gebhart/patrepeval huggingface dataset:
Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs (2019)

Abstract Background Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). However, the advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified. Results We performed whole genome methyl-seq on diverse normal cells and tissues and three types of cancers (multiple myeloma, lymphoma, glioblastoma multiforme). After excluding imprinting, the data pinpointed 15,114 high-confidence ASM differentially methylated regions (DMRs), of which 1,842 contained SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies were increased 5 to 9-fold in cancers vs. matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancers showed increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor (TF) binding motifs were similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes tracked with de novo ASM in the cancers. Allele-specific TF binding from ChIP-seq was enriched among ASM loci, but most ASM DMRs lacked such annotations, and some were found in otherwise uninformative “chromatin deserts”. Conclusions ASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and TF binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, neuropsychiatric, and neoplastic diseases. Custom genome browser tracks with annotated ASM loci can be viewed at a UCSC browser session hosted by our laboratory ( https://bit.ly/tycko-asm )
EXPRESSION OF THE INTERLEUKIN 2 RECEPTOR β CHAIN (p75) IN RENAL TRANSPLANTATION—APPLICABILITY OF ANTMNTERLEUKIN-2 RECEPTOR β CHAIN MONOCLONAL ANTIBODY (1991)

The interaction of interleukin 2 with specific cellular receptors plays an essential role in the allostimulated proliferation and differentiation of T cells. Recent chemical linking studies have demonstrated that the human high-affinity IL-2 receptor is a membrane complex composed of at least two distinct subunits, which are the p55 (alpha-chain) and p75 (beta-chain) subunits. The IL-2R beta chain is supposed to play a role in the signal transduction of IL-2, but the exact mechanism is still unknown. In this study, we investigated the effects of a newly established anti-IL-2R beta chain monoclonal antibody (MoAb, TU-27) on the induction of cytotoxic T lymphocytes (CTLs) using the cell-mediated lympholysis (CML) assay. TU-27 in combination with H-31, a MoAb directed against the IL-2R alpha chain, produced inhibition of cytotoxicity, while TU-27 alone could not inhibit cytotoxicity, while TU-27 alone could not inhibit cytotoxicity at any concentration. TU-27 plus H-31 prevented the expansion of CD4+ cells and CD8++ cells in mixed lymphocyte culture (MLC). Furthermore, we examined the serial changes in the expression of the IL-2R beta chain on peripheral blood lymphocytes from renal transplant recipients using two-color immunofluorescence flow cytometry, so as to investigate correlations between IL-2R beta chain expression and the occurrence of allograft rejection. Here, we report that the IL-2R beta chain is expressed on CD4-positive (CD4+) cells and strongly CD8-positive (CD8(+)+) cells in association with acute rejection, indicating that IL-2R beta chain expression appears to increase on alloreactive T cells.
Predictive Value of Capnography for Suspected Diabetic Ketoacidosis in the Emergency Department (2013)

Capnography values greater than 24.5 mmHg accurately allow the exclusion of DKA in ED patients suspected of that diagnosis. Capnography levels lower that 24.5 mmHg were unable to differentiate between DKA and other disease entities.
The paediatric Bohler's angle and crucial angle of Gissane: a case series (2011)

We have presented the normal values of Bohler's angle and the crucial angle of Gissane in a paediatric population. These values may provide a useful comparison to assist with the management of the paediatric calcaneal fracture.
Botulinum Neurotoxins (BoNTs)—Antibody and Vaccine (2018)

Botulism, caused by exposure to one or more of the eight serotypes of botulinum neurotoxins (BoNTs) (BoNT/A through H), is often fatal without rapid treatment. [...].
Computational model of the human eye for intelligent systems (2010)

The knowledge of the spatiotemporal sensitivity of the human eye can be essential for those practical applications where the communication of an informatical system and a human subject can be crucial (topics: cognitive informatics, cognitive infocommunication), such as intelligent video-coding, driving assistant systems or intelligent instrumental boards. In this paper we will present the spatiotemporal sensitivity of the human eye for achromatic stimuli at photopic light levels. To our knowledge, it is the first comprehensive model that: (1) considers the spatiotemporal transfer function of P and M ganglion cells along the retina, (2) contains the fast adaptation mechanisms (contrast gain control and luminance gain control) and (3) discusses the role of the receptor and post-receptor light adaptation separately.
Confidence-driven Weighted Retraining for Predicting Safety-Critical Failures in Autonomous Driving Systems (2022)

Safe handling of hazardous driving situations is a task of high practical relevance for building reliable and trustworthy cyber-physical systems such as autonomous driving systems. This task necessitates an accurate prediction system of the vehicle's confidence to prevent potentially harmful system failures on the occurrence of unpredictable conditions that make it less safe to drive. In this paper, we discuss the challenges of adapting a misbehavior predictor with knowledge mined during the execution of the main system. Then, we present a framework for the continual learning of misbehavior predictors, which records in-field behavioral data to determine what data are appropriate for adaptation. Our framework guides adaptive retraining using a novel combination of in-field confidence metric selection and reconstruction error-based weighing. We evaluate our framework to improve a misbehavior predictor from the literature on the Udacity simulator for self-driving cars. Our results show that our framework can reduce the false positive rate by a large margin and can adapt to nominal behavior drifts while maintaining the original capability to predict failures up to several seconds in advance.
Theory of Ferroelectric Nanoparticles in Nematic Liquid Crystals (2009)

Recent experiments have reported that ferroelectric nanoparticles have drastic effects on nematic liquid crystals-increasing the isotropic-nematic transition temperature by about 5 K, and greatly increasing the sensitivity to applied electric fields. To understand these effects, we develop a theory for the statistical mechanics of ferroelectric nanoparticles in liquid crystals. This theory predicts the enhancements of liquid-crystal properties, in good agreement with experiments. These predictions apply even when electrostatic interactions are partially screened by moderate concentrations of ions.
On the development of an information system for monitoring user opinion and its role for the public (2022)

Abstract Social media services and analytics platforms are rapidly growing. A large number of various events happen mostly every day, and the role of social media monitoring tools is also increasing. Social networks are widely used for managing and promoting brands and different services. Thus, most popular social analytics platforms aim for business purposes while monitoring various social, economic, and political problems remains underrepresented and not covered by thorough research. Moreover, most of them focus on resource-rich languages such as the English language, whereas texts and comments in other low-resource languages, such as the Russian and Kazakh languages in social media, are not represented well enough. So, this work is devoted to developing and applying the information system called the OMSystem for analyzing users’ opinions on news portals, blogs, and social networks in Kazakhstan. The system uses sentiment dictionaries of the Russian and Kazakh languages and machine learning algorithms to determine the sentiment of social media texts. The whole structure and functionalities of the system are also presented. The experimental part is devoted to building machine learning models for sentiment analysis on the Russian and Kazakh datasets. Then the performance of the models is evaluated with accuracy, precision, recall, and F1-score metrics. The models with the highest scores are selected for implementation in the OMSystem. Then the OMSystem’s social analytics module is used to thoroughly analyze the healthcare, political and social aspects of the most relevant topics connected with the vaccination against the coronavirus disease. The analysis allowed us to discover the public social mood in the cities of Almaty and Nur-Sultan and other large regional cities of Kazakhstan. The system’s study included two extensive periods: 10-01-2021 to 30-05-2021 and 01-07-2021 to 12-08-2021. In the obtained results, people’s moods and attitudes to the Government’s policies and actions were studied by such social network indicators as the level of topic discussion activity in society, the level of interest in the topic in society, and the mood level of society. These indicators calculated by the OMSystem allowed careful identification of alarming factors of the public (negative attitude to the government regulations, vaccination policies, trust in vaccination, etc.) and assessment of the social mood.
Molecular Fingerprint of High Fat Diet Induced Urinary Bladder Metabolic Dysfunction in a Rat Model (2013)

Thus, high-fat diet is sufficient to induce significant remodelling of the urinary bladder and alterations of the molecular fingerprint. Our findings give new insights into obesity related bladder dysfunction and identified proteins that may indicate novel pathophysiological mechanisms and therefore constitute new drug targets.
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR (2021)

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.
Pyk2- and Src-Dependent Tyrosine Phosphorylation of PDK1 Regulates Focal Adhesions (2003)

3-Phosphoinositide-dependent protein kinase 1 (PDK1) is a signal integrator that activates the AGC superfamily of serine/threonine kinases. PDK1 is phosphorylated on tyrosine by oxidants, although its regulation by agonists that stimulate G-protein-coupled receptor signaling pathways and the physiological consequences of tyrosine phosphorylation in this setting have not been fully identified. We found that angiotensin II stimulates the tyrosine phosphorylation of PDK1 in vascular smooth muscle in a calcium- and c-Src-dependent manner. The calcium-activated tyrosine kinase Pyk2 acts as a scaffold for Src-dependent phosphorylation of PDK1 on Tyr9, which permits phosphorylation of Tyr373 and -376 by Src. This critical function of Pyk2 is further supported by the observation that Pyk2 and tyrosine-phosphorylated PDK1 colocalize in focal adhesions after angiotensin II stimulation. Importantly, infection of smooth muscle cells with a Tyr9 mutant of PDK1 inhibits angiotensin II-induced tyrosine phosphorylation of paxillin and focal adhesion formation. These observations identify a novel interaction between PDK1 and Pyk2 that regulates the integrity of focal adhesions, which are major compartments for integrating signals for cell growth, apoptosis, and migration.
VITA-an autonomous road vehicle (ARV) for collision avoidance in traffic (2003)

Describes results of the autonomous Daimler-Benz test vehicle VITA (vision technology application). The basic structure of the vehicle is introduced. The computer vision based applications, ranging from lane keeping, obstacle detection, stop+go and lane change to intersection control are briefly explained. Ongoing research work in the Daimler-Benz PROMETHEUS subproject is mentioned.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Learning Contextual Embeddings for Knowledge Graph Completion (2017)

Knowledge Graphs capture entities and their relationships. However, many knowledge graphs are afflicted by missing data. Recently, embedding methods have been used to alleviate this issue via knowledge graph completion. However, most existing methods only consider the relationship in triples, even though contextual relation types, consisting of the surrounding relation types of a triple, can substantially improve prediction accuracy. Therefore, we propose a contextual embedding method that learns the embeddings of entities and predicates while taking contextual relation types into account. The main benefits of our approach are: (1) improved scalability via a reduced number of epochs needed to achieve comparable or better results with the same memory complexity, (2) higher prediction accuracy (an average of 14%) compared to the related algorithms, and (3) high accuracy for both missing entity and predicate predictions. The source code and the YAGO43k dataset of this paper can be found from (https://github.ncsu.edu/cmoon2/kg).
In vitroAnticancer Activities of Some Triterpene Glycosides from Holothurians of Cucumariidae, Stichopodidae, Psolidae, Holothuriidae and Synaptidae families (2016)

Triterpene glycosides isolated from holothurians are natural products known to possess cytotoxic properties against cancer cells. However, their anticancer prophylactic activity has not been studied sufficiently. The anticancer prophylactic; cytotoxic, and pro-apoptotic properties of 18 triterpene glycosides, as well as their effects on the transcriptional activities of activator protein-I (AP-1) and nuclear factor-KB (NF-KB), were examined using methods that included EGF-induced JB6 C141 P' cell transformation in soft agar, flow cytometry, MTS assessment of cell viability, and a luciferase activity assay. The compounds inhibited EGF-induced neoplastic JB6 C141 P' cell transformation in soft agar and caused apoptosis and necrosis of human HL-60 and THP-I leukemia cells. AP- and NF-KB were involved in the cellular response to the treatment by the compounds. Conclusion: glycosides isolated from holothurians of Cucumariidae, Stichopodidae, Psolidae, Holothuriidae and Synaptidae families have potential for development as new antitumor agents and as instruments to study AP-I and NF-kB.
Intramolecular versus intermolecular bonding in amidoantimony dimers; syntheses and structures of {Sb(NMe2)[µ-N(mpy)]}2(mpy = 4-methylpyridin-2-yl) and [Sb(NMe2){µ-N[C6H2(OMe)3-3,4,5]}]2 (1994)

The reaction of Sb(NMe2)3 with 2-amino-4-methylpyridine (1 : 1 ratio) produced {Sb(NMe2)[µ-N (mpy)]}2(mpy = 4-methylpyridin-2-yl) which forms unassociated dimers in which relatively weak intramolecular Sb ⋯ N interactions are present [2.891(5)Å], whereas a similar reaction with 3,4,5-trimethoxyaniline produced [Sb(NMe2){µ-N[C6H2(OMe)3-3,4,5]}]2in which the dimer units are associated into a loosely linked polymer by intermolecular chelating MoO ⋯ Sb interactions [3.500(5)Å].
Reductive aminations of ketones and aldehydes using borane–pyridine (1984)

Borane–pyridine is introduced as a cheap and readily available alternative to sodium cyanotrihydroborate for the purpose of the reductive amination of a wide variety of carbonyl compounds. It does not suffer from the severe toxicity associated with sodium cyanotrihydroborate.
A unified platform for data driven web applications with automatic client-server partitioning (2007)

Data-driven web applications are usually structured in three tiers with different programming models at each tier. This division forces developers to manually partition application functionality across the tiers, resulting in complex logic, suboptimal partitioning, and expensive re-partitioning of applications. In this paper, we introduce a unified platform for automatic partitioning of data-driven web applications. Our approach is based on Hilda[41, 46], a high-level declarative programming language with a unified data and programming model for all the layers of the application. Based on run-time properties of the application, Hilda's run time system automatically partitions the application between the tiers to improve response time while adhering to memory and/ or processing constraints at the clients. We evaluate our methodology with traces from a real application and with TPC-W, and our results show that automatic partitioning outperforms manual partitioning without the associated development overhead.
3D System Integration Technologies (2006)

Electronic interconnection and packaging is mainly performed in a planar, 2D design style. Further miniaturization and performance enhancement of electronic systems will more and more require the use of 3D interconnection schemes. Key technologies for realizing true 3D interconnect schemes are the realization of vertical connections, either through the Si-die or through the multilayer interconnect with embedded die. Different applications require different complexities of 3D-interconnectivity. Therefore, different technologies may be used. These can be categorized as a more traditional packaging approach, a wafer-level-packaging, WLP ('above' passivation), approach and a foundry level ('below' passivation) approach. We define these technologies as respectively 3D-SIP, 3D-WLP and 3D-SIC. In this paper, these technologies are discussed in more detail
Severe adverse events during sirolimus “off‐label” therapy for vascular anomalies (2021)

Most SAEs are observed in the first year of sirolimus therapy; however, SAEs can also occur after a longer treatment period. SAEs are potentially life threatening, especially in early infancy. Presence of other risk factors, that is, underlying vascular anomaly or immune status, may contribute to the risk of SAEs. Sirolimus is an important therapeutic option for vascular anomalies, but patients and physicians need to be aware that adequate monitoring is necessary, especially in patients with complex lymphatic anomalies that are overrepresented in our cohort of SAEs.
On the tightness of Marton's regions for semi-additive broadcast channels (2009)

We study cost constrained side-information channels, where the cost function depends on a state which is known only to the encoder. In the additive noise case, we bound the capacity loss due to not knowing the cost state at the decoder and show that it is small under various assumptions, and goes to zero in the limit of weak noise. This model plays an important role in the (non-degraded) broadcast channel. In the semi-additive noise case, we bound the gap between the best known single letter achievable region and the true capacity region, using tools developed for the first problem. In the limit of weak noise, we show that the bounds coincide, thus we get the complete characterization of the capacity region.
ChemInform Abstract: UNTERSUCHUNGEN UEBER DIE ISOXAZOLCHEMIE 5. MITT. DIE N‐ALKYLIERUNG UND N‐ACYLIERUNG VON 5‐AMINO‐3‐(5‐NITRO‐2‐FURYL)‐ISOXAZOLEN (1971)

Abstract Durch Reaktion des Nitrofurylderivates (I) mit den Natriumsalzen von Nitrilen (II) wurde eine Reihe von Furylisoxazolen (III) hergestellt, diese wurden mit Natriumhydrid in Tetrahydrofuran in die Natriumverbindungen (IV) umgewandelt und durch aufeinanderfolgende Einwirkung von Alkylierungs‐ und Acylierungsmitteln zu den verschiedenen Monoalkyl‐, Dialkyl‐, Acyl‐, Diacyloder Alkylacylderivate umgesetzt.
Synthesis and Antifungal Activities of Myristic Acid Analogs (1996)

Myristic acid analogs that are putative inhibitors of N-myristoyl-transferase were tested in vitro for activity against yeasts (Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans) and filamentous fungi (Aspergillus niger). Several (+/-)-2-halotetradecanoic acids including (+/-)-2-bromotetradecanoic acid (14c) exhibited potent activity against C. albicans (MIC = 39 microM), C. neoformans (MIC = 20 microM), S. cerevisiae (MIC = 10 microM), and A. niger (MIC < 42 microM) in RPMI 1640 media. Improved synthetic methods have been developed for the synthesis of 12-fluorododecanoic acid (12a) and 12-chlorododecanoic acid (12c). Three novel fatty acids, 12-chloro-4-oxadodecanoic acid (8a), 12-phenoxydodecanoic acid (12i), and 11-(4-iodophenoxy)-undecanoic acid (13d) were also synthesized and tested.
Effect of cholestyramine on the absorption of vitamin D 3 and calcium (1969)

The absorption of 10 mug doses of vitamin D(3)-(3)H in rats was found to be decreased by the addition of cholestyramine to the diet in an amount sufficient to cause steatorrhoea. Studies in vitro suggested that the effect of cholestyramine was due to its known ability to bind bile salts and thus disrupt micelles containing vitamin D. The absorption of 1 mg (47)calcium chloride was similar in both control and cholestyramine-fed rats, whether estimated by the whole body counting or the faecal excretion technique. These findings show that the administration of cholestyramine causes a reduction in the absorption of vitamin D(3)-(3)H but not of radiocalcium.