gebhart/patrepeval huggingface dataset:
Scoring functions and enrichment: a case study on Hsp90 (2007)

Overall, we demonstrate the validity of virtual screening as a method for identifying new leads from a pool of ligands with similar physicochemical properties and we believe that the outcome of this study provides useful insight into the setting up of a suitable docking and scoring protocol, resulting in enrichment of 'target active' compounds.
Abstract 056: The Impact of Periostin as A Regulator of Cardiac Remodeling (2013)

Background: Periostin (PN) is a matricellular protein that is induced by mechanostress and regulates organ remodeling. We previously documented that over-expression of full-length periostin (periostin1:Pn1) resulted in ventricular dilation with enhanced interstitial collagen deposition. Controversially, supplement of PN splicing variant lacking exon 17 (periostin2:Pn2) was reported to accelerate cardiac repair with the induction of cardiomyocyte proliferation and angiogenesis. The aim of this study was to investigate the different roles of PN splicing isoforms in cardiac remodeling. Methods: Coronary ligation was employed to induce cardiac remodeling in rat. A neutralizing antibody against exon17 (Pn1Ab) was injected intravenously every 6 days until day 21. Mice were followed ultrasonographically and then euthanized for histological analysis at day 56. In vitro study, the effect of each PN splicing isoform was assessed in rat cardiac fibroblast and HUVEC. Results: Administration of Pn1Ab resulted in 24.1 % decrease in infarct size and 38.2 % decrease in fibrotic area at day 56 post-operation (n=21, P&lt;0.05). Consistently, echocardiography demonstrated 26.3 % better ejection fraction (P&lt;0.05). Inhibition of fibrosis was associated with suppressed fibrosis-related gene expression such as collagen I, collagen III and TGF-beta1. Importantly, the number of myofibroblasts was significantly reduced in the Pn1Ab group, while neither cardiomyocyte proliferation nor angiogenesis was detected. In vitro study, Pn2 administration for HUVEC induced proliferation and tube formation however Pn1 did not. Pn1 administration accelerated maturation of myofibroblast more than Pn2. Conclusions: Pn1Ab preserved cardiac function through anti-fibrotic effect without cardiomyocyte proliferation and angiogenesis. Specific blockade of Pn1 without Pn2 will potentially lead to new therapeutic targets on a molecular basis to limit cardiac remodeling.
Enhanced and inhibited visible spontaneous emission by atoms in a confocal resonator. (1987)

We report the alteration of visible spontaneous emission by atoms coupled to the degenerate modes of a confocal resonator. The partial emission rate into the resonator modes is enhanced by a factor of 19 when the resonator is tuned to the atomic transition frequency and inhibited by a factor of 42 when it is detuned. This results in a fractional increase of 1.6% and decrease of 0.5%, respectively, in the total spontaneous emission rate, which we verify by monitoring changes in the intensity of light emitted out the sides of the resonator as it is tuned.
Generative Classifiers as a Basis for Trustworthy Computer Vision. (2020)

With the maturing of deep learning systems, trustworthiness is becoming increasingly important for model assessment. We understand trustworthiness as the combination of explainability and robustness. Generative classifiers (GCs) are a promising class of models that are said to naturally accomplish these qualities. However, this has mostly been demonstrated on simple datasets such as MNIST, SVHN and CIFAR in the past. In this work, we firstly develop an architecture and training scheme that allows for GCs to be trained on the ImageNet classification task, a more relevant level of complexity for practical computer vision. The resulting models use an invertible neural network architecture and achieve a competetive ImageNet top-1 accuracy of up to 76.2%. Secondly, we show the large potential of GCs for trustworthiness. Explainability and some aspects of robustness are vastly improved compared to standard feed-forward models, even when the GCs are just applied naively. While not all trustworthiness problems are solved completely, we argue from our observations that GCs are an extremely promising basis for further algorithms and modifications, as have been developed in the past for feedforward models to increase their trustworthiness. We release our trained model for download in the hope that it serves as a starting point for various other generative classification tasks in much the same way as pretrained ResNet models do for discriminative classification.
Magnetic Resonance Fingerprinting Reconstruction Using Recurrent Neural Networks (2019)

Magnetic Resonance Fingerprinting (MRF) is an imaging technique acquiring unique time signals for different tissues. Although the acquisition is highly accelerated, the reconstruction time remains a problem, as the state-of-the-art template matching compares every signal with a set of possible signals. To overcome this limitation, deep learning based approaches, e.g. Convolutional Neural Networks (CNNs) have been proposed. In this work, we investigate the applicability of Recurrent Neural Networks (RNNs) for this reconstruction problem, as the signals are correlated in time. Compared to previous methods based on CNNs, RNN models yield significantly improved results using in-vivo data.
Lightweight thermal energy recovery system based on shape memory alloys: a DOE ARPA-E initiative (2012)

Over 60% of energy that is generated is lost as waste heat with close to 90% of this waste heat being classified as low grade being at temperatures less than 200&deg;C. Many technologies such as thermoelectrics have been proposed as means for harvesting this lost thermal energy. Among them, that of SMA (shape memory alloy) heat engines appears to be a strong candidate for converting this low grade thermal output to useful mechanical work. Unfortunately, though proposed initially in the late 60's and the subject of significant development work in the 70's, significant technical roadblocks have existed preventing this technology from moving from a scientific curiosity to a practical reality. This paper/presentation provides an overview of the work performed on SMA heat engines under the US DOE (Department of Energy) ARPA-E (Advanced Research Projects Agency - Energy) initiative. It begins with a review of the previous art, covers the identified technical roadblocks to past advancement, presents the solution path taken to remove these roadblocks, and describes significant breakthroughs during the project. The presentation concludes with details of the functioning prototypes developed, which, being able to operate in air as well as fluids, dramatically expand the operational envelop and make significant strides towards the ultimate goal of commercial viability.
Uptake and translocation of imidacloprid, clothianidin and flupyradifurone in seed‐treated soybeans (2015)

This study enhances our understanding of the uptake and distribution of insecticides used as seed treatments in soybean. The uptake and translocation of these insecticides differed in response to soil moisture stress. © 2015 Society of Chemical Industry.
Hydrolytic Stability of Hydrazones and Oximes (2008)

O toppt N, nicht aber N+: Hydrazone und Oxime sind gängige, doch leicht hydrolysierbare Verbindungen. Die Hydrolysestabilitäten isostruktureller Hydrazone und von einem Oxim wurden bei pD 5.0–9.0 untersucht. Die Geschwindigkeitskonstante der säurekatalysierten Hydrolyse war beim Oxim fast 103-mal kleiner als bei einfachen Hydrazonen, und ein Trialkylhydrazoniumion (durch Kondensation gebildet) war noch stabiler als das Oxim. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z802651_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Tools for real-time signal-processing research (1993)

The use of digital signal processing (DSP) devices for real-time communication applications is discussed. The authors comment on distinguishing aspects of DSP architecture, describing not so much individual processors as those features common to DSPs and distinct from modern general-purpose processors. They describe three DSP32xx-based machines that support DSP algorithm implementation: SURF-board, HoBo, and DSP3. They also described rtpi, a source-code debugger for workstations and for the AT&T DSP32C signal-processor integrated circuit, and dspx, a collection of subroutines and host programs that provides an execution environment for DSPs akin to the UNIX environment. These tools facilitate the transfer of algorithms from mainframes or workstations to DSP hardware. Included are case studies of two real-time implementations: the low-delay CELP (LD-CELP) speech coder and the decoder side of the perceptual audio coder (PAC), an algorithm that compresses CD-quality audio into a 128-kb/s stream without perceptible distortion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 Å resolution. Conservation of solvent sites in RNase-A high-resolution structures (1993)

The X-ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2'-CMP) has been determined at 1.6 A resolution and refined by restrained least squares to R = 0.17 for 11 945 reflections. Binding of the inhibitor molecule to the protein is confirmed to be in the productive mode associated with enzyme activity. A study of conserved solvent sites amongst high-resolution structures in the same crystal form reveals a stabilizing water cluster between the N and C termini.
Molecular subtype specific efficacy of MEK inhibitors in pancreatic cancers (2017)

Pancreatic cancer is an increasing cause of cancer related death worldwide. KRAS is the dominant oncogene in this cancer type and molecular rationale would indicate, that inhibitors of the downstream target MEK could be appropriate targeted agents, but clinical trials have failed so far to achieve statistically significant benefit in unselected patients. We aimed to identify predictive molecular biomarkers that can help to define subgroups where MEK inhibitors might be beneficial alone or in combination. Next-generation sequencing data of 50 genes in three pancreatic cancer cell lines (MiaPaCa2, BxPC3 and Panc1) were analyzed and compared to the molecular profile of 138 clinical pancreatic cancer samples to identify the molecular subtypes of pancreatic cancer these cell lines represent. Luminescent cell viability assay was used to determine the sensitivity of cell lines to kinase inhibitors. Western blot was used to analyze the pathway activity of the examined cell lines. According to our cell viability and pathway activity data on these model cell lines only cells harboring the rare G12C KRAS mutation and low EGFR expression are sensitive to single MEK inhibitor (trametinib) treatment. The common G12D KRAS mutation leads to elevated baseline Akt activity, thus treatment with single MEK inhibitors fails. However, combination of MEK and Akt inhibitors are synergistic in this case. In case of wild-type KRAS and high EGFR expression MEK inhibitor induced Akt phosphorylation leads to trametinib resistance which necessitates for MEK and EGFR or Akt inhibitor combination treatment. In all we provide strong preclinical rational and possible molecular mechanism to revisit MEK inhibitor therapy in pancreatic cancer in both monotherapy and combination, based on molecular profile analysis of pancreatic cancer samples and cell lines. According to our most remarkable finding, a small subgroup of patients with G12C KRAS mutation may still benefit from MEK inhibitor monotherapy.
Differential release of chromatin-bound IL-1α discriminates between necrotic and apoptotic cell death by the ability to induce sterile inflammation (2010)

IL-1alpha, like IL-1beta, possesses multiple inflammatory and immune properties. However, unlike IL-1beta, the cytokine is present intracellularly in healthy tissues and is not actively secreted. Rather, IL-1alpha translocates to the nucleus and participates in transcription. Here we show that intracellular IL-1alpha is a chromatin-associated cytokine and highly dynamic in the nucleus of living cells. During apoptosis, IL-1alpha concentrates in dense nuclear foci, which markedly reduces its mobile nature. In apoptotic cells, IL-1alpha is retained within the chromatin fraction and is not released along with the cytoplasmic contents. To simulate the in vivo inflammatory response to cells undergoing different mechanisms of death, lysates of cells were embedded in Matrigel plugs and implanted into mice. Lysates from cells undergoing necrosis recruited cells of the myeloid lineage into the Matrigel, whereas lysates of necrotic cells lacking IL-1alpha failed to recruit an infiltrate. In contrast, lysates of cells undergoing apoptotic death were inactive. Cells infiltrating the Matrigel were due to low concentrations (20-50 pg) of the IL-1alpha precursor containing the receptor interacting C-terminal, whereas the N-terminal propiece containing the nuclear localization site failed to do so. When normal keratinocytes were subjected to hypoxia, the constitutive IL-1alpha precursor was released into the supernatant. Thus, after an ischemic event, the IL-1alpha precursor is released by hypoxic cells and incites an inflammatory response by recruiting myeloid cells into the area. Tissues surrounding the necrotic site also sustain damage from the myeloid cells. Nuclear trafficking and differential release during necrosis vs. apoptosis demonstrate that inflammation by IL-1alpha is tightly controlled.
Contacts for monolithic 3D architecture: Study of Ni0.9Co0.1 silicide formation (2016)

In this work, we studied the solid-state reaction between a Ni <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.9</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.1</sub> film and a silicon substrate. NiCo silicide is considered to substitute Ni- and NiPt-based silicides in 3D integration in order to extend the bottom transistor thermal stability. Thanks to the combined analysis of sheet resistance data, X-ray reflectivity spectra modelling, X-ray diffraction and wavelength dispersive X-ray fluorescence analyses on Ni <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.9</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.1</sub> /Si samples annealed at various temperatures, we were able to describe the phase sequence of the NiCo silicide formation.
Vertical 3D NAND Flash Memory Technology (2011)

We've developed Bit Cost Scalable (BiCS) flash technology as a three-dimensional memory for the future ultra high density storage devices, which extremely reduces the chip costs by vertically stacking memory arrays with punch and plug process. We've advanced it into Pipe-shaped BiCS flash memory introducing U-shaped NAND string structure, to improve operation window, speed and reliability. 32 G bit test chips with 16 stacked layers by 60nm P-BiCS flash process have been fabricated, and the functionality of Multi-Level-Cell (MLC) operation has been successfully demonstrated. P-BiCS is the most promising candidate of three-dimensional ultra high density data storage memories.
Is the left atrial appendage more than a simple appendage? (2009)

The left atrial appendage (LAA) is a cardiac structure with unique anatomic and functional features. It is significantly more than a simple chamber appended to the left atrium (LA), differing from the LA in structure, function, and hormonal activity. Unfortunately, it is the source of more than 90% of cardiac-based emboli, particularly in atrial fibrillation, mandating lifelong anticoagulation. Percutaneous LAA exclusion was developed to limit or eliminate cardioembolic events in patients with atrial fibrillation. Benign healing of the appendage occurs without adverse hemodynamic effects, and with no residual surface thrombus or tissue damage. The feasibility of this treatment is now established, suggesting that percutaneous therapy is safe, practical and possibly effective to eliminate the need for anticoagulation and significantly reduce cardioembolic events.
Supplementary Table S1 from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine (2023)

&lt;p&gt;Characteristics of patients enrolled to PancSeq protocol&lt;/p&gt;
Cell Therapy for Lung Diseases. Report from an NIH–NHLBI Workshop, November 13–14, 2012 (2013)

The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health convened the Cell Therapy for Lung Disease Working Group on November 13-14, 2012, to review and formulate recommendations for future research directions. The workshop brought together investigators studying basic mechanisms and the roles of cell therapy in preclinical models of lung injury and pulmonary vascular disease, with clinical trial experts in cell therapy for cardiovascular diseases and experts from the NHLBI Production Assistance for Cell Therapy program. The purpose of the workshop was to discuss the current status of basic investigations in lung cell therapy, to identify some of the scientific gaps in current knowledge regarding the potential roles and mechanisms of cell therapy in the treatment of lung diseases, and to develop recommendations to the NHLBI and the research community on scientific priorities and practical steps that would lead to first-in-human trials of lung cell therapy.
OTOMO: Electric wheelchair-type remote communication mobility (2022)

OTOMO is a mobility system that uses telepresence technology to communicate with a passenger in an electric wheelchair and a driver in remote to experience the sensation that they are moving together in the same space. The driver in remote wears an HMD and operates a controller made of a PVC balloon 1.2 m in diameter. The driver feels as if they are a dwarf by operating the 1.2-meter-diameter controller with their entire body while viewing a magnified video of the wheelchair’s surroundings on the HMD. The passenger in the electric wheelchair gives instructions while watching the dwarf-sized driver projected in the cockpit at the front of the vehicle. Driving experiments using OTOMO confirmed interactive communication between the driver and passenger.
Laser ablation sampling system and method (2023)

A method and system for sampling a solid sample material can include the step of mounting the sample material on a support. A sample surface is coated with a surface treatment composition in a dry deposition process. A solvent supply conduit for supplying solvent to the sample surface and a solvent exhaust conduit for withdrawing solvent from the sample surface can be provided. Solvent is flowed from the solvent supply conduit to the surface treatment composition and the sample surface such that the solvent contacts the surface treatment composition. A laser beam is directed from a laser source to the sample and the surface treatment composition. The laser beam will ablate the sample and the surface treatment composition in portions intersected by the laser beam. Ablated sample material enters the solvent liquid and will be transported with the solvent away from the sample surface through the solvent exhaust conduit.
Supplementary Figures 1-7 from Simultaneous Targeting of Two Distinct Epitopes on MET Effectively Inhibits MET- and HGF-Driven Tumor Growth by Multiple Mechanisms (2023)

&lt;p&gt;Supplementary figure 1. Sym015 inhibits viability of cell lines in a synergic manner; Supplementary figure 2. The Sym015 antibodies Hu9338 and Hu9006 bind to 2nd or 3rd blades of MET and block HGF binding; Supplementary figure 3. Sym015 induces MET internalization and degradation in MKN-45 cells; Supplementary figure 4. Sym015 induces MET internalization and degradation in EBC-1 cells; Supplementary figure 5. Sym015 induces MET degradation in MKN-45 and EBC-1 cells; Supplementary figure 6. Sym015 inhibits signaling by MET in EBC-1 cells; Supplementary figure 7. Sym015 inhibits motility of EBC-1&lt;/p&gt;
ChemInform Abstract: Synthesis of Unsymmetrical 2,8‐ and 2,9‐Dihalo‐1,10‐phenanthrolines and Derivatives. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Host Specificity ofRhizobium leguminosarumis Determined by the Hydrophobicity of Highly Unsaturated Fatty Acyl Moieties of the Nodulation Factors (1995)

The nodE genes of Rhizobium leguminosarum bvs, trifolii and viciae strains are the major determinants of the host range of nodulation, Using mass spectrometry we have analyzed the structures of the major and minor lipooligosaccharides produced by two R, leguminosarum strains that differ only in the origin of the nod genes, The strain containing the nod genes of R. l. by. viciae produces lipo-chitin oligosaccharide (LCO) molecules that contain the common cis-vaccenyl (C18:1) or a highly unsaturated acyl (C18:4) group that is determined by nodE (Spaink et al, Nature 354:125-130, 1991), Here we show that, in addition, minor quantities of analogous molecules that contain different common fatty acyl groups such as stearyl (C18:0), palmityl (C16:0), and palmitoyl (C16:1) groups are produced, The set of LCOs produced by the strain containing the R. l. by. trifolii nod genes is similar, but major differences are found in the length and unsaturation of the fatty acyl groups of various LCOs. The R. l, by. trifolii strain does not produce LCO molecules that contain the C18:4 fatty acyl group. Instead, a complex mixture of other unsaturated fatty acyl groups containing either two, three, or four double bonds is produced, These novel fatty acyl groups are more hydrophobic than the C18:4 fatty acyl group found in by. viciae, as judged by highperformance liquid chromatography retention times, probably as a result of the longer carbon chain length, the lack of a cis double bond, or both, Another difference is that the relative amount of highly unsaturated fatty acid-containing LCOs produced by R. l. by. trifolii is much smaller An isogenic R. l. by. trifolii strain containing a Tn5 insertion in the nodE gene only produces LCOs containing the common fatty acyl groups and not the highly unsaturated types, The results indicate that the difference in the host range of the R. l. bvs, viciae and trifolii is determined by the overall hydrophobicity of the highly unsaturated fatty acyl moieties of LCOs rather than by a specific structural feature.