gebhart/patrepeval huggingface dataset:
Site-Directed Mutagenesis of Residues in a Conserved Region of Bovine Aspartyl (Asparaginyl) β-Hydroxylase: Evidence That Histidine 675 Has a Role in Binding Fe2+ (1996)

The roles in catalysis of several residues in bovine aspartyl (asparaginyl) beta-hydroxylase that are located in a region of homology among alpha-ketoglutarate-dependent dioxygenases were investigated using site-directed mutagenesis. Previous studies have shown that when histidine 675, an invariant residue located in this highly conserved region, was mutated to an alanine residue, no enzymatic activity was detected. A more extensive site-directed mutagenesis study at position 675 has been undertaken to define the catalytic role of this essential residue. The partial hydroxylase activity observed with some amino acid replacements for histidine 675 correlates with the potential to coordinate metals and not with size, charge, or hydrophobic character. Furthermore, the increase in Km for Fe2+ observed with the H675D and H675E mutant enzymes can account for their partial activities relative to wild type. No significant changes in the Km for alpha-ketoglutarate (at saturating Fe2+) or Vmax were observed for these mutants. These results support the conclusion that histidine 675 is specifically involved in Fe2+ coordination. Further site-directed mutagenesis of other highly conserved residues in the vicinity of position 675 demonstrates the importance of this region of homology in catalysis for Asp (Asn) beta-hydroxylase and, by analogy, other alpha-ketoglutarate-dependent dioxygenases.
Pilot study assessment of dynamic vascular changes in breast cancer with near-infrared tomography from prospectively targeted manipulations of inspired end-tidal partial pressure of oxygen and carbon dioxide (2013)

The dynamic vascular changes in the breast resulting from manipulation of both inspired end-tidal partial pressure of oxygen and carbon dioxide were imaged using a 30 s per frame frequency-domain near-infrared spectral (NIRS) tomography system. By analyzing the images from five subjects with asymptomatic mammography under different inspired gas stimulation sequences, the mixture that maximized tissue vascular and oxygenation changes was established. These results indicate maximum changes in deoxy-hemoglobin, oxygen saturation, and total hemoglobin of 21, 9, and 3%, respectively. Using this inspired gas manipulation sequence, an individual case study of a subject with locally advanced breast cancer undergoing neoadjuvant chemotherapy (NAC) was analyzed. Dynamic NIRS imaging was performed at different time points during treatment. The maximum tumor dynamic changes in deoxy-hemoglobin increased from less than 7% at cycle 1, day 5 (C1, D5) to 17% at (C1, D28), which indicated a complete response to NAC early during treatment and was subsequently confirmed pathologically at the time of surgery.
Design of an 8-tap CMOS lock-in pixel with lateral electric field charge modulator for highly time-resolved imaging (2017)

Recently, CMOS time-resolved imaging devices are being widely used for scientific and medical applications. A fluorescence lifetime imaging microscopy (FLIM), which is a powerful analysis tool in fundamental physics as well as in the life science, is a typical application for the time-resolved imaging devices. For better time-resolution in the lock-in pixel design, a multi-tap pixel architecture is very effective and useful. In this paper, we have proposed an 8-tap CMOS lock-in pixel with lateral electric field charge modulator (LEFM) and demonstrated the effectiveness of designed pixel by CAD simulation. The proposed pixel makes possible to measure the highly time-resolved images with a high signal to noise ratio (SNR) and to observe various images of cells even if a sample has a multi-lifetime component. An 8-tap time-resolved CMOS image sensor chip is developed by 0.11&mu;m 1P4M CIS process technology.
Center of Excellence in Aerospace Manufacturing Automation (1983)

Abstract : Air Force support of a Center of Excellence at Stanford University has provided the impetus and core for a major new entity, the Center for Automation and Manufacturing Science (CAMS). The new center draws from two well- known research groups at Stanford: the Robotics Group of Stanford's Artificial Intelligence Laboratory and the Automatic Control Group of Stanford's Department of Aeronautics and Astronautics. Ten professors and some 50 graduate students are participating in CAMS activities. CAMS in turn is the first of a new complex of centers at Stanford involved in the manufacturing enterprise: the Stanford Institute for Manufacturing and Automation (SIMA). Strong industrial interaction is a primary objective of SIMA. In our Air Force program we are focusing on robotic aspects of automation. Our goal is to make fundamental contributions to the underlying set of technologies that will enable the next generation of industrial robots to be far more capable than today's - will enable them to be lightweight, limber, deft, facile, quick, friendly, low-powered, seeing, sensing, thinking machines that can reason and strategize- can carry out tasks assigned at a high conceptual level. Specifically, our research focus is on fast, precise control of lightweight (flexible) manipulators, sensing, especially optical and tactile sensing, intelligent systems for robot task management, and computer vision for robot management. We are addressing the question of how to provide manipulator control so good that a whole new generation of manipulators can be developed-manipulators that are much lighter and far more facile than anything today's control systems could stably manage.
Rapid, ultra-low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy in metastatic castration-resistant prostate cancer (mCRPC). (2017)

144 Background: Although cell free DNA (cfDNA) profiling by next generation sequencing (NGS) holds great promise for precision oncology, the inability to estimate tumor content a priori typically results in ultra-deep sequencing (e.g. 10,000x) based approaches—often at limited loci—to ensure accurate assessment of cfDNA samples where tumor content can be &lt; 0.1%. However, a large subset of patients with advanced cancers, where most precision oncology is applied, have much greater cfDNA tumor content. Methods: Here we demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) on benchtop sequencers as a precision medicine screening strategy based on ultra-low coverage (~0.005x) tumor content determination through genome-wide copy number alteration (CNA) profiling using 48 plasma cfDNA samples from patients with advanced cancer. Results: Using this approach, we identified therapeutically relevant focal CNAs in 13 of 48 (27%) cfDNA samples from patients with metastatic cancer, including 11 of 36 (31%) from patients with mCRPC. We further show that PRINCe is effective at whole genome coverages as low as 0.005x. Combining PRINCe with targeted multiplexed-PCR NGS of the same cfDNA enables mutation and CNA assessment using effective coverage as low as 25x based on calibrating sequencing depth to cfDNA tumor content. Lastly, PRINCe identifies pre-treatment cfDNA copy number profiles that can be used for inexpensive disease monitoring. Conclusions: Taken together, our screening approach enables broadly applicable cfDNA based precision oncology for patients with advanced cancer through rapid, inexpensive identification of therapeutically relevant CNAs and pre-treatment genomic profiles for disease monitoring, while also guiding additional cfDNA profiling approaches to reserve costly ultra-deep approaches for patients with very low cfDNA tumor content.
Using Remendable Polymers for Aerospace Composite Structures (2011)

The work described in this research focuses on the development of a single-component remendable polymer suitable for integration into aerospace composite structures. The structural polymer can be used as a replacement matrix material in fiberreinforced composites and allows for in-situ site-specific healing of delamination and matrix cracking when combined with a small volume fraction of heat-assisting materials such as magnetic particles. Whereas previous studies focused on the optimal volume fraction and composition of magnetic particles, and the healing of cracks in carbon-fiber composite coupons, current studies focus on the barriers to adopt this material in a aircraft manufacturing environment. These barriers include the (1) the extensive labor involved in producing a limited quantity of Mendomer (1-3 grams), (2) the evolution and entrapment of voids for all but exquisitely controlled environments, and (3) the low melting temperature (ca. 125°C) of the material when compared against high-temperature matrix systems. Proprietary steps have been formulated to increase raw material yield, reduce viscosity, and increase the glass transition temperature. Interests have also been motivated by reducing costs and adhering to conventional composite fabrication techniques. Research has also involved the investigation of automated damage detection to locate the site of damage for further healing, followed by automated healing since the ultimate goal of this research is to develop an autonomously healing composite system. However, a remendable composite is in itself valuable where its successful incorporation will reduce the need for part replacement and maintenance as well as increase the longevity and reliability of the structure.
Table S1 from EMP2 Is a Novel Regulator of Stemness in Breast Cancer Cells (2023)

&lt;p&gt;Selected functional pathways enriched with EMP2 mRNA based on TCGA data.&lt;/p&gt;
Abstract LB-25: Regulation of Np63α by IκB kinase-β (2010)

Abstract The p53 family (p53, p73, p63) plays an instrumental role in the cellular stress response, including induction of cell cycle arrest and apoptosis in response to DNA damage. In addition to p63 and p73 isotypes capable of transactivating downstream target gene expression (TA isotypes), both genes also express dominant negative inhibitory isoforms, such as ΔNp63α. ΔNp63 is degraded in response to DNA damaging agents, thereby enabling an effective cellular response to genotoxic agents. Here, we identify a key molecular mechanism underlying the regulation of ΔNp63α expression in response to extrinsic stimuli, such as chemotherapeutic agents or TNF-α. We show that ΔNp63α interacts with IκB kinase (IKK), a multisubunit protein kinase that consists of two catalytic subunits, IKKα and IKKβ, and a regulatory subunit, IKKγ (NEMO-NF-κB essential modifier). We find that IKK kinase promotes ubiquitin-mediated proteasomal degradation of ΔNp63α, whereas a kinase-deficient mutant IKK -K44A fails to do so. Cytokine- or chemotherapy-induced stimulation of IKKβ leads to degradation of ΔNp63α and augments trans-activation of p53 family-induced genes involved in the cellular response to DNA damage. Conversely, inhibition of IKKβ with a NEMO-binding peptide or siRNA-mediated silencing IKKβ expression attenuates cytokine- or chemotherapy induced degradation of ΔNp63α. These data demonstrate that IKKβ plays an essential role in regulating ΔNp63α in response to extrinsic stimuli. Our findings suggest that the activation of IKK may be a mechanism by which levels of ΔNp63α are reduced, thereby rendering the cells susceptible to cell death in the face of cellular stress or DNA damage. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-25.
Kronos: a workflow assembler for genome analytics and informatics (2016)

Abstract Background The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into ‘best practices’ for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results We present Kronos , a software platform for automating the development and execution of reproducible, auditable and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. Resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications which can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, promoting and facilitating reproducible research and comparative analyses. We introduce a framework for building Kronos components which function as shareable, modular nodes in Kronos workflows. Conclusion The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon AWS machine images. It is free, open source and available through PyPI (Python Package Index) and https://github.com/jtaghiyar/kronos .
Basic Understanding of the Role of the Interfacial Inversion Layer in the Operation of Silicon Solar Cells with a-Si/c-Si Heterojunction (HIT) (2013)

Valence band offset and valence band bending at the p+ hydrogenated amorphous silicon/n-type crystalline silicon (a-Si:H(p+)/n_c-Si) interface in heterojunction silicon solar cells (HIT) induce a p+ inversion layer which pushes the pn junction 20-25 nm deep in the c-Si side. The heavily hole populated interfacial inversion layer acts as the HIT cell emitter while the ultrathin amorphous silicon layer is the front contact. The impact of doping level and dangling bond defects in the a-Si:H layer and of interface states on the inversion layer properties is investigated by means of AFORS-HET simulations. Apart from the electric field created by the conduction band offset, the HIT cell performs like a c-Si solar cell which has an inversion layer emitter matching that of the HIT cell, with an open circuit voltage of 733 mV. The latter rolls off at relatively large interface (front surface) recombination velocity. Increasing the a-Si:H(p+) doping level modifies the peak hole concentration in the inversion layer and increases the front surface field. On the other hand, c-Si cell with an ultrathin dopant diffused emitter having also the same emitter hole profile sees its performance degraded at relatively low surface reombination because it suffers from bandgap narrowing and from doping dependent mobility degradation and has no front surface field. Inserting an ultrathin intrinsic or lowly doped a-Si:H spacer between a-Si:H(p+) and c-Si provides less hole population in the inversion layer which reduces Auger recombination and improves the open circuit voltage at low surface recombination to 735 mV despite the less effective front surface field.
An Evaluation of Water Quality at Fort Monmouth, New Jersey, Using the EPANET Model. (1995)

Abstract: Under the Facilities Engineering Applications Program, the U.S. Army Corps of Engineers wanted to test the capability of the EPANET computer model for evaluating water quality in water distribution systems. Fort Monmouth, New Jersey, has experienced low chlorine residuals levels. The EPANET model was calibrated using hydrant flow tests to predict chlorine die-off in the distribution system at the Fort. The model was then used to compare the effects of flushing and chlorine addition to improve water quality. Because of the high chlorine die-off rates in warm weather, it appears that chlorine addition is the only way to significantly improve chlorine residuals during summer months.
Identification of proteins of the yeast protein map using genetically manipulated strains and peptide-mass fingerprinting. (1996)

In this study we used genetically manipulated strains in order to identify polypeptide spots of the protein map of Saccharomyces cerevisiae. Thirty-two novel polypeptide spots were identified using this strategy. They corresponded to the product of 23 different genes. We also explored the possibilities of using peptide-mass fingerprinting for the identification of proteins separated on our gels. According to this strategy, proteins contained in spots are digested with trypsin and the masses of generated peptides are determined by matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). The peptide masses are then used to search a yeast protein database for proteins that match the experimental data. Application of this strategy to previously identified polypeptide spots gave evidence of the feasibility of this approach. We also report predictions on the identities of nine unknown spots using MALDI-MS.
Metal-graphite reagents in carbohydrate chemistry. 8. The scope and limitations of the use of zinc/silver-graphite in the synthesis of carbohydrate-derived substituted hex-5-enals and pent-4-enals [Erratum to document cited in CA114(15):143819g] (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-graphite reagents in carbohydrate chemistry. 8. The scope and limitations of the use of zinc/silver-graphite in the synthesis of carbohydrate-derived substituted hex-5-enals and pent-4-enals [Erratum to document cited in CA114(15):143819g]Alois Fuerstner, Denis Jumbam, Judith Teslic, and Hans WeidmannCite this: J. Org. Chem. 1991, 56, 20, 5965Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/jo00020a054https://doi.org/10.1021/jo00020a054research-articleACS PublicationsRequest reuse permissionsArticle Views107Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Real-time smoke and flame detection in video (2006)

A novel method to detect smoke and/or flame by processing the video data generated by an ordinary camera monitoring a scene is proposed. It is assumed the camera is stationary. Since the smoke is semi-transparent, edges of image frames start loosing their sharpness and this leads to a decrease in the high frequency content of the image. To determine the smoke, the background of the scene is estimated and decrease of high frequency energy of the scene is monitored using the spatial wavelet transforms of the current and the background images. For the detection of flames, in addition to ordinary motion and color clues, flicker analysis is also carried out by analyzing the video in wavelet domain. These clues are combined to reach a final decision.
Joint Symbol-Level Precoding and Sub-Block-Level RIS Design for Dual-Function Radar-Communications (2023)

In the symbol-level precoding (SLP) based wireless systems, the reconfigurable intelligent surface (RIS) is usually configured on a block level, which causes a mismatch to the SLP design in terms of update rate. Although it is expected that updating both the RIS and precoding on the symbol level could boost the system performance, the requirements for synchronization and system overhead will become demanding inevitably. In this paper, we consider the RIS-aided dual-function radar-communication (DFRC) system and investigate the benefit of increasing the RIS updating frequency. We jointly design the SLP and RIS to maximize the target illumination power while satisfying the power budget and the multiuser multiple input single output (MU-MISO) communication quality of service (QoS) requirements, where the RIS is updated multiple times in a block (at a sub-block level). Through the simulation results, we demonstrate the optimized trade-off between system performance and RIS update rate.
Mechanical assessment of two hybrid plate designs for pancarpal canine arthrodesis under cyclic loading (2023)

Pancarpal canine arthrodesis (PCA) sets immobilization of all three carpal joints <i>via</i> dorsal plating to result in bony fusion. Whereas the first version of the plate uses a round hole (RH) for the radiocarpal (RC) screw region, its modification into an oval hole (OH) in a later version improves versatility in surgical application. The aim of this study was to mechanically investigate the fatigue life of the PCA plate types implementing these two features-PCA-RH and PCA-OH. Ten PCA-RH and 20 PCA-OH stainless steel (316LVM) plates were assigned to three study groups (n = 10). All plates were pre-bent at 20° and fixed to a canine forelimb model with simulated radius, RC bone and third metacarpal bone. The OH plates were fixed with an RC screw inserted either most proximal (OH-P) or most distal (OH-D). All specimens were cyclically tested at 8 Hz under 320 N loading until failure. Fatigue life outcome measures were cycles to failure and failure mode. Cycles to failure were higher for RH plate fixation (695,264 ± 344,023) <i>versus</i> both OH-P (447,900 ± 176,208) and OH-D (391,822 ± 165,116) plate configurations, being significantly different between RH and OH-D, <i>p</i> = 0.03. No significant difference was detected between OH-P and OH-D configurations, <i>p</i> = 0.09. Despite potential surgical advantages, the shorter fatigue life of the PCA-OH plate design may mitigate its benefits compared to the plate design with a round radiocarpal screw hole. Moreover, the failure risk of plates with an oval hole is increased regardless from the screw position in this hole. Based on these findings, the PCA plate with the current oval radiocarpal screw hole configuration cannot be recommended for clinical use.