gebhart/patrepeval huggingface dataset:
Microinductor-Fused Atomic Force Microscopy Cantilevers for Dynamic Imaging and Multimodal Manipulation (2021)

ABSTRACT Recent advances in atomic force microscopy (AFM) imaging and force spectroscopy have demonstrated improvements in rapid acquisition of quantitative data for applications in materials science, surface characterization, and biology. However, conventional AFM technology is limited in detection sensitivity and the ability to excite at off-resonance frequencies restricting broad utility of the technology. Here we demonstrate new AFM cantilevers fabricated with a planar microcoil at the tip region, which can be used to generate or sense highly-localized magnetic fields. Torsion/bending actuation of the cantilevers is accomplished with simple experimental configurations, enabling quantitative and simultaneous mapping of both stiffness and friction at the sample surface with more than one order of magnitude improvement in compositional contrast. Our method is compatible with commercial AFM systems, allowing us to clearly resolve small stiffness and friction variations in copolymer and biological samples that were difficult to detect by conventional AFM methods. In combination with fluorescence microscopy, we also generated localized fields to selectively stimulate and monitor structural changes in viable cells with nm-scale detail. Hybrid AFM cantilevers may be useful to characterize a broad range of complex material surfaces, in addition to combined physical and chemical analyses of single cells and biological microenvironments.
The impact of routing policy on Internet paths (2002)

The impact of routing policy on Internet paths is poorly understood. In theory, the policy can inflate shortest-router-hop paths. To our knowledge, the extent of this inflation has not been previously examined. Using a simplified model of the routing policy in the Internet, we obtain approximate indications of the impact of policy routing on Internet paths. Our findings suggest that the routing policy does impact the length of Internet paths significantly. For instance, in our model of the routing policy, some 20% of Internet paths are inflated by more than five router-level hops.
Abstract 2517: Hybrid benzofused-biaryl polyamides with selective telomeric G-quadruplex stabilization potential (2011)

Abstract Guanine-rich nucleic acids can fold into four-stranded G-quadruplex structures which are found in telomeric DNA repeats as well as in sequences in the promoter and other regulatory regions of genes. Small molecules that can selectively bind and stabilize quadruplex structure are of increasing significance as potential anticancer agents. We recently reported a series of novel biaryl polyamides with significant selectively towards G-quadruplex compared to duplex DNA, and modest selectivity between different quadruplex types such as c-kit1, c-kit2 and HT4 (Chemical Commun., 4097, 2009). These molecules were based on a distamycin scaffold but included biaryl building blocks in place of pyrroles to switch preference from duplex to quadruplex DNA. This alteration in shape ensured that the molecules had low affinity for duplex DNA while increasing their interaction with G-quadruplex structure, since the ligands had similar dimensions. We have now synthesized a 34-member second-generation biaryl polyamide library based on the previously obtained structural information. Initial assessment of the G-quadruplex interaction of library members was carried out using a FRET-based melting assay. Two compounds (KN-88 and KN-119) containing hybrid benzofused and biaryl building blocks provided significant selective stabilization of human Telomeric G-quadruplex. At 1 µM they stabilize human Telomeric G-quadruplex by 21 and 18 °C, respectively, while showing insignificant affinity for duplex DNA. FRET competition assays with C-kit quadruplexes and CT DNA further confirmed selective stabilization of telomeric quadruplexes. CD titrations of KN-88 and KN-119 with h-telo, c-kit1 and c-kit2 quadruplex-forming DNA sequences showed concentration-dependent enhancement of major CD signals, and in some cases the ligands induced the folding of a particular quadruplex structure. Kd values for KN-88 and KN-119 for telomeric quadruplex sequences were determined by CD titration and were found to be 2.8 × 106 and 7.0 × 106, respectively. Short-term growth inhibitory experiments against a panel of tumour cell lines (MiaPaCa2, A549, MCF7, HeLa, U87MG and A431) gave low micromolar IC50 values for these two compounds, and significant selectivity for tumour cell lines compared to the non-tumour fibroblast WI38 cell line. Given their low molecular weight, good water solubility and cellular penetration properties, molecules of this type have potential as therapeutic agents and reagents that can selectively probe quadruplex structure and/or selectively down-regulate signaling pathways in cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2517. doi:10.1158/1538-7445.AM2011-2517
Thiazinotrienomycins, New Ansamycin Group Antibiotics. (1995)

New triene-ansamycins designated thiazinotrienomycins A, B, C, D and E were isolated from culture broth of Streptomyces sp. MJ672-m3 for their activities against cervical cancer cell lines. The structures and some biological and biochemical properties of the antibiotics were determined.
Fracture of the Occipital Condyle as an Incidental Finding during CT-Evaluation of a Maxillary Fracture (1994)

A 43-year-old male presented with blunt facial trauma after a motor-vehicle accident. CT-evaluation revealed a right-sided maxillary fracture and a fracture of the left occipital condyle. The fracture of the occipital condyle is potentially unstable and fatal cases have been described. Plain radiographs are not diagnostic. This occipital condyle fracture was an incidental finding during CT-evaluation of a maxillary fracture and is probably the first case with coronary CT scans of this type of fracture.
P3‐179: Development of an Indicator Cell Assay for Blood‐Based Diagnosis of Alzheimer’s Disease (2016)

We have developed the Indicator Cell Assay Platform™ (iCAP™), a broadly applicable tool for blood-based diagnostics that uses cultured cells as biosensors, capitalizing on their innate ability to integrate and respond to weak, multicomponent signals in noisy environments. To develop an assay, standardized indicator cells are exposed in vitro to serum from normal or diseased subjects and their global differential response patterns are used to train a reliable, cost-effective disease classifier based on a small number of features. In a feasibility study with 50 serum samples, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified 95% of samples from Huntington’s disease mice as non-carriers of ALS (p-Value=2.09E-50). We initiated development of a preliminary iCAP for early detection of Alzheimer’s disease (AD). We analyzed plasma samples from diseased patients with preclinical or early symptomatic stage AD (N=38), and normal healthy controls (N=20). Classes were defined based on CDR scores and CSF Abeta-42 levels. Indicator cells for this experiment were neurons derived from induced pluripotent stem cells (iPSCs) (from Cellular Dynamics International (CDI)). Global cellular responses to plasma were used to generate AD classifiers using support vector machine-based disease classification. The iCAP detected early-stage AD with 72% cross-validated accuracy (p-Value=3.10E-3). iCAP features were enriched for disease-related genes, supporting the assay’s relevance for disease research. This work establishes a paradigm for capitalizing on the natural ability of cultured cells to detect and respond to weak disease signatures for early detection of AD from blood. As the iCAP yields multicomponent disease signatures, it has potential applications for diagnosis and disease tracking of AD with utility for clinical diagnostics and drug development.
julia: v0.4.0-rc2 (2015)

All major 0.4 changes are in, we continue with bugfixes and backports toward a final 0.4 release. A prepared tarball (the output of make light-source-dist) is attached below in julia-0.4.0-rc1_fa52609644.tar.gz, use this if a source tarball is desired, as it contains a small amount of preparation that a simple archive of the git repository does not. For source builds in restricted environments (e.g. no network access) use the output of make full-source-dist attached below in julia-0.4.0-rc1_fa52609644-full.tar.gz as it already contains all dependencies pre-downloaded and ready for compilation.
Abstract 75: Somatic Overexpression and Knockdown in Mice to Identify Causal Genes Underlying 26 Lipid-associated Loci (2013)

Genome-wide association studies (GWAS) have identified 95 loci in the human genome that harbor common variants associated with plasma lipid traits. Of the 95 loci, 17 harbor genes known to cause monogenic lipid disorders and collectively a third of them contain genes with characterized roles in lipid metabolism. Therefore in the majority of loci the causal genes are unknown. We selected 32 genes, not previously implicated in lipid metabolism and representing a total of 26 loci, to test for their ability to modify plasma lipid concentrations upon somatic overexpression in vivo. We utilized adeno-associated virus serotype 8 (AAV8) to overexpress the selected genes specifically in the livers of both C57BL/6 mice and in an appropriate humanized mouse model (either mice expressing human apolipoprotein A-I for HDL loci or Apobec1-knockout, Ldlr haploinsufficient mice expressing human apolipoprotein B-100 for triglyceride and LDL loci). Approximately half of the genes tested reproducibly affected plasma lipids. For 13 of the interrogated loci the lipid-associated variants also correlated with expression variations of the respective genes in liver (liver expression quantitative trait loci-eQTLs). We demonstrate a causal role for 7 of these 13 genes. The overexpression of these 7 genes not only affected the predicted lipid class, but additionally exerted its effect in the predicted direction in 6 of 7 cases (Tmem57, Slc39a8, Ppp1r3b, Vkorc1, Tbkbp1 and Ube2l3). Additionally for a subset of the examined genes we proceeded to develop small interfering RNA (siRNA) nanoparticles that were particularly targeted to the liver. We were able to obtain robust knockdown for a significant number of genes and, in several cases, observe reciprocal effects on plasma lipids from our overexpression and knockdown studies. This work has identified several novel lipid regulators, whose further investigation can uncover novel mechanisms and pathways controlling plasma lipids.
Increase in diameters of vasospastic intracranial arteries by intraarterial papaverine administration (1998)

In all treatment groups an increase was found in the average arterial diameters ranging from 2.8 to 73.9%, with a mean increase of 26.5%. Increases in diameter were observed in proximal, intermediate, and distal arteries. The timing of treatments ranged from Day 3 to Day 19 post-SAH, and there was no relationship between timing and arterial responsiveness (r = -0.06). There was a moderately good correlation between the degree of vasospasm in an artery and its responsiveness to papaverine (r = -0.54, -0.66, and -0.66, for proximal, intermediate, and distal arteries, respectively). The effect of papaverine did not persist until the following day in patients in whom repeated angiography was performed.
The LOCATA Challenge Data Corpus for Acoustic Source Localization and Tracking (2018)

Algorithms for acoustic source localization and tracking are essential for a wide range of applications such as personal assistants, smart homes, tele-conferencing systems, hearing aids, or autonomous systems. Numerous algorithms have been proposed for this purpose which, however, are not evaluated and compared against each other by using a common database so far. The IEEE-AASP Challenge on sound source localization and tracking (LOCATA) provides a novel, comprehensive data corpus for the objective benchmarking of state-of-the-art algorithms on sound source localization and tracking. The data corpus comprises six tasks ranging from the localization of a single static sound source with a static microphone array to the tracking of multiple moving speakers with a moving microphone array. It contains real-world multichannel audio recordings, obtained by hearing aids, microphones integrated in a robot head, a planar and a spherical microphone array in an enclosed acoustic environment, as well as positional information about the involved arrays and sound sources represented by moving human talkers or static loudspeakers.
SPHEREx: NASA's near-infrared spectrophotometric all-sky survey (2020)

SPHEREx, the Spectro-Photometer for the History of the Universe, Epoch of Reionization, and ices Explorer, is a NASA MIDEX mission planned for launch in 2024. SPHEREx will carry out the first all-sky spectral survey at wavelengths between 0.75µm and 5µm with spectral resolving power ~40 between 0.75 and 3.8µm and ~120 between 3.8 and 5µm At the end of its two-year mission, SPHEREx will provide 0.75-to-5µm spectra of each 6.”2x6.”2 pixel on the sky - 14 billion spectra in all. This paper updates an earlier description of SPHEREx presenting changes made during the mission's Preliminary Design Phase, including a discussion of instrument integration and test ow and a summary of the data processing, analysis, and distribution plans.
Research of Surface Generation Mechanisms in Single-Point Diamond Turning (2007)

One of the remarkable achievements of nanotechnology is the ability to achieve nanometric surface finishes in single-point diamond turning of high-precision components for complex optical surfaces. A better understanding of the surface generation mechanisms is of prime importance for the development for the prediction of the surface roughness. This paper presents a study of mechanisms of nano-surface generation in single-point diamond turning of various types of materials.
Cyclit‐Reaktionen, XVI. Synthese von Varianten des Valiolamins (1987)

Abstract In das Enon 2 kann mit dem Anion des 5‐Methyl‐1,3,5‐dithiazinans 3 eine Seitenkette unter Bildung von 4 eingeführt werden, aus dem nach Spaltung und Reduktion das Hydroxymethyl‐verzweigte Inosit‐Derivat 6 erhältlich ist. Epoxidierung von 6 führt zum Epoxid 10 , das nach Benzylierung zu 12 mit Natriumazid in das Epoxidöffnungsprodukt 14 überführbar ist. Die Hydrierung von 14 ergibt das hydroxylierte Valiolamin‐Derivat 16 . Die aus 18 erhältliche Ulose 19 kann mit Hydroxylamin in die Oxime 20 und 21 umgewandelt werden. Die Hydrierung der Oxime führt zu den Aminen 22, 23 und 25 . Nach der Entblockierung ergeben diese die Hydrochloride der drei Varianten des Valiolamins 26 , 27 und 28 .
1550nm all-fiber interferometer for partial discharge detection in oil-insulated power transformer (2006)

A fiber-interferometric sensor realized with standard telecommunication components operating at 1550nm is developed to detect acoustic emissions from partial discharges in oilinsulated transformers. Sensor performance is compared with typical electric measurement in realistic harsh environment.
Deep Crash Detection From Vehicular Sensor Data With Multimodal Self-Supervision (2021)

The ability to detect vehicle accidents from on-board sensor data is of the utmost importance to provide prompt assistance to prevent injuries and fatalities. In this article, we present a novel deep learning method capable of analyzing time series recorded from Inertial Measurement Units (IMU) and GPS devices to recognize the presence of an accident along with its severity. We propose a neural architecture capable of exploiting the different sensor streams (i.e., acceleration, gyroscope, and GPS speed), a multimodal contrastive self-supervised training procedure, and an ad-hoc stack of data augmentation techniques, specifically designed to counteract the extreme class imbalance and to improve the generalization capabilities of the whole pipeline. The proposed method has been validated against several state-of-the-art methods on a large and highly imbalanced dataset, composed of more than 200 thousand time series collected from US vehicles, with different vehicle sizes and traveling on different types of road. Our method achieves an average-precision score (AP) of 0.9 in the detection of crashes and 0.76 in the detection of severe crashes, significantly outperforming all the other approaches, and has small footprint and latency, so that it can easily be deployed on embedded devices.
hnRNP A1-mediated translational regulation of the G quadruplex-containing RON receptor tyrosine kinase mRNA linked to tumor progression (2016)

The expression and role of RNA binding proteins (RBPs) controlling mRNA translation during tumor progression remains largely uncharacterized. Analysis by immunohistochemistry of the expression of hnRNP A1, hnRNPH, RBM9/FOX2, SRSF1/ASF/SF2, SRSF2/SC35, SRSF3/SRp20, SRSF7/9G8 in breast tumors shows that the expression of hnRNP A1, but not the other tested RBPs, is associated with metastatic relapse. Strikingly, hnRNP A1, a nuclear splicing regulator, is also present in the cytoplasm of tumor cells of a subset of patients displaying exceedingly worse prognosis. Expression of a cytoplasmic mutant of hnRNP A1 leads to increased translation of the mRNA encoding the tyrosine kinase receptor RON/MTS1R, known for its function in tumor dissemination, and increases cell migration in vitro. hnRNP A1 directly binds to the 5' untranslated region of the RON mRNA and activates its translation through G-quadruplex RNA secondary structures. The correlation between hnRNP A1 and RON tumoral expression suggests that these findings hold clinical relevance.
Image to Image Translation for Domain Adaptation (2018)

We propose a general framework for unsupervised domain adaptation, which allows deep neural networks trained on a source domain to be tested on a different target domain without requiring any training annotations in the target domain. This is achieved by adding extra networks and losses that help regularize the features extracted by the backbone encoder network. To this end we propose the novel use of the recently proposed unpaired image-to-image translation framework to constrain the features extracted by the encoder network. Specifically, we require that the features extracted are able to reconstruct the images in both domains. In addition we require that the distribution of features extracted from images in the two domains are indistinguishable. Many recent works can be seen as specific cases of our general framework. We apply our method for domain adaptation between MNIST, USPS, and SVHN datasets, and Amazon, Webcam and DSLR Office datasets in classification tasks, and also between GTA5 and Cityscapes datasets for a segmentation task. We demonstrate state of the art performance on each of these datasets.
ChemInform Abstract: Synthesis of Pyrrolidines and Pyrroles by Tandem Amination/Cyanation/Alkylation and Amination/Oxidation Sequences. (2015)

Abstract A three component tandem reaction of primary amino‐tethered alkynes gives α‐CN substituted pyrrolidines in good regioselectivities.
NMR characterization of erodible copolymers (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNMR characterization of erodible copolymersEyal Ron, Edith Mathiowitz, George Mathiowitz, Abram Domb, and Robert LangerCite this: Macromolecules 1991, 24, 9, 2278–2282Publication Date (Print):April 29, 1991Publication History Published online1 May 2002Published inissue 29 April 1991https://pubs.acs.org/doi/10.1021/ma00009a024https://doi.org/10.1021/ma00009a024research-articleACS PublicationsRequest reuse permissionsArticle Views304Altmetric-Citations53LEARN 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
OUP accepted manuscript (2021)

CRISPR-Cas9 is an RNA-guided DNA endonuclease involved in bacterial adaptive immunity and widely repurposed for genome editing in human cells, animals and plants. In bacteria, RNA molecules that guide Cas9's activity derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-Cas2 CRISPR integrase. How cells generate the specific lengths of DNA required for integrase capture is a central unanswered question of type II-A CRISPR-based adaptive immunity. Here, we show that an integrase supercomplex comprising guide RNA and the proteins Cas1, Cas2, Csn2 and Cas9 generates precisely trimmed 30-base pair DNA molecules required for genome integration. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming by a mechanism that is independent of the guide RNA sequence. These results show that Cas9 possesses a distinct catalytic capacity for generating immunological memory in prokaryotes.
Methylation in the Core-promoter Region of the Chondromodulin-I Gene Determines the Cell-specific Expression by Regulating the Binding of Transcriptional Activator Sp3 (2004)

Transcriptional regulation of cell- and stage-specific genes is a crucial process in the development of mesenchymal tissues. Here we have investigated the regulatory mechanism of the expression of the chondromodulin-I (ChM-I) gene, one of the chondrocyte-specific genes, in osteogenic cells using osteosarcoma (OS) cells as a model. Methylation-specific sequence analyses revealed that the extent of methylation in the core-promoter region of the ChM-I gene was correlated inversely with the expression of the ChM-I gene in OS primary tumors and cell lines. 5-Aza-deoxycytidine treatment induced the expression of the ChM-I gene in ChM-I-negative OS cell lines, and the induction of expression was associated tightly with the demethylation of cytosine at -52 (C(-52)) in the middle of an Sp1/3 binding site to which the Sp3, but not Sp1, bound. The replacement of C(-52) with methyl-cytosine or thymine abrogated Sp3 binding and also the transcription activity of the genomic fragment including C(-52). The inhibition of Sp3 expression by small interfering RNA reduced the expression of the ChM-I gene in ChM-I-positive normal chondrocytes, indicating Sp3 as a physiological transcriptional activator of the ChM-I gene. These results suggest that the methylation status of the core-promoter region is one of the mechanisms to determine the cell-specific expression of the ChM-I gene through the regulation of the binding of Sp3.