gebhart/patrepeval huggingface dataset:
Abstract C151: Systematic discovery of cancer dependencies through deep coverage pshRNA screens (2015)

Abstract Large scale cancer genome sequencing efforts, such as TCGA, revealed the landscape of genomic alterations across many tumor types, but the functional relevance of these alterations and genetic interdependencies cannot be fully assessed from these datasets. Thus, functional genomic screens, such as pooled shRNA 9pshRNA) screens, hold great promise to systematically identify cancer dependencies. However, RNAi discovery screens have been plagued by off target effects causing false positive results and possibly masking on-target effects. In order to address the previous problems with RNAi screens for cancer target discovery, we conducted a large scale pshRNA screening campaign targeting 7500 genes at a depth of 20 shRNAs per gene, across more than 300 cell lines of the cancer cell line encyclopedia (CCLE). The substantial shRNA and cell line depth in this screen significantly increased the robustness of results relative to previous published screens, and allowed the more robust identification of cancer dependencies. Moreover, integration of those growth phenotypes with known features of the cancer cell line encyclopedia (CCLE) enabled the identification of biomarkers (genetic, epigenetic, or proteomic) that correlate with sensitivity, and thus permitted discovery of synthetic lethal relationships. The increased depth provides a robust data set that can be used to find and validate new drug targets as well as infer pathway membership of novel genes by simple phenotypic similarity. The findings of this screen will be presented here. Citation Format: Michael Schlabach, Eric Billy, Konstantinos Mavrakis, Greg Hoffman, Tobias Schmelzle, Francesco Hofmann, Nicholas Keen, Frank Stegmeier, William Sellers. Systematic discovery of cancer dependencies through deep coverage pshRNA screens. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C151.
Debunking the July Effect Myth (2016)

Los Angeles County University of Southern California (LAC+USC) Medical Center Los Angeles, CA [email protected] The authors disclose no conflict of interest.
Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination (2023)

Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.
Synthesis of glycosyl phosphates using the Fraser-Reid activation (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of glycosyl phosphates using the Fraser-Reid activationPatrick Pale and George M. WhitesidesCite this: J. Org. Chem. 1991, 56, 14, 4547–4549Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/jo00014a043https://doi.org/10.1021/jo00014a043research-articleACS PublicationsRequest reuse permissionsArticle Views284Altmetric-Citations27LEARN 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
Thyroid hormone inhibits pulmonary fibrosis through enhancement of mitochondrial function in alveolar epithelial cells (2016)

Background: Idiopathic Pulmonary Fibrosis (IPF) lungs are characterized by increased numbers of damaged mitochondria. Thyroid hormone (TH) is critical for maintenance of mitochondrial homeostasis during stress responses, but its role in lung fibrosis is unknown. Objective: To determine the role of TH signaling in lung fibrosis. Methods and Results: Reanalysis of the Lung Genomic Research Consortium (LGRC) dataset revealed that DIO2 was among the most significantly increased genes in IPF lungs compared to controls (9 fold, p < 0.001). DIO2 mRNA, protein and enzymatic activity were significantly increased in IPF lungs compared to controls (8, 3 and 3.5-fold, respectively p < 0.001). Genetic ablation of DIO2 or inhibition of TH synthesis by propylthiouracil enhanced bleomycin-induced lung fibrosis as assessed by significant increases in: a) hydroxyproline (1.35-fold, p < 0.05), b) Masson Trichrome staining and c) modified Ashcroft score (2fold, p < 0.05). Aerosolized TH delivery reversed bleomycininduced fibrosis as assessed by significant reductions in: a) hydroxyproline (1.4 fold, p < 0.05) and b) Masson Trichrome staining (Figure). Bleomycin injury caused mitochondrial dysfunction in primary murine alveolar type II epithelial cells (AECIIs) while TH therapy reversed these abnormalities and induced regulators of mitochondrial function, peroxisome proliferator-activated receptor gamma coactivator alpha (PPARGC1A) and PTENinduced putative kinase 1 (PINK1) (1.5-and 1.8-fold, respectively, p < 0.05). TH treatment did not blunt fibrosis in PPARGC1A or PINK1 knockout mice, suggesting that TH anti-fibrotic effects are mediated through PPARGC1A and PINK1. Conclusions: We conclude that TH treatment is protective against fibrotic lung injury through restoration of AECIIs mitochondrial homeostasis and may represent an effective therapy for IPF.
Should Postmastectomy Radiotherapy to the Chest Wall and Regional Lymph Nodes Be Standard for Patients with 1–3 Positive Lymph Nodes? (2011)

The indication for adjuvant postmastectomy radiotherapy (PMRT) in breast cancer patients with small tumors and 1-3 macrometastases in the axilla remains a controversial issue, despite the recommendation that PMRT should be applied in these patients in the most recent overview by the Early Breast Cancer Trialists' Collaborative Group. In this report, we discuss the available data on the benefit from PMRT in patients diagnosed with N1 breast cancer. Based on this, we recommend adjuvant PMRT to the chest wall and regional lymph nodes in patients diagnosed with early node-positive breast cancer.
<italic>Bradyrhizobium elkanii</italic> Induces Outer Cortical Root Swelling in Soybean (1995)

When soybean roots were inoculated with Bradyrhizobium elkanii USDA76, USDA94 or USDA31, a localized swelling of the root outer cortical cells was observed within 10 days after inoculation. This phenotype was designated outer cortical swelling (OCS). OCS was not observed in roots inoculated with B.japonicum USDA110 or USDA122. Therefore, the OCS response appears to be specific for B. elkanii. To determine the involvement of the nodulation genes in OCS formation, we constructed a nod- mutant, strain USDA94δNOD, of B. elkanii USDA94 in which the nodD2D1KABC genes were deleted. An OCS response was observed on roots inoculated with USDA94δNOD, indicating that the lipo-chitin nodulation signals synthesized by the nodABC gene products are not required for OCS formation.
Design of a network-based mobile gait rehabilitation system (2012)

In this paper, a network-based mobile gait rehabilitation system is proposed for improved mobility and tele-rehabilitation. In this system, an Internet-based body sensor network is employed for health monitoring and a local highspeed wireless network is developed to achieve precise control of the gait rehabilitation device, which is a compact rotary elastic actuator (cRSEA). A new wireless protocol called MBStarPlus is proposed to achieve a high sampling rate and real-time communication. To deal with packet loss in the wireless network, a modified linear quadratic Gaussian (LQG) controller is combined with a disturbance observer (DOB) to control the cRSEA over the wireless network. Successful system integration and promising experimental results validate both the system design and proposed control algorithm. The plan for clinical testing with the proposed system is discussed.
Novel dihydrobenzofuro[4,5-b][1,8]naphthyridin-6-one derivative, MHY-449, induces cell cycle arrest and apoptosis via the downregulation of Akt in human lung cancer cells (2015)

The anticancer properties of MHY-449, a novel dihydrobenzofuro[4,5-b][1,8]naphthyridin-6-one derivative, in various human cancer cell lines have been previously reported. The aim of the present study was to investigate the activities of MHY-449 on human lung cancer cells in order to elucidate its underlying molecular mechanisms of action. The result showed that MHY-449 treatment inhibited cell growth in a time- and concentration‑dependent manner. Specifically, MHY-449 induced cell cycle arrest at the S phase, and the resulting increased sub-G1 fraction led to the induction of apoptosis, as determined by flow cytometric analysis and DNA fragmentation. In addition, MHY-449 was shown to induce alterations in the ratio of Bax/Bcl-2 protein expression, and contribute to the loss of mitochondrial membrane potential. These cellular events then triggered the caspase cascade and subsequent poly(ADP‑ribose) polymerase cleavage. The apoptotic cell death induced by MHY-449 was inhibited by pretreatment with Z-VAD‑FMK, a pan-caspase inhibitor. Moreover, MHY-449 downregulated the phosphorylation of Akt, and the phosphatidylinositol-3 kinase/Akt inhibitor LY294002 was found to enhance its induction of apoptosis. Taken together, the results suggested that MHY-449 exerts anticancer effects by promoting cell cycle arrest and apoptosis via the downregulation of Akt. Based on these data, MHY-449 serves as a potential candidate in the chemoprevention and/or treatment of lung cancer.
Supplementary Figure S1 from Safety, Outcomes, and T-Cell Characteristics in Patients with Relapsed or Refractory MDS or CMML Treated with Atezolizumab in Combination with Guadecitabine (2023)

&lt;p&gt;Median overall survival was longer among patients whose T cells harbored ASXL1 mutations (green) than for those without the mutation (red) or with only myeloid mutations (blue), but ASXL1 mutation status was not associated with survival in a univariate analysis by the logrank test (p=0.11). In a multivariate analysis using a Cox proportional model and adjusted by age at study entry, gender, diagnosis, and the number of prior treatment regimens, ASXL1 was significantly associated with survival (p=0.001 based on likelihood ratio test).&lt;/p&gt;
Coherent structures in turbulent boundary layers with adverse pressure gradients (2010)

The coherent structures in turbulent boundary layers (TBLs) subjected to adverse pressure gradients (APGs) were investigated by analyzing a database of direct numerical simulations. The equilibrium adverse pressure gradient flows were established by using a power law free-stream distribution. The population trends of the spanwise vortices show that the outer regions of the APG TBLs are densely populated with hairpin-like vortices. These vortical structures induce low-momentum regions in the middle of the boundary layers, which result in an outer peak in the Reynolds shear stress. The 3-D features of the hairpin packets were deduced from their spatial characteristics in the spanwise-wall-normal plane. The conditionally averaged velocity fields show that there are counter-rotating v &amp; w swirling motions that represent cross-sectional evidences of the packets. Moreover, two-point correlations and linear stochastic estimations were used to provide statistical information about the hairpin packet motions in the cross-stream planes of the APG TBLs.
Automobile Pollution Is a Disease (1991)

Brief article printed on a grocery bag in Benicia, CA.
Evidence for Gas Exchange in Single-Bubble Sonoluminescence (1998)

In this Letter we describe measurements of the light emission evolution for single-bubble sonoluminescence. In particular, we show that the evolution of intensity for an air bubble depends on whether or not the bubble has previously been in a steady sonoluminescence state. Our results provide strong experimental evidence in support of the recent hypothesis that an air bubble undergoing single-bubble sonoluminescence in water transitions to an argon bubble.
Serum cholesterol levels and suicidal tendencies in psychiatric inpatients. (1994)

Our findings may imply that an association exists between cholesterol, suicide, and depression.
Thermal-Power Delivery Network Co-Analysis for Multi-Die Integration (2018)

In this paper, we present a thermal-power delivery network (PDN) co-analysis framework to analyze various multi-die integration schemes. In the proposed approach, we capture the interdependencies between temperature distribution of the dice in a package and the supply voltage noise. We use standalone thermal and PDN analyses as references to compare our co-analysis results. Using a multi-die package and a bridge-based 2.5-D package case studies, our analysis shows a 10-12% overestimation in steady-state temperature and power supply noise.
Highly Specific Sigma Receptor Ligands Exhibit Anti-Viral Properties in SARS-CoV-2 Infected Cells (2021)

(1) Background: There is a strong need for prevention and treatment strategies for COVID-19 that are not impacted by SARS-CoV-2 mutations emerging in variants of concern. After virus infection, host ER resident sigma receptors form direct interactions with non-structural SARS-CoV-2 proteins present in the replication complex. (2) Methods: In this work, highly specific sigma receptor ligands were investigated for their ability to inhibit both SARS-CoV-2 genome replication and virus induced cellular toxicity. This study found antiviral activity associated with agonism of the sigma-1 receptor (e.g., SA4503), ligation of the sigma-2 receptor (e.g., CM398), and a combination of the two pathways (e.g., AZ66). (3) Results: Intermolecular contacts between these ligands and sigma receptors were identified by structural modeling. (4) Conclusions: Sigma receptor ligands and drugs with off-target sigma receptor binding characteristics were effective at inhibiting SARS-CoV-2 infection in primate and human cells, representing a potential therapeutic avenue for COVID-19 prevention and treatment.
Vesicle Membrane Thickness in Aqueous Dispersions of Block Copolymer Blends (2008)

ADVERTISEMENT RETURN TO ISSUECommunication to the...Communication to the EditorNEXTVesicle Membrane Thickness in Aqueous Dispersions of Block Copolymer BlendsKevin P. Davis†, Timothy P. Lodge†‡, and Frank S. Bates*†View Author Information Department of Chemical Engineering and Materials Science and Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455* To whom correspondence should be addressed: e-mail [email protected]†Department of Chemical Engineering and Materials Science.‡Department of Chemistry.Cite this: Macromolecules 2008, 41, 22, 8289–8291Publication Date (Web):October 24, 2008Publication History Received21 August 2008Revised8 October 2008Published online25 October 2008Published inissue 25 November 2008https://pubs.acs.org/doi/10.1021/ma801902zhttps://doi.org/10.1021/ma801902zrapid-communicationACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views1799Altmetric-Citations25LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Copolymers,Membranes,Micelles,Thickness,Vesicles Get e-Alerts
Expression of functional mGlu5 metabotropic glutamate receptors in human melanocytes (2000)

Cultured human melanocytes express mGlu5 metabotropic glutamate (mGlu) receptors, as shown by RT-PCR, immunocytochemistry, Western blot analysis, and measurement of agonist-stimulated polyphosphoinositide hydrolysis. The mGlu5 receptor agonists (S)-3,5-dihydroxyphenylglycine and quisqualate increased [3H-methyl]thymidine incorporation and melanocyte proliferation in subconfluent cultures, but impaired cell viability in confluent cultures. Both effects were prevented by 2-methyl-6-(2-phenyl-1-ethynyl)-pyridine, a potent and highly selective mGlu5 receptor antagonist. Agonists of other mGlu receptor subtypes (such as the mGlu2/3 receptor agonist, 2S,2′R,3′R-2–2′,3′-dicarboxycyclopropylglycine, or the mGlu4/6/7/8 receptor agonist, L-2-amino-4-phosphonobutanoate) or selective agonists of ionotropic glutamate receptors (N-methyl-D-aspartate, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate, and kainate) did not affect melanocyte proliferation or viability. The presence of a receptor for glutamate, the major excitatory neurotransmitter, in human melanocytes is intriguing. mGlu5 receptors may be involved in the control of melanocyte proliferation (and perhaps in other functions), but harbor a potential toxicity and may therefore contribute to cell damage under pathological conditions. J. Cell. Physiol. 183:364–372, 2000. © 2000 Wiley-Liss, Inc.
NeILF++: Inter-Reflectable Light Fields for Geometry and Material Estimation (2023)

We present a novel differentiable rendering framework for joint geometry, material, and lighting estimation from multi-view images. In contrast to previous methods which assume a simplified environment map or co-located flashlights, in this work, we formulate the lighting of a static scene as one neural incident light field (NeILF) and one outgoing neural radiance field (NeRF). The key insight of the proposed method is the union of the incident and outgoing light fields through physically-based rendering and inter-reflections between surfaces, making it possible to disentangle the scene geometry, material, and lighting from image observations in a physically-based manner. The proposed incident light and inter-reflection framework can be easily applied to other NeRF systems. We show that our method can not only decompose the outgoing radiance into incident lights and surface materials, but also serve as a surface refinement module that further improves the reconstruction detail of the neural surface. We demonstrate on several datasets that the proposed method is able to achieve state-of-the-art results in terms of geometry reconstruction quality, material estimation accuracy, and the fidelity of novel view rendering.
Maximum Likelihood Structured Covariance Matrix Estimation and connections to SBL: A Path to Gridless DoA Estimation (2022)

In this paper, we revisit the framework for maximum likelihood estimation (MLE) as applied to parametric models with an aim to estimate the parameter of interest in a gridless manner. The approach has inherent connections to the sparse Bayesian learning (SBL) formulation, and naturally leads to the problem of structured matrix recovery (SMR). We therefore pose the parameter estimation problem as a SMR problem, and recover the parameter of interest by appealing to the Carathéodory-Fejér result on decomposition of positive semi-definite Toeplitz matrices. We propose an iterative algorithm to estimate the structured covariance matrix; each iteration solves a semi-definite program. We numerically compare the performance with other gridless schemes in literature and demonstrate the superior performance of the proposed technique.
Threat of Racial and Economic Inequality Increases Preference for Algorithm Decision-Making (2021)

Artificial intelligence (AI) algorithms hold promise to reduce inequalities across race and socioeconomic status. One of the most important domains of racial and economic inequalities is medical outcomes; Black and low-income people are more likely to die from many diseases. Algorithms can help reduce these inequalities because they are less likely than human doctors to make biased decisions. Unfortunately, people are generally averse to algorithms making important moral decisions—including in medicine—undermining the adoption of AI in healthcare. Here we use the COVID-19 pandemic to examine whether the threat of racial and economic inequality increases the preference for algorithm decision-making. Four studies (N=2,819) conducted in the United States and Singapore show that emphasizing inequality in medical outcomes increases the preference for algorithm decision-making for triage decisions. These studies suggest that one way to increase the acceptance of AI in healthcare is to emphasize the threat of inequality and its negative outcomes associated with human decision-making.
Performance of linear interpolation-based MIMO detection for MIMO-OFDM systems (2004)

Detection of MIMO signals presents a formidable computation challenge due to the inherent complexity incurred by matrix-type wireless fading channels. When combined with OFDM, the MIMO detection over frequency-selective fading channels is divided into that over each flat-fading subchannel. Since this is usually done on per subchannel basis, it implies significant hardware cost. This work proposes the use of linear interpolation to exploit the correlation among adjacent subchannels. Since the weight matrices on non-pilot subchannels are linearly interpolated from those of pilot subchannels, the computation overhead is greatly reduced. This is particularly effective when the subchannel bandwidth is much smaller than the coherence bandwidth of the channel. Simulation using MMSE MIMO detection shows that, by keeping the product of interpolation factor and normalized RMS delay spread within a certain limit, linear interpolation can result in minimum degradation of system performance up to a practical SNR level of 20 dB to 25 dB.