gebhart/patrepeval huggingface dataset:
Human Chk1 expression is dispensable for somatic cell death and critical for sustaining G2 DNA damage checkpoint. (2003)

Mammalian Chk1 is an essential kinase for embryonic development and plays an important role in the cellular response to DNA damage. However, it remains unclear whether inhibition of Chk1 induces apoptosis in somatic cells. The uncertainty has become a critical issue for rationale design of Chk1 mechanism-based anticancer drugs. Here we show that Chk1 small interfering RNA (siRNA) effectively eliminates Chk1 protein expression without altering the cell cycle profile or inducing apoptosis in various human cancer cell lines under normal conditions. In the presence of DNA-damaging agents, however, Chk1 siRNA alone is sufficient to abrogate the DNA damage-induced G(2) checkpoint and significantly enhance apoptosis. Cell cycle kinetic profiles show that abrogation of G(2) arrest is mediated through shortening of the checkpoint. We also demonstrate that Chk1 siRNA enhances DNA damage-induced apoptosis in p53-deficient cancer cell lines and augments the growth inhibition conferred by DNA-damaging agents. These findings imply that Chk1 inhibitors will have low cytotoxicity on their own and can enhance the efficacy of DNA-damaging drugs.
P3–064: Characterizing the Alzheimer's disease prefrontal cortex transcriptome by multiple RNA‐sequencing (2013)

The goal of this project is to elucidate what, if any, transcriptomic differences are associated with the Alzheimer's disease state in the prefrontal cortex. Specifically, not only would we would like to determine which mRNAs are differentially expressed, but we would also like to examine differences in all non-coding RNAs (short and long), including those that are not currently annotated. Total RNA was extracted from human prefrontal cortex samples. Using a modified version of the Illumina strand-specific small RNA sequencing protocol, two types of cDNA libraries were produced. The first set of libraries are simply small RNAs as indicated by Illumina's protocol. The second set comprise a whole transcriptome library, where total RNA was subjected to a Ribominus treatment in order to deplete ribosomal RNA, and then fragmented before being used in the strand-specific (RNA ligation) protocol. We obtained a total of 31,000,000 unique reads covering the small RNA transcriptomes of 7 distinct samples. Among the small RNAs we were able to quantify are microRNAs, tRNA-fragments, and small RNAs derived from a variety of non-coding RNAs in the cell. Sixteen of the microRNAs are differentially expressed in the AD prefrontal cortex. We also found that many tRNA-derived small RNAs are differentially expressed in AD. Intriguingly, we found 42 completely unannotated small RNA loci that are differentially expressed in AD. In addition, we obtained70,000,000 unique reads covering the non-ribosomal RNA transcriptome across the same samples. Using this data we inferred that 121 protein-coding mRNAs and 66 non-coding RNAs are differentially expressed in AD. Overrepresented among the ncRNAs are molecules such as snoRNAs. The differential expression of tRNA-derived RNAs merits further investigation as these show the greatest degree of difference. The mRNAs found to be different in the whole transcriptome are highly consistent with what is known about the AD state, but there are several interesting new candidates that have not been reported, including several noncoding RNAs.
Synthesis and mesomorphic properties of naphth-2-yl 2-pyridylmethyl ketones and their copper (II) complexes (1996)

Abstract The synthesis, characterization and mesomorphic properties of a homologous series of 6-alkoxy naphth-2-yl 2-pyridylmethyl ketones and their copper(II) complexes are reported. All the ligands and their copper complexes, with exception of the lowest homologues, exhibit enantiotropic mesophases. According to textural observations, the ligands display nematic and smectic transitions depending on the length of the alkoxy chain on the pyridine moiety, while the mesogenic complexes show exclusively smectic transitions. In comparison with the phenyl analogues, stabilization of the mesophase and a greater tendency to smectic ordering through incorporation of the naphthyl group into the molecules is confirmed.
Material Development for Tooling Applications Using Big Area Additive Manufacturing (BAAM) (2015)

Techmer Engineered Solutions (TES) is working with Oak Ridge National Laboratory (ORNL) to develop materials and evaluate their use for ORNL's recently developed Big Area Additive Manufacturing (BAAM) system for tooling applications. The first phase of the project established the performance of some commercially available polymer compositions deposited with the BAAM system. Carbon fiber reinforced ABS demonstrated a tensile strength of nearly 10 ksi, which is sufficient for a number of low temperature tooling applications.
Recent Advances in Atomic Layer Deposition (2016)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTRecent Advances in Atomic Layer DepositionNeil P. Dasgupta, Han-Bo-Ram Lee, Stacey F. Bent, and Paul S. WeissView Author Information University of Michigan, Ann Arbor, Michigan Incheon National University, Incheon, KoreaCite this: Chem. Mater. 2016, 28, 7, 1943–1947Publication Date (Web):April 12, 2016Publication History Published online12 April 2016Published inissue 12 April 2016https://pubs.acs.org/doi/10.1021/acs.chemmater.6b00673https://doi.org/10.1021/acs.chemmater.6b00673editorialACS PublicationsCopyright © 2016 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views7919Altmetric-Citations75LEARN 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 PDF (195 KB) Get e-AlertscloseSUBJECTS:Atomic layer deposition,Deposition,Electrodes,Oxides,Thin films Get e-Alerts
Carbon Nanotubes, Phthalocyanines and Porphyrins: Attractive Hybrid Materials for Electrocatalysis and Electroanalysis (2009)

The manuscript discusses different ways of forming hybrid materials between single (SWCNT) or multi (MWCNT) walled carbon nanotubes and biomimetic compounds such as metalloporphyrins, metallophthalocyanines and other MN4 complexes. The hybrid materials are employed for electrocatalysis of reactions such as oxygen and hydrogen peroxide reduction, nitric oxide oxidation, oxidation of thiols and other pollutants. Methods of characterizing the hybrid materials such as cyclic voltammetry (CV), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM) are discussed.
Biopolymer based nanocomposite ionogels: high performance, sustainable and solid electrolytes (2013)

Ionogels based on a chemically cross-linked polysaccharide matrix and a hydrophobic ionic liquid offer a sustainable alternative to petrochemical-based polymer electrolytes.
Supplementary Figure Legends from Reversal of NK-Cell Exhaustion in Advanced Melanoma by Tim-3 Blockade (2023)

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NeurOCS: Neural NOCS Supervision for Monocular 3D Object Localization (2023)

Monocular 3D object localization in driving scenes is a crucial task, but challenging due to its ill-posed nature. Estimating 3D coordinates for each pixel on the object surface holds great potential as it provides dense 2D-3D geometric constraints for the underlying PnP problem. However, high-quality ground truth supervision is not available in driving scenes due to sparsity and various artifacts of Lidar data, as well as the practical infeasibility of collecting per-instance CAD models. In this work, we present NeurOCS, a framework that uses instance masks and 3D boxes as input to learn 3D object shapes by means of differentiable rendering, which further serves as supervision for learning dense object coordinates. Our approach rests on insights in learning a category-level shape prior directly from real driving scenes, while properly handling single-view ambiguities. Furthermore, we study and make critical design choices to learn object coordinates more effectively from an object-centric view. Altogether, our framework leads to new state-of-the-art in monocular 3D localization that ranks 1st on the KITTI-Object benchmark among published monocular methods.
An Unprecedented Approach to 4,5-Disubstituted Pyrimidine Derivatives by a ZnCl2-Catalyzed Three-Component Coupling Reaction (2009)

We have developed a ZnCl(2)-catalyzed three-component coupling reaction involving a variety of functionalized enamines, triethyl orthoformate, and ammonium acetate, which leads to the production of 4,5-disubstituted pyrimidine derivatives in a single step. The procedure can be successfully applied to the efficient synthesis of mono- and disubstituted pyrimidine derivatives, using methyl ketone derivatives instead of enamines.
The Communications Scheduler: A Task Scheduling Mitigation For A Closed Loop Adaptive System (2005)

This paper describes the Communications Scheduler, an adaptive system mitigation designed to scheduler incoming messages to improve message comprehension and situation awareness. The U.S. Army is currently defining the roles of the 2010-era Future Force Warrior (FFW) program, which seeks to push information exchange requirements to the lowest levels and posits that with enhanced capabilities a squad can cover the battlefield in the same way that a platoon now does. Among other capabilities, the application of a full range of netted communications and collaborative situational awareness will afford the FFW unparalleled knowledge and expand the effect of the Future Force three dimensionally. It is expected that in a highly networked environment the sheer magnitude of communication traffic could overwhelm the individual soldier. The Honeywell Augmented Cognition team has developed the Communications Scheduler, a task scheduling mitigation driven by real-time neurophysiological and physiological measurements of human cognitive state, which is used to augment the work environment to improve human-automation joint performance. Evaluations have shown over at least a 100 % improvement in message comprehension an situation awareness.
Exploring and troubleshooting istio issues (2019)

Cloud computing gave rise to a Cloud-native[1] approach for operating application software in the cloud, whereby applications are segmented into micro-services that can be designed and deployed independently of each other. This significantly increases application maintainability, reduces time to market, and helps leveraging cloud computing model. On the other hand, this approach increases the system level complexity of the application and poses new challenges, such as how services discover each other, and how application handles individual service upgrades. To support cloud-native paradigm, new development, deployment, and orchestration tools are created. One of such tools is Istio [2] service mesh, built to connect, secure, control, and observe services. While immensely useful to application developers, Istio is an additional layer in cloud compute platform software stack and is thus prone to failure or misuse.
Palladium-Catalyzed Suzuki-Type Cross-Couplings of Iodocyclopropanes with Boronic Acids:  Synthesis of trans-1,2-Dicyclopropyl Alkenes (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPalladium-Catalyzed Suzuki-Type Cross-Couplings of Iodocyclopropanes with Boronic Acids: Synthesis of trans-1,2-Dicyclopropyl AlkenesAndré B. Charette and André GirouxView Author Information Département de Chimie, Université de Montréal, Québec H3C 3J7, Canada Cite this: J. Org. Chem. 1996, 61, 25, 8718–8719Publication Date (Web):December 13, 1996Publication History Received31 July 1996Published online13 December 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo9614654https://doi.org/10.1021/jo9614654rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2263Altmetric-Citations81LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Anions,Coupling reactions,Cross coupling reaction,Organic compounds,Vinyl Get e-Alerts
ChemInform Abstract: Preparation of Carbocyclic, Phosphonate Analogues of Cyclic Adenosine Monophosphate (cAMP). (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Invasive fungal infection of the central nervous system in a patient with acute myeloid leukaemia. (2012)

A fast improvement in the clinical condition of the patient after the applied antifungal therapy and the regression of lesions in the central nervous system shown in the imaging studies confirmed our final diagnosis.
Physical mechanisms of longitudinal vortices formation, appearance of zones with high heat fluxes and early transition in hypersonic flow over delta wing with blunted leading edges (2016)

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Simulation study of the ability of a computationally‐designed peptide to recognize target tRNALys3 and other decoy tRNAs (2016)

In this paper, we investigate the ability of our computationally-designed peptide, Pept10 (PNWNGNRWLNNCLRG), to recognize the anticodon stem and loop (ASL) domain of the hypermodified tRNA<sup>Lys3</sup> (mcm<sup>5</sup> s<sup>2</sup> U<sub>34</sub> ,ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> ), a reverse transcription primer of HIV replication. Five other ASLs, the singly modified ASL<sup>Lys3</sup> (ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> ), ASL<sup>Lys3</sup> (s<sup>2</sup> U<sub>34</sub> ), ASL<sup>Lys3</sup> (Ψ<sub>39</sub> ), ASL<sup>Lys1,2</sup> (t<sup>6</sup> A<sub>37</sub> ), and ASL<sup>Glu</sup> (s<sup>2</sup> U<sub>34</sub> ), were used as decoys. Explicit-solvent atomistic molecular dynamics simulations were performed to examine the process of binding of Pept10 with the target ASL<sup>Lys3</sup> (mcm<sup>5</sup> s<sup>2</sup> U<sub>34</sub> ,ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> ) and the decoy ASLs. Simulation results demonstrated that Pept10 is capable of recognizing the target ASL<sup>Lys3</sup> (mcm<sup>5</sup> s<sup>2</sup> U<sub>34</sub> ,ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> ) as well as one of the decoys, ASL<sup>Lys3</sup> (Ψ<sub>39</sub> ), but screens out the other four decoy ASLs. The interchain van der Waals (VDW) and charge-charge (ELE + EGB) energies for the two best complexes were evaluated to shed light on the molecular recognition mechanism between Pept10 and ASLs. The results indicated that Pept10 recognizes and binds to the target ASL<sup>Lys3</sup> (mcm<sup>5</sup> s<sup>2</sup> U<sub>34</sub> ,ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> ) through residues W<sub>3</sub> and R<sub>7</sub> which interact with the nucleotides mcm<sup>5</sup> s<sup>2</sup> U<sub>34</sub> , U<sub>35</sub> , and ms<sup>2</sup> t<sup>6</sup> A<sub>37</sub> via the interchain VDW energy. Pept10 also recognizes the decoy ASL<sup>Lys3</sup> (Ψ<sub>39</sub> ) through residue R<sub>14</sub> which contacts the nucleotide U<sub>36</sub> via the interchain VDW energy. Regardless of the type of ASL, the positively charged arginines on Pept10 are attracted to the negatively charged phosphate linkages on the ASL via the interchain ELE + EGB energy, thereby enhancing the binding affinity.
Gene therapy for treatment of cerebral ischemia using defective herpes simplex viral vectors (2001)

Significant advances have been made over the past few years concerning the cellular and molecular events underlying neuron death. Recently, it is becoming increasingly clear that some of the genes induced during cerebral ischemia may actually serve to rescue the cell from death. However, the injured cell may not be capable of expressing protein at levels high enough to be protective. One of the most exciting arenas of such interventions is the use of viral vectors to deliver potentially neuroprotective genes at high levels. Neurotrophic herpes simplex viral strains are an obvious choice for gene therapy to the brain, and we have utilized bipromoter vectors that are capable of transferring various genes to neurons. Using this system in experimental models of stroke, cardiac arrest and excitotoxicity, we have found that it is possible to enhance neuron survival against such cerebral insults by over-expressing genes that target various facets of injury. These include energy restoration by the glucose transporter (GLUT-1), buffering calcium excess by calbindin, preventing protein malfolding or aggregation by stress proteins and inhibiting apoptotic death by BCL-2. We show that in some cases, gene therapy is also effective after the onset of injury, and also address whether successful gene therapy necessarily spares function. Although gene therapy is limited to the few hundred cells the vector is capable of transfecting, we consider the possibility of such gene therapy becoming relevant to clinical neurology in the future.
Vehicle speed prediction using a cooperative method of fuzzy Markov model and auto-regressive model (2017)

Vehicle speed prediction can benefit a wide range of vehicle control designs, especially for fuel economy applications. This paper shows a computationally light vehicle short term speed predictor designed for on-board implementation, using minimal information of speed measurement only. The predictor generalizes historical speed data's underlying pattern and predicts from probability aspect. One novelty of the method is the usage of fuzzy modeling to eliminate the resolution limitation in vehicle acceleration state definition, classification, and prediction. The method uses Auto-regressive (AR) model to capture vehicle speed data's short term dynamics, and classifies the data into multiple acceleration states by fuzzy membership. In the prediction process, acceleration measurements are mapped to the Markov states by fuzzy encoding, and future acceleration states are predicted by Markov transition. Deterministic speed prediction is calculated from the trained AR models, which are selected by fuzzy state membership similarity. The developed predictor is tested with a vehicle's real urban driving data, and the effectiveness of the incorporated techniques is verified by a comparison study.
Virtual-freezing fluorescence imaging flow cytometry with 5-aminolevulinic acid stimulation and antibody labeling for detecting all forms of circulating tumor cells (2023)

Circulating tumor cells (CTCs) are precursors to cancer metastasis. In blood circulation, they take various forms such as single CTCs, CTC clusters, and CTC-leukocyte clusters, all of which have unique characteristics in terms of physiological function and have been a subject of extensive research in the last several years. Unfortunately, conventional methods are limited in accurately analysing the highly heterogeneous nature of CTCs. Here we present an effective strategy for simultaneously analysing all forms of CTCs in blood by virtual-freezing fluorescence imaging (VIFFI) flow cytometry with 5-aminolevulinic acid (5-ALA) stimulation and antibody labeling. VIFFI is an optomechanical imaging method that virtually freezes the motion of fast-flowing cells on an image sensor to enable high-throughput yet sensitive imaging of every single event. 5-ALA stimulates cancer cells to induce the accumulation of protoporphyrin (PpIX), a red fluorescent substance, making it possible to detect all cancer cells even if they show no expression of the epithelial cell adhesion molecule, a typical CTC biomarker. Although PpIX signals are generally weak, VIFFI flow cytometry can detect them by virtue of its high sensitivity. As a proof-of-principle demonstration of the strategy, we applied cancer cells spiked in blood to the strategy to demonstrate image-based detection and accurate classification of single cancer cells, clusters of cancer cells, and clusters of a cancer cell(s) and a leukocyte(s). To show the clinical utility of our method, we used it to evaluate blood samples of four breast cancer patients and four healthy donors and identified EpCAM-positive PpIX-positive cells in one of the patient samples. Our work paves the way toward the determination of cancer prognosis, the guidance and monitoring of treatment, and the design of antitumor strategies for cancer patients.
Nanostenciling for fabrication and interconnection of nanopatterns and microelectrodes (2007)

Stencil lithography is used for patterning and connecting nanostructures with metallic microelectrodes in ultrahigh vacuum. Microelectrodes are fabricated by static stencil deposition through a thin silicon nitride membrane. Arbitrary nanoscale patterns are then deposited at a predefined position relative to the microelectrodes, using as a movable stencil mask an atomic force microscopy (AFM) cantilever in which apertures have been drilled by focused ion beam. Large scale AFM imaging, combined with the use of a high precision positioning table, allows inspecting the microelectrodes and positioning the nanoscale pattern with accuracy better than 100nm.