color Theoretical Aspects of Pseudocoloring RGB-Based Colormaps HSI-Based Colormaps Experimental Results Performance Evaluation Conclusion References
Web-Enabled System Dynamics Model for Error and Change Management on Concurrent Design and Construction Projects (2006)

Construction projects are uncertain and complex in nature often because of iterative cycles caused by errors and changes. These errors and changes impair project performance and, consequently, cause schedule and cost overruns to be prevalent. Iterative cycles are more detrimental when design and construction are concurrent and often force activities to proceed without complete information. In an effort to address this issue, this paper presents the information technology aspect of the dynamic planning and control methodology (DPM), which provides a mechanism that will analyze the impact of negative iterative cycles on construction performance. In order to guarantee a smooth application of this method to real-world projects, DPM has been developed by integrating several existing methods around a core system dynamic model for quality and change management and then implementing these methods into a web-based collaborative environment. A case project, applying the developed web-based DPM, shows great potential in facilitating on-site decision making by virtue of its support of data analysis as well as real-time information sharing.
Hydrothermal Synthesis of SnO<sub>2</sub> Structures with Various Morphologies in the Presence of Different Alcoholic Co-Solvents (2016)

The addition of certain co-solvents to the hydrothermal synthesis starting solution can greatly alter morphology and enhance different morphology dependent properties of the synthesized material. While ethanol is the most common co-solvent used for the synthesis of various SnO 2 nano/microstructures by hydro/solvothermal process, it is not clear how the use of some other alcoholic co-solvents (for example, methanol or isopropanol) affect morphology and properties of SnO 2 , especially if synthesis is done under similar conditions as in the case of ethanol co-solvent. In the present study, we investigated how the use of various alcoholic co-solvents (methanol, ethanol, 2-propanol, ethylene glycol and glycerol) affects crystal structure, morphology and specific surface area of the hydrothermally synthesized SnO 2 . Additionally, sensitivity towards 100 ppm ethanol of the synthesized materials was tested. The formation of nanoparticles, rod-cluster structures and spherical SnO 2 structures were observed depending on the alcoholic co-solvent used. The highest sensitivity (~22 at 250 °C) showed the material that was synthesized in the presence of ethanol co-solvent.
Dobutamine Enhances Cardiodepressant Effects of Receptor-Mediated Coronary Endothelial Stimulation (1997)

Dobutamine enhances the cardiodepressant effect on myocardial contractile performance of receptor-mediated coronary endothelial stimulation in transplant recipients and in patients with dilated nonischemic cardiomyopathy. This enhancement could result from a potentiating interaction of the relaxation-hastening effect exerted by beta-adrenergic stimulation and by mediators released from the coronary endothelium, such as nitric oxide.