gebhart/patrepeval huggingface dataset:
Mitochondrial and nuclear DNA defects in Saccharomyces cerevisiae with mutations in DNA polymerase γ associated with progressive external ophthalmoplegia (2005)

A number of nuclear mutations have been identified in a variety of mitochondrial diseases including progressive external ophthalmoplegia (PEO), Alpers syndrome and other neuromuscular and oxidative phosphorylation defects. More than 50 mutations have been identified in POLG, which encodes the human mitochondrial DNA (mtDNA) polymerase gamma, PEO and Alpers patients. To rapidly characterize the effects of these mutations, we have developed a versatile system that enables the consequences of homologous mutations, introduced in situ into the yeast mtDNA polymerase gene MIP1, to be evaluated in vivo in haploid and diploid cells. Overall, distinct phenotypes for expression of each of the mip1-PEO mutations were observed, including respiration-defective cells with decreased viability, dominant-negative mutant polymerases, elevated levels of mitochondrial and nuclear DNA damage and chromosomal mutations. Mutations in the polymerase domain caused the most severe phenotype accompanied by loss of mtDNA and cell viability, whereas the mutation in the exonuclease domain showed mild dominance with loss of mtDNA. Interestingly, the linker region mutation caused elevated mitochondrial and nuclear DNA damage. The cellular processes contributing to these observations in the mutant yeast cells are potentially relevant to understanding the pathologies observed in human mitochondrial disease patients.
Mechanism for the Water-to-Air Transfer and Concentration of Bacteria (1970)

Air bubbles breaking at the air-water interface can remove bacteria that concentrate in the surface microlayer and eject the bacteria into the atmosphere. The bacterial concentrations (numbers per milliliter) in the drops ejected from the bubbles may, depending on drop size, be from 10 to 1000 times that of the water in which the bubbles burst.
Shear‐wave statics using receiver functions (2002)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2002Shear‐wave statics using receiver functionsAuthors: Dirk‐Jan van ManenJohan RobertssonAndrew CurtisRalf FerberHanneke PaulssenDirk‐Jan van ManenDept. of Geophysics, Utrecht University, The Netherlands, Johan RobertssonWesternGeco Oslo Technology Centre, Asker, Norway, Andrew CurtisSchlumberger Cambridge Research, Cambridge, United Kingdom, Ralf FerberSchlumberger Cambridge Research, Cambridge, United Kingdom, and Hanneke PaulssenDept. of Geophysics, Utrecht University, The Netherlandshttps://doi.org/10.1190/1.1816925 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816925FiguresReferencesRelatedDetailsCited byComparative analysis of C-wave receiver static estimation in onshore dataJulián Vargas, Jorge Monsegny, William Agudelo*, and Luis Montes13 March 2014Shear wave statics using receiver functionsGeophysical Journal International, Vol. 153, No. 3 SEG Technical Program Expanded Abstracts 2002ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2002 Pages: 2478 publication data© 2002 Copyright © 2002 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 03 Jan 2005 CITATION INFORMATION Dirk‐Jan van Manen, Johan Robertsson, Andrew Curtis, Ralf Ferber, and Hanneke Paulssen, (2002), "Shear‐wave statics using receiver functions," SEG Technical Program Expanded Abstracts : 1412-1415. https://doi.org/10.1190/1.1816925 Plain-Language Summary PDF DownloadLoading ...
The tobacco-specific carcinogen NNK induces pulmonary tumorigenesis via nAChR/Src/STAT3-mediated activation of the renin-angiotensin system and IGF-1R signaling (2023)

The renin-angiotensin (RA) system has been implicated in lung tumorigenesis without detailed mechanistic elucidation. Here, we demonstrate that exposure to the representative tobacco-specific carcinogen nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) promotes lung tumorigenesis through deregulation of the pulmonary RA system. Mechanistically, NNK binding to the nicotinic acetylcholine receptor (nAChR) induces Src-mediated signal transducer and activator of transcription 3 (STAT3) activation, resulting in transcriptional upregulation of angiotensinogen (AGT) and subsequent induction of the angiotensin II (AngII) receptor type 1 (AGTR1) signaling pathway. In parallel, NNK concurrently increases insulin-like growth factor 2 (IGF2) production and activation of IGF-1R/insulin receptor (IR) signaling via a two-step pathway involving transcriptional upregulation of IGF2 through STAT3 activation and enhanced secretion from intracellular storage through AngII/AGTR1/PLC-intervened calcium release. NNK-mediated crosstalk between IGF-1R/IR and AGTR1 signaling promoted tumorigenic activity in lung epithelial and stromal cells. Lung tumorigenesis caused by NNK exposure or alveolar type 2 cell-specific Src activation was suppressed by heterozygous Agt knockout or clinically available inhibitors of the nAChR/Src or AngII/AGTR1 pathways. These results demonstrate that NNK-induced stimulation of the lung RA system leads to IGF2-mediated IGF-1R/IR signaling activation in lung epithelial and stromal cells, resulting in lung tumorigenesis in smokers.
Facilitating Knowledge Maintenance of Clinical Guidelines and Protocols (2004)

Clinical protocols and guidelines are widely used in the medi-cal domain to improve disease management techniques. Different software systems are in development to support the de-sign and the execution of such guidelines. The bottleneck in the guideline software developing process is the transformation of the text-based clinical guidelines into a formal representation, which can be used by the execution software. This paper introduces a method and a tool that was designed to provide a solution for that bottleneck. The so-called Guideline Markup Tool (GMT) facilitates the translation of guidelines into a formal representation written in XML. This tool enables the protocol designer to create links between the original guideline and its formal representation and ease the editing of guidelines applying design patterns in the form of macros. The usefulness of our approach is illustrated using GMT to edit Asbru protocols. We performed a usability study with eight participants to examine the usefulness of the GMT and of the Asbru macros, which showed that the proposed approach is very appropriate to author and maintain clinical guidelines.
Towards Multi-Purpose Wireless Sensor Networks (2005)

Current wireless sensor network (WSN) architectures are based on the assumption that all sensor nodes are participating in a single global task. In many scenarios, however it will be desirable to use a single sensor network for multiple concurrent applications. In order to enable such multipurpose WSNs efficiently, delimiting each application to its specific set of relevant nodes is one of the key issues that needs to be solved. We present scoping as a general concept for the creation and maintenance of network-wide node subsets and describe a flexible and modular architecture that meets the requirements of multi-purpose WSNs.
Effects of Al and N2 Flow Sequences on the Interface Formation of AlN on Sapphire by EVPE (2017)

The interface formation mechanisms of AlN films on sapphire substrates grown by the elementary source vapor phase epitaxy (EVPE) method, which is a new AlN bulk fabrication method using Al and N2 as precursors, are investigated. Supplying N2 after the substrate temperature reaches the growth temperature [Process N2(GT)] causes the interface to become rough due to the thermal decomposition of sapphire. Self-separation occasionally occurs with the Process N2(GT), suggesting that the rough interface generates self-separating films with little strain. On the other hand, supplying N2 beginning at room temperature forms a relatively smooth interface with voids, which can be realized by the reaction between a nitrided sapphire surface and an Al source.
Controlled Synthesis of Conjugated Polymers and Block Copolymers (2017)

This chapter includes an in-depth understanding of the actual polymerization mechanism, the controlled polymerization of other and more challenging monomers, the synthesis of different kinds of copolymers, and the fabrication of end-functionalized polymers. The first and most widely used method to obtain a controlled polymerization of conjugated polymers relies on the association of the catalyst to the polymer chain. The mechanism of CTP was unraveled via the PT synthesis based on Kumada couplings. Soon after the discovery of the controlled synthesis of poly(thiophene)s, it was found that KCTP was also applicable to poly(p-phenylene)s (PPPs). In a Negishi coupling, the monomers possess both an organozinc moiety and a halide function. The development of a controlled polymerization allows the implementation of functional groups at the beginning as well as the end of each polymer chain. Besides postpolymerization reactions or the use of functionalized initiators, functional end groups can also be incorporated through end-capping.
Increasing Burden of Nursing Care on the Treatment of COVID-19 Patients in the Aging Society: Analyses During the First to the Third Wave of Pandemic in Kyoto City, Japan (2021)

<b>Background:</b> The coronavirus disease 2019 (COVID-19) pandemic is associated with a heavy burden on patient's mental and physical health, regional healthcare resources, and global economic activity. An aging society such as Japan has many retirement homes and long-term stay hospitals for the elderly and their inhabitants. During the COVID-19 pandemic, disease clusters are often identified in retirement homes and long-term stay hospitals. Although we hypothesize that additional burdens of nursing care for elderly patients will reinforce the anxiety and exhaustion of medical staff and healthcare resources in the aging society, the actual situation is not well understood. In this study, we aimed to evaluate the current situation and countermeasures of the COVID-19 pandemic in the aging society. <b>Methods:</b> We reviewed COVID-19 patients who required hospitalization at the National Hospital Organization Kyoto Medical Center, a 600-bed capacity hospital located in Kyoto, Japan, between 1 April 2020 and 31 March 2021. We assessed the characteristics of the COVID-19 patients, disease severity, duration of hospitalization, outcome at discharge, degree of activities of daily living (ADLs), and complications unique to elderly patients. <b>Results:</b> We enrolled 118 patients who required hospitalization during the study period. Approximately 40% of the patients were aged ≥ 80 years. Dementia (27.1%) was the most prevalent underlying disease, followed by diabetes mellitus (23.7%) and chronic kidney disease (23.7%). Approximately 60% of hospitalized COVID-19 patients had impaired ADL at admission. The COVID-19 patients aged 80 years or older required significantly more longer-term hospitalization than the COVID-19 patients aged under 80 years (15.5 ± 8.2 vs. 13.1 ± 7.7, <i>P</i> = 0.032). In elderly patients aged 80 years or older, approximately 50% of patients had geriatric mental disorders, and approximately 70% had bedridden status and feeding difficulty. Poor ADL at admission was significantly associated with COVID-19 mortality (Odds ratio, 5.6; 95% confidence interval, 1.04-45.2; <i>p</i>-value = 0.044). <b>Conclusions:</b> The proportion of elderly patients aged 80 years or older was relatively high during the hospitalization for COVID-19. Poor ADL at admission in these elderly patients was significantly associated with poor prognosis of COVID-19. We should keep in mind that healthcare workers are forced to have an additional burden of nursing care in the aging society during the COVID-19 pandemic. Therefore, interventions to reduce the burden are urgently required.
Near optimal detection of complex signals with unknown parameters (2002)

We consider the problem of detecting complex signals with uncertain parameters including amplitude and phase. For one class of problems the optimal solution is a three-layer neural network with an infinite number of intermediate nodes. We investigate several finite size structures which approximate the output of the optimal detector and deliver near optimal detection performance with reduced complexity. Training these structures is shown to have an interpretation in terms of minimizing cross entropy.
Improving deep neural networks for LVCSR using rectified linear units and dropout (2013)

Recently, pre-trained deep neural networks (DNNs) have outperformed traditional acoustic models based on Gaussian mixture models (GMMs) on a variety of large vocabulary speech recognition benchmarks. Deep neural nets have also achieved excellent results on various computer vision tasks using a random “dropout” procedure that drastically improves generalization error by randomly omitting a fraction of the hidden units in all layers. Since dropout helps avoid over-fitting, it has also been successful on a small-scale phone recognition task using larger neural nets. However, training deep neural net acoustic models for large vocabulary speech recognition takes a very long time and dropout is likely to only increase training time. Neural networks with rectified linear unit (ReLU) non-linearities have been highly successful for computer vision tasks and proved faster to train than standard sigmoid units, sometimes also improving discriminative performance. In this work, we show on a 50-hour English Broadcast News task that modified deep neural networks using ReLUs trained with dropout during frame level training provide an 4.2% relative improvement over a DNN trained with sigmoid units, and a 14.4% relative improvement over a strong GMM/HMM system. We were able to obtain our results with minimal human hyper-parameter tuning using publicly available Bayesian optimization code.
Simian Virus 40 DNA Replication In Vitro: Specificity of Initiation and Evidence for Bidirectional Replication (1985)

We recently described a soluble cell-free system derived from monkey cells that is capable of replicating exogenous plasmid DNA molecules containing the simian virus 40 (SV40) origin of replication (J.J. Li, and T.J. Kelly, Proc. Natl. Acad. Sci. U.S.A. 81:6973-6977, 1984). Replication in the system is completely dependent upon the addition of the SV40 large T antigen. In this report we describe additional properties of the in vitro replication reaction. Extracts prepared from cells of several nonsimian species were tested for the ability to support origin-dependent replication in the presence of T antigen. The activities of extracts derived from human cell lines HeLa and 293 were approximately the same as those of monkey cell extracts. Chinese hamster ovary cell extracts also supported SV40 DNA replication in vitro, but the extent of replication was approximately 1% of that observed with human or monkey cell extracts. No replication activity was detectable in extracts derived from BALB/3T3 mouse cells. The ability of these extracts to support replication in vitro closely parallels the ability of the same cells to support replication in vivo. We also examined the ability of various DNA molecules containing sequences homologous to the SV40 origin to serve as templates in the cell-free system. Plasmids containing the origins of human papovaviruses BKV and JCV replicated with an efficiency 10 to 20% of that of plasmids containing the SV40 origin. Plasmids containing Alu repeat sequences (BLUR8) did not support detectable DNA replication in vitro. Circular DNA molecules were found to be the best templates for DNA replication in the cell-free system; however, linear DNA molecules containing the SV40 origin also replicated to a significant extent (10 to 20% of circular molecules). Finally, electron microscopy of replication intermediates demonstrated that the initiation of DNA synthesis in vivo takes place at a unique site corresponding to the in vivo origin and that replication is bidirectional. These findings provide further evidence that replication in the cell-free system faithfully mimics SV40 DNA replication in vivo.
XeF4 as a Ligand for a Metal Ion (2009)

Abstract Edles Molekül : [Mg(XeF 2 )(XeF 4 )](AsF 6 ) 2 ist die erste Koordinationsverbindung, in der XeF 4 als an ein Metallzentrum gebundener Ligand vorliegt. Es ist auch die erste bekannte Verbindung, in der XeF 2 und XeF 4 gemeinsam an dasselbe Metallzentrum binden (siehe Struktur; lila Xe, grün F, grau Mg, gelb As). magnified image
Proton magnetic resonance relaxation studies on the structure of mixed micelles of Triton X-100 and dimyristoylphosphatidylcholine (1975)

Proton magnetic resonance and gel chromatographic studies on mixtures of phospholipid and the nonionic surfactant Triton X-200 have shown that at temperatures above the thermotropic phase transition of the phospholipid and below the cloud point of Triton, mixed micelles are present at molar ratios above about 2:1 Triton/phospholipid. Proton T1 and T2 (from line widths) relaxation times are reported for protons in Triton micelles and in mixed micelles of Triton and dimyristoylphosphatidylcholine at a molar ratio of 3:1 Triton/phospholipid. The T1 values and their temperature dependence and the activation energies of the various Triton proton groups appear to reflect internal motions of the Triton molecules in the micelle. Measurements of the T1/T2 ratio and frequency dependence (55-220 MHz) suggest that the hydrophobic tert-butyl group in Triton is observed under extreme narrowing conditions. The T1 and T2 values of Triton are unchanged in the presence of phosphatidylcholine. The T1 values of various protons of dimyristoylphosphatidylcholine in mixed micelles are similar to those reported for the phospholipid in sonicated vesicles, which are used as membrane models, and presumably the same coupled trans-gauche motions dominate. The T2 values for the terminal methyl and choline methyl protons in the phospholipid are longer than those reported for these groups in vesicles. Hence, the motion of the phospholipid in the mixed micelles appears to be less restricted than in vesicles. T1 measurements in H20/D20 mixtures are consistent with the idea that water does not penetrate the hydrophobic core of the mixed micelles, while water does solvate the polar oxyethylene and choline methyl groups. Titration with Mn2+ confirms that the oxyethylene and choline methyl groups are on the exterior of the mixed micelle while the hydrophobic groups are located in the micellar interior.
Network Security: Data and Voice Communications (1995)

From the Publisher:
Network Security is the first comprehensive hands-on guide to securing data and voice networks from both internal and external security threats. Starting with the basics, this practical reference quickly brings the reader up to speed on such timely topics as conducting effective security audits; security risks inherent in connecting to the Internet; protecting your network from the latest viruses; incorporating the latest government encryption initiatives and policies; managing passwords, encryption, authentication, and access control; and how to construct firewalls to keep hackers out of your system. Packed with real-life examples, this working reference includes a product selection checklist covering a wide variety of security hardware and software products currently available.
Biochemical characterization and tissue distribution of hamster complement C1s (1991)

Several mAb (PG11, NG7, and ED4) against hamster complement C1s were obtained. PG11 and NG7 were shown to cross-react with human and rat C1s. By using an immunohistochemical method, we examined localization of C1s in tissues of hamsters and rats. Present results revealed a widespread yet specific staining of hamster C1s which is associated with endoderm-, mesoderm-, and neuroectoderm-derived cells. For example, chondrocyte of hyaline cartilage and surface epithelium of the stomach were strongly positive. Intestinal epithelium, muscle cells, pia mater and epithelium of the choroid plexus of the ventricle, and hepatocytes were also stained. The synthesis of hamster C1s in these organs was confirmed by RNA blot hybridization. Secretion of C1s into the culture medium was revealed by immunoblot analysis in cell lines of hepatocytes, kidney cells, and myoblasts of rat or hamster.
3-Dimensional Examination of the Adult Mouse Subventricular Zone Reveals Lineage-Specific Microdomains (2012)

Recent studies suggest that the subventricular zone (SVZ) of the lateral ventricle is populated by heterogeneous populations of stem and progenitor cells that, depending on their exact location, are biased to acquire specific neuronal fates. This newly described heterogeneity of SVZ stem and progenitor cells underlines the necessity to develop methods for the accurate quantification of SVZ stem and progenitor subpopulations. In this study, we provide 3-dimensional topographical maps of slow cycling "stem" cells and progenitors based on their unique cell cycle properties. These maps revealed that both cell populations are present throughout the lateral ventricle wall as well as in discrete regions of the dorsal wall. Immunodetection of transcription factors expressed in defined progenitor populations further reveals that divergent lineages have clear regional enrichments in the rostro-caudal as well as in the dorso-ventral span of the lateral ventricle. Thus, progenitors expressing Tbr2 and Dlx2 were confined to dorsal and dorso-lateral regions of the lateral ventricle, respectively, while Mash1+ progenitors were more homogeneously distributed. All cell populations were enriched in the rostral-most region of the lateral ventricle. This diversity and uneven distribution greatly impede the accurate quantification of SVZ progenitor populations. This is illustrated by measuring the coefficient of error of estimates obtained by using increasing section sampling interval. Based on our empirical data, we provide such estimates for all progenitor populations investigated in this study. These can be used in future studies as guidelines to judge if the precision obtained with a sampling scheme is sufficient to detect statistically significant differences between experimental groups if a biological effect is present. Altogether, our study underlines the need to consider the SVZ of the lateral ventricle as a complex 3D structure and define methods to accurately assess neural stem cells or progenitor diversity and population sizes in physiological or experimental paradigms.
Incorporation of Lysyl-tRNA Synthetase into Human Immunodeficiency Virus Type 1 (2001)

During human immunodeficiency virus type 1 (HIV-1) assembly, tRNA(Lys) isoacceptors are selectively incorporated into virions and tRNA(Lys)3 is used as the primer for reverse transcription. We show herein that the tRNA(Lys)-binding protein, lysyl-tRNA synthetase (LysRS), is also selectively packaged into HIV-1. The viral precursor protein Pr55gag alone will package LysRS into Pr55gag particles, independently of tRNA(Lys). With the additional presence of the viral precursor protein Pr160gag-pol, tRNA(Lys) and LysRS are both packaged into the particle. While the predominant cytoplasmic LysRS has an apparent M(r) of 70,000, viral LysRS associated with tRNA(Lys) packaging is shorter, with an apparent M(r) of 63,000. The truncation occurs independently of viral protease and might be required to facilitate interactions involved in the selective packaging and genomic placement of primer tRNA.