gebhart/patrepeval huggingface dataset:
High-throughput robust single-cell DNA methylation profiling with sciMETv2 (2022)

DNA methylation is a key epigenetic property that drives gene regulatory programs in development and disease. Current single-cell methods that produce high quality methylomes are expensive and low throughput without the aid of extensive automation. We previously described a proof-of-principle technique that enabled high cell throughput; however, it produced only low-coverage profiles and was a difficult protocol that required custom sequencing primers and recipes and frequently produced libraries with excessive adapter contamination. Here, we describe a greatly improved version that generates high-coverage profiles (~15-fold increase) using a robust protocol that does not require custom sequencing capabilities, includes multiple stopping points, and exhibits minimal adapter contamination. We demonstrate two versions of sciMETv2 on primary human cortex, a high coverage and rapid version, identifying distinct cell types using CH methylation patterns. These datasets are able to be directly integrated with one another as well as with existing snmC-seq2 datasets with little discernible bias. Finally, we demonstrate the ability to determine cell types using CG methylation alone, which is the dominant context for DNA methylation in most cell types other than neurons and the most applicable analysis outside of brain tissue.
WISDOM2013: A Large-scale Web Information Analysis System (2013)

We demonstrate our large-scale web information analysis system called WISDOM2013, which consists of several deep semantic analysis systems such as a factoid QA, a non-factoid QA and a sentiment analyzer, and a software platform on which its semantic analysis systems can be applied to a billion-page-scale web archive. The software platform has an extendable architecture, and we are planning to enhance WISDOM2013 in the future by adding more semantic analysis systems and inference mechanisms.
Fish, Fish Oils and Cardioprotection: Promise or Fish Tale? (2018)

Fish and commercially available fish oil preparations are rich sources of long-chain omega-3 polyunsaturated fatty acids. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are the most important fatty acids in fish oil. Following dietary intake, these fatty acids get incorporated into the cell membrane phospholipids throughout the body, especially in the heart and brain. They play an important role in early brain development during infancy, and have also been shown to be of benefit in dementia, depression, and other neuropsychiatric disorders. Early epidemiologic studies show an inverse relationship between fish consumption and the risk of coronary heart disease. This led to the identification of the cardioprotective role of these marine-derived fatty acids. Many experimental studies and some clinical trials have documented the benefits of fish oil supplementation in decreasing the incidence and progression of atherosclerosis, myocardial infarction, heart failure, arrhythmias, and stroke. Possible mechanisms include reduction in triglycerides, alteration in membrane fluidity, modulation of cardiac ion channels, and anti-inflammatory, anti-thrombotic, and anti-arrhythmic effects. Fish oil supplements are generally safe, and the risk of toxicity with methylmercury, an environmental toxin found in fish, is minimal. Current guidelines recommend the consumption of either one to two servings of oily fish per week or daily fish oil supplements (around 1 g of omega-3 polyunsaturated fatty acids per day) in adults. However, recent large-scale studies have failed to demonstrate any benefit of fish oil supplements on cardiovascular outcomes and mortality. Here, we review the different trials that evaluated the role of fish oil in cardiovascular diseases.
Information extraction and manipulation threats in crowd-powered systems (2014)

Crowd-powered systems have become a popular way to augment the capabilities of automated systems in real-world settings. Many of these systems rely on human workers to process potentially sensitive data or make important decisions. This puts these systems at risk of unintentionally releasing sensitive data or having their outcomes maliciously manipulated. While almost all crowd-powered approaches account for errors made by individual workers, few factor in active attacks on the system. In this paper, we analyze different forms of threats from individuals and groups of workers extracting information from crowd-powered systems or manipulating these systems' outcomes. Via a set of studies performed on Amazon's Mechanical Turk platform and involving 1,140 unique workers, we demonstrate the viability of these threats. We show that the current system is vulnerable to coordinated attacks on a task based on the requests of another task and that a significant portion of Mechanical Turk workers are willing to contribute to an attack. We propose several possible approaches to mitigating these threats, including leveraging workers who are willing to go above and beyond to help, automatically flagging sensitive content, and using workflows that conceal information from each individual, while still allowing the group to complete a task. Our findings enable the crowd to continue to play an important part in automated systems, even as the data they use and the decisions they support become increasingly important.
The Potential Use of Antibiotics Against Helicobacter pylori Infection: Biopharmaceutical Implications (2022)

<i>Helicobacter pylori</i> (<i>H. pylori</i>) is a notorious, recalcitrant and silent germ, which can cause a variety of debilitating stomach diseases, including gastric and duodenal ulcers and gastric cancer. This microbe predominantly colonizes the mucosal layer of the human stomach and survives in the inhospitable gastric microenvironment, by adapting to this hostile milieu. In this review, we first discuss <i>H. pylori</i> colonization and invasion. Thereafter, we provide a survey of current curative options based on polypharmacy, looking at pharmacokinetics, pharmacodynamics and pharmaceutical microbiology concepts, in the battle against <i>H. pylori</i> infection.
Challenges and solutions on pre-assembly processes for thinned 3D wafers with micro-bumps on the backside (2014)

In 3D IC technology, temporary bonding systems and stacking/assembly process are identified as critical elements given all the concerns on wafer handling amidst BEOL processes and how to do the stacking as best as one could in so many different schemes. In between the temporary bonding systems and stacking/assembly process, is a group and series of processes that link the two. This is collectively and commonly known as the pre-assembly process. This paper presents the in-house pre-assembly 3D IC process flow for thinned wafer with micro-bumps on the backside along with the different challenges on materials and processes on each step. Most importantly, this paper reports on a solution found that enabled pre-assembly process to successfully provide a bridge from temporary bonding systems to stacking/assembly process: a UV dicing tape that can handle the complexities at hand when processing thinned 3D IC wafers with backside micro bumps in pre-assembly integration.
Cross-reactive and mono-reactive SARS-CoV-2 CD4+ T cells in prepandemic and COVID-19 convalescent individuals (2021)

Class II tetramer reagents for eleven common DR alleles and a DP allele prevalent in the world population were used to identify SARS-CoV-2 CD4+ T cell epitopes. A total of 112, 28 and 42 epitopes specific for Spike, Membrane and Nucleocapsid, respectively, with defined HLA-restriction were identified. Direct ex vivo staining of PBMC with tetramer reagents was used to define immunodominant and subdominant T cell epitopes and estimate the frequencies of these T cells in SARS-CoV-2 exposed and naïve individuals. Majority of SARS-CoV-2 epitopes identified have <67% amino acid sequence identity with endemic coronaviruses and are unlikely to elicit high avidity cross-reactive T cell responses. Four SARS-CoV-2 Spike reactive epitopes, including a DPB1*04:01 restricted epitope, with ≥67% amino acid sequence identity to endemic coronavirus were identified. SARS-CoV-2 T cell lines for three of these epitopes elicited cross-reactive T cell responses to endemic cold viruses. An endemic coronavirus Spike T cell line showed cross-reactivity to the fourth SARS-CoV-2 epitope. Three of the Spike cross-reactive epitopes were subdominant epitopes, while the DPB1*04:01 restricted epitope was a dominant epitope. Frequency analyses showed Spike cross-reactive T cells as detected by tetramers were present at relatively low frequency in unexposed people and only contributed a small proportion of the overall Spike-specific CD4+ T cells in COVID-19 convalescent individuals. In total, these results suggested a very limited number of SARS-CoV-2 T cells as detected by tetramers are capable of recognizing ccCoV with relative high avidity and vice versa. The potentially supportive role of these high avidity cross-reactive T cells in protective immunity against SARS-CoV-2 needs further studies.
Discovery of a low-mass companion inside the debris ring surrounding the F5V star HD 206893 (2016)

Aims. Uncovering the ingredients and the architecture of planetary systems is a very active field of research that has fuelled many new theories on giant planet formation, migration, composition, and interaction with the circumstellar environment. We aim at discovering and studying new such systems, to further expand our knowledge of how low-mass companions form and evolve.
Data from Monitoring Therapeutic Response to Anti-FAP CAR T Cells Using [<sup>18</sup>F]AlF-FAPI-74 (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Despite the success of chimeric antigen receptor (CAR) T-cell therapy against hematologic malignancies, successful targeting of solid tumors with CAR T cells has been limited by a lack of durable responses and reports of toxicities. Our understanding of the limited therapeutic efficacy in solid tumors could be improved with quantitative tools that allow characterization of CAR T–targeted antigens in tumors and accurate monitoring of response.&lt;/p&gt;Experimental Design:&lt;p&gt;We used a radiolabeled FAP inhibitor (FAPI) [&lt;sup&gt;18&lt;/sup&gt;F]AlF-FAPI-74 probe to complement ongoing efforts to develop and optimize FAP CAR T cells. The selectivity of the radiotracer for FAP was characterized &lt;i&gt;in vitro&lt;/i&gt;, and its ability to monitor changes in FAP expression was evaluated using rodent models of lung cancer.&lt;/p&gt;Results:&lt;p&gt;[&lt;sup&gt;18&lt;/sup&gt;F]AlF-FAPI-74 showed selective retention in FAP&lt;sup&gt;+&lt;/sup&gt; cells &lt;i&gt;in vitro&lt;/i&gt;, with effective blocking of the uptake in presence of unlabeled FAPI. &lt;i&gt;In vivo&lt;/i&gt;, [&lt;sup&gt;18&lt;/sup&gt;F]AlF-FAPI-74 was able to detect FAP expression on tumor cells as well as FAP&lt;sup&gt;+&lt;/sup&gt; stromal cells in the tumor microenvironment with a high target-to-background ratio. We further demonstrated the utility of the tracer to monitor changes in FAP expression following FAP CAR T-cell therapy, and the PET imaging findings showed a robust correlation with &lt;i&gt;ex vivo&lt;/i&gt; analyses.&lt;/p&gt;Conclusions:&lt;p&gt;This noninvasive imaging approach to interrogate the tumor microenvironment represents an innovative pairing of a diagnostic PET probe with solid tumor CAR T-cell therapy and has the potential to serve as a predictive and pharmacodynamic response biomarker for FAP as well as other stroma-targeted therapies. A PET imaging approach targeting FAP expressed on activated fibroblasts of the tumor stroma has the potential to predict and monitor therapeutic response to FAP-targeted CAR T-cell therapy.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/clincancerres/article/doi/10.1158/1078-0432.CCR-22-2565" target="_blank"&gt;See related commentary by Weber et al., p. 5241&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Temperature Evolution in Nanoscale Carbon-Based Memory Devices Due to Local Joule Heating (2017)

Tetrahedral amorphous (ta-C) carbon-based memory devices have recently gained traction due to their good scalability and promising properties like nanosecond switching speeds. However, cycling endurance is still a key challenge. In this paper, we present a model that takes local fluctuations in sp <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$^{2}$ </tex-math></inline-formula> and sp <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$^{3}$</tex-math></inline-formula> content into account when describing the conductivity of ta-C memory devices. We present a detailed study of the conductivity of ta-C memory devices ranging from ohmic behavior at low electric fields to dielectric breakdown. The study consists of pulsed switching experiments and device-scale simulations, which allows us for the first time to provide insights into the local temperature distribution at the onset of memory switching.
Human Performance in Six Degree of Freedom Input Control (2002)

This thesis investigates human performance in relation to various dimensions of 6 degree of freedom (DOF) interfaces, including device resistance, transfer functions, muscles groups and joints, and input display formats. These dimensions are analysed respectively in terms of human proprioception and control feel, mental processing in forming control actions, motor and sensory cortex representation, and the nature of various visual depth cues. A series of five experiments are presented. Experiment 1 examined isotonic versus isometric resistance modes and position versus rate control transfer functions. A strong interaction was found between the resistance mode and the transfer function: in position control, the isotonic device outperformed the isometric device; whereas in rate control, the isometric device outperformed the isotonic device. Experiments 2 and 3 studied isometric versus elastic devices in rate control. When optimised between two opposing factors, i.e. proprioception and compatibility, the elastic device had performance advantages over the isometric device at the early stage of learning. Experiment 3 also revealed users' control strategies in terms of attentional priority to each degree of freedom. Experiment 4 investigated the effects of different joints and muscle groups on 6 DOF manipulation. The results showed that the participation of fingers significantly improved task performance. Experiment 5 studied the visual representation of users’ input control actions. It was found that partial occlusion through semi-transparency in 3D, a rather novel graphic technique, was strongly beneficial. The major conclusions of the thesis can be summarised briefly as: (1) The physical properties of a 6 DOF input device should provide rich feedback so that the user can easily feel her control actions proprioceptively and thus learn the task quickly. (2) To the extent possible, fine small muscle groups and joints should be included in the operation of input devices. (3) The transfer function used to interface a device with the computer should be compatible with the physical device. (4) The visual representation of the user’s actions should be designed to allow immediate exteroceptive feedback and the application of semitransparency serves this purpose well.
Seeing Early Signs of Alzheimer's Disease Through the Lens of the Eye (2016)

Translation of these findings to clinical diagnosis could lead to earlier therapeutic interventions and, consequently, better chances to delay or halt AD progression.
Semantic Correspondence Across 3D Models for Example-based Modeling (2017)

Modeling 3D shapes is a specialized skill not affordable to most novice artists due to its complexity and tediousness. At the same time, databases of complex models ready for use are becoming widespread, and can help the modeling task in a process called example-based modeling. We introduce such an example-based mesh modeling approach which, contrary to prior work, allows for the replacement of any localized region of a mesh by a region of similar semantics (but different geometry) within a mesh database. For that, we introduce a selection tool in a space of semantic descriptors that co-selects areas of similar semantics within the database. Moreover, this tool can be used for part-based retrieval across the database. Then, we show how semantic information improves the assembly process. This allows for modeling complex meshes from a coarse geometry and a database of more detailed meshes, and makes modeling accessible to the novice user.
Gene alterations in epigenetic modifiers and JAK-STAT signaling are frequent in breast implant-associated ALCL. (2019)

The oncogenic events involved in breast implant-associated anaplastic large cell lymphoma (BI-ALCL) remain elusive. To clarify this point, we have characterized the genomic landscape of 34 BI-ALCLs (15 tumor and 19 in situ subtypes) collected from 54 BI-ALCL patients diagnosed through the French Lymphopath network. Whole-exome sequencing (n = 22, with paired tumor/germline DNA) and/or targeted deep sequencing (n = 24) showed recurrent mutations of epigenetic modifiers in 74% of cases, involving notably KMT2C (26%), KMT2D (9%), CHD2 (15%), and CREBBP (15%). KMT2D and KMT2C mutations correlated with a loss of H3K4 mono- and trimethylation by immunohistochemistry. Twenty cases (59%) showed mutations in ≥1 member of the JAK/STAT pathway, including STAT3 (38%), JAK1 (18%), and STAT5B (3%), and in negative regulators, including SOCS3 (6%), SOCS1 (3%), and PTPN1 (3%). These mutations were more frequent in tumor-type samples than in situ samples (P = .038). All BI-ALCLs expressed pSTAT3, regardless of the mutational status of genes in the JAK/STAT pathway. Mutations in the EOMES gene (12%) involved in lymphocyte development, PI3K-AKT/mTOR (6%), and loss-of-function mutations in TP53 (12%) were also identified. Copy-number aberration (CNA) analysis identified recurrent alterations, including gains on chromosomes 2, 9p, 12p, and 21 and losses on 4q, 8p, 15, 16, and 20. Regions of CNA encompassed genes involved in the JAK/STAT pathway and epigenetic regulators. Our results show that the BI-ALCL genomic landscape is characterized by not only JAK/STAT activating mutations but also loss-of-function alterations of epigenetic modifiers.
ChemInform Abstract: Catalytic Carbon‐Carbon Coupling by Palladium Complexes: Heck Reactions (1997)

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.
The Effect of <i>Bifidobacterium lactis</i> on the Growth of Infants: A Pooled Analysis of Randomized Controlled Studies (2009)

The analysis suggests that B. lactis may have a positive effect on growth in vulnerable populations, specifically in infants born to mothers with HIV.
MAUDE: inferring expression changes in sorting-based CRISPR screens (2020)

Improved methods are needed to model CRISPR screen data for interrogation of genetic elements that alter reporter gene expression readout. We create MAUDE (Mean Alterations Using Discrete Expression) for quantifying the impact of guide RNAs on a target gene's expression in a pooled, sorting-based expression screen. MAUDE quantifies guide-level effects by modeling the distribution of cells across sorting expression bins. It then combines guides to estimate the statistical significance and effect size of targeted genetic elements. We demonstrate that MAUDE outperforms previous approaches and provide experimental design guidelines to best leverage MAUDE, which is available on https://github.com/Carldeboer/MAUDE.
Magnetic field responses of auditory cortex to produced speech (1999)

Several behavioral and brain imaging studies have demonstrated a significant interaction between speech reception and speech production. In this study, the dynamics of modulation of auditory cortical responses to speech during self-production and feedback alteration were examined. Magnetic field recordings were obtained from both hemispheres of subjects who spoke while hearing controlled versions of their feedback via earphones. These responses were compared to magnetic field recordings made while subjects listened to a tape recording of their production. The amplitude of the tape playback was adjusted to be equal to the amplitude of produced speech. Successful recordings of evoked responses to both self-produced and tape-recorded speech were obtained free of movement-related artifacts. In all subjects, a progressive differentiation in the dynamics of the responses to self-produced speech and to recorded speech was observed. In several subjects, a clear bilateral suppression of amplitude of the peak response 100 ms after stimulus onset was also observed. Feedback alteration enhanced the evoked response to produced speech. [Work supported by the McDonnell-Pew Foundation, the Coleman Fund, HRI, and Scientific Learning Corp.]
Acyclic stereoselection. 29. Stereoselection in the Michael addition reaction. 1. The Mukaiyama-Michael reaction (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcyclic stereoselection. 29. Stereoselection in the Michael addition reaction. 1. The Mukaiyama-Michael reactionClayton H. Heathcock, Mark H. Norman, and David E. UehlingCite this: J. Am. Chem. Soc. 1985, 107, 9, 2797–2799Publication Date (Print):May 1, 1985Publication History Published online1 May 2002Published inissue 1 May 1985https://doi.org/10.1021/ja00295a037RIGHTS & PERMISSIONSArticle Views986Altmetric-Citations89LEARN 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 InReddit PDF (356 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
ChemInform Abstract: THE MECHANISM OF INTERSYSTEM CROSSING AND RING CLOSURE OF THE TRIPLET 1,8‐NAPHTHOQUINODIMETHANE BIRADICAL (1980)

Abstract Bei der Photolyse der Azomethane (I) können ESR‐ spektroskopisch die intermediären Carbene (II) nicht beobachtet werden aufgrund der sehr schnellen Umlagerung zu den Biradikalen (III).
Disturbance-suppressed ReRAM write algorithm for high-capacity and high-performance memory (2014)

In this paper, the mechanism of write disturbance, a unique phenomenon in high density ReRAM, is experimentally identified and quantified using fabricated test array. Based on the analysis, disturbance-suppressed ReRAM write algorithm is proposed to prove the feasibility of future high-capacity and high-performance ReRAM memory for NAND applications. By appropriately controlling WL and BL bias, surge current that causes write disturbance is successfully suppressed so that the overall cell distribution was narrowed down by more than 70%.
Preliminary experience of the estimation of cerebral perfusion pressure using transcranial Doppler ultrasonography (2001)

The device is of potential benefit for intermittent or continuous monitoring of brain perfusion pressure in situations where the direct measurement is not available or its reliability is in question.