gebhart/patrepeval huggingface dataset:
Binding energy shifts for nitrogen‐containing graphene‐based electrocatalysts – experiments and DFT calculations (2016)

A detailed analysis of the physiochemical nature, thermodynamic properties, and electrochemical characterization of N motifs present in self‐assembled nitrogen functionalized transition metal and nitrogen doped graphene pyrolyzed materials has been conducted in this study. First principle density‐functional‐theory calculations were performed to assess the thermochemistry of Fe–N x and graphitic‐N defects and to predict N1s core‐level‐shifts. Combining this prediction with our X‐ray photoelectron spectroscopy and rotating ring disk electrode experiments, we find that graphitic‐N contributes significantly to hydrogen peroxide formation in oxygen reduction reactions, while materials containing nitrogen coordinated transition metal result in the complete reduction of oxygen to water. Lastly, we show how the synergy of experimental, electrochemical, and computational approaches can accelerate the accurate identification and characterization of nitrogen functionalized graphene moieties present in pyrolyzed electrocatalysts for fuel cells. Copyright © 2016 John Wiley &amp; Sons, Ltd.
Solving the Straggler Problem with Bounded Staleness (2018)

Many important applications fall into the broad class of <em>iterative convergent </em>algorithms. Parallel implementations of these algorithms are naturally expressed using the Bulk Synchronous Parallel (BSP) model of computation. However, implementations using BSP are plagued by the straggler problem, where every transient slowdown of any given thread can delay all other threads. This paper presents the<em> Stale Synchronous Parallel </em>(SSP) model as a generalization of BSP that preserves many of its advantages, while avoiding the straggler problem. Algorithms using SSP can execute efficiently, even with significant delays in some threads, addressing the oft-faced straggler problem.
Mathematical modeling of chemotaxis and glial scarring around implanted electrodes (2015)

It is well known that the implantation of electrodes for deep brain stimulation or microelectrode probes for the recording of neuronal activity is always accompanied by the response of the brain’s immune system leading to the formation of a glial scar around the implantation sites. The implantation of electrodes causes massive release of adenosine-5′-triphosphate (ATP) and different cytokines into the extracellular space and activates the microglia. The released ATP and the products of its hydrolysis, such as ADP and adenosine, become the main elements mediating chemotactic sensitivity and motility of microglial cells via subsequent activation of P2Y _2,12 as well as A3A/A2A adenosine receptors. The size and density of an insulating sheath around the electrode, formed by microglial cells, are important criteria for the optimization of the signal-to-noise ratio during microelectrode recordings or parameters of electrical current delivered to the brain tissue. Here, we study a purinergic signaling pathway underlying the chemotactic motion of microglia towards implanted electrodes as well as the possible impact of an anti-inflammatory coating consisting of the interleukin-1 receptor antagonist. We present a model describing the formation of a stable aggregate around the electrode due to the joint chemo-attractive action of ATP and ADP and the mixed influence of extracellular adenosine. The bioactive coating is modeled as a source of chemo-repellent located near the electrode surface. The obtained analytical and numerical results allowed us to reveal the dependences of size and spatial location of the insulating sheath on the amount of released ATP and estimate the impact of immune suppressive coating on the scarring process.
J044011 Effect of High-Speed Laser Cutting Process on Mechanical Behavior of CFRTP (2012)

Carbon fiber reinforced thermo plastics (CFRTP), which is expected to reduce the weight of transportations and is made higher speed and lower cost than these of CFRP (thermosetting plastics), was cut by a CO_2 gas laser (10μm, 800W, 20kHz, lm/min), CW single-mode fiber laser (1.07[im, 300W or 2000W, CW, lm/min or 7m/min) and a machining with a cemented carbide end milling. Although the high-power laser cutting processes make it possible to improve cutting rate of CFRTP, the laser-cut specimens clearly showed a thermal damage with a heat-affected zone (HAZ) identified by a micro X-ray CT analysis. These specimens were lower tensile strjpnth and fatigue strjpnth than milling-cut specimens. In laser-cut specimens, specimens cut by the CO_2 gas laser exhibited the lowest strjpnth of all processes. And, the 2000W CW single-mode fiber laser (7m/min), which is the highest cutting speed and the shortest waveljpnths, was reduced the degradation of strjpnth as compared with the 300W CW single-mode fiber laser (lm/min) and the CO_2 gas laser.
ChemInform Abstract: Synthesis and Structure of ITQ‐3, the First Pure Silica Polymorph with a Two‐Dimensional System of Straight Eight‐Ring Channels. (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.
Improving the Sensitivity and Specificity of Tumor Contrast in Fluorescence Imaging by Employing an Untargeted Fluorescent Reporter (2012)

A dual-reporter fluorescence imaging approach is presented that can quantify biomarker expression in vivo. The approach was also demonstrated to provide better tumor contrast compared to targeted fluorescence uptake alone.
<title>Preliminary performance characteristics of a dual-energy KCD</title> (1995)

A kinestatic charge detector (KCD) with segmented signal-collection fingers was constructed to evaluate the dual-energy x-ray imaging performance of a KCD. The front segments of the KCD signal-collectors produce a digital low-energy image and the back segments produce a digital high-energy image. A gap between the front and back signal-collectors is used as a filter to increase the separation between the mean energies absorbed in the front and back segments. Preliminary measurements have been performed on the dual-energy KCD to determine its dual-energy imaging characteristics. The KCD output signal has been measured as a function of depth in the chamber. The ion drift velocity, modulation transfer function (MTF), detective quantum efficiency (DQE) and Wiener spectrum have been determined for both the front (low-energy) and back (high-energy) signal detection regions of the KCD.
Data from Selective and Potent Raf Inhibitors Paradoxically Stimulate Normal Cell Proliferation and Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;Raf inhibitors are under clinical investigation, specifically in patients with tumor types harboring frequent activating mutations in B-Raf. Here, we show that cell lines and tumors harboring mutant B-Raf were sensitive to a novel series of Raf inhibitors (e.g., &lt;sup&gt;V600E&lt;/sup&gt;B-Raf A375, IC&lt;sub&gt;50&lt;/sub&gt; on cells = 2 nmol/L; ED&lt;sub&gt;50&lt;/sub&gt; on tumor xenografts = 1.3 mg/kg). However, in cells and tumors with wild-type B-Raf, exposure to Raf inhibitors resulted in a dose-dependent and sustained activation of mitogen-activated protein kinase signaling. In some of these cell lines, Raf inhibition led to entry into the cell cycle, enhanced proliferation, and significantly stimulated tumor growth &lt;i&gt;in vivo&lt;/i&gt;. Inhibition with structurally distinct Raf inhibitors or isoform-specific small interfering RNA knockdown of Raf showed that these effects were mediated directly through Raf. Either A-Raf or C-Raf mediated the Raf inhibitor–induced mitogen-activated protein kinase pathway activation in an inhibitor-specific manner. These paradoxical effects of Raf inhibition were seen in malignant and normal cells &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Hyperplasia of normal epithelial cells in the esophagus and the stomach was evident in mice with all efficacious Raf inhibitors (&lt;i&gt;n&lt;/i&gt; = 8) tested. An implication of these results is that Raf inhibitors may induce unexpected normal cell and tumor tissue proliferation in patients. Mol Cancer Ther; 9(8); 2399–410. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Germline BRCA2 gene mutations in patients with apparently sporadic pancreatic carcinomas. (1996)

Germline mutations in BRCA2 predispose carriers to the development of breast, ovarian, and a variety of other cancers. The original localization of the BRCA2 gene was aided by its homozygous deletion in a pancreatic carcinoma; indeed, an excess of pancreatic carcinoma has been seen in some BRCA2 cancer families. To determine the involvement of BRCA2 in pancreatic carcinomas, we screened for BRCA2 alterations in an unselected panel of 41 adenocarcinomas of the pancreas (30 pancreatic adenocarcinoma xenografts and 11 pancreatic cancer cell lines). Of the 15 (27%) that had allelic loss at the BRCA2 locus, 4 (9.8%) had abnormalities in the second allele upon screening of the entire BRCA2 gene by in vitro synthesized protein assay. Three of the four mutations were considered germline in origin (7.3% overall; two were confirmed in normal tissue, and one was the 6174delT mutation from the pancreatic cancer cell line CAPAN-1, for which normal tissue was unavailable). The identification of two 6174delT mutations in this series prompted us to evaluate the prevalence of this mutation in an overlapping consecutive series of 245 patients who underwent pancreatoduodenectomy for adenocarcinoma of the pancreas. Sequence analysis of this limited region of the gene identified two additional mutations: (a) one additional germline 6174delT mutation (2 of 245, 0.8% overall); and (b) a second nearby germline 6158insT mutation. One of the patients with a germline mutation had a single relative with breast cancer, and another had a single relative with prostate cancer. None had a family history of pancreatic cancer. The incidence of germline BRCA2 mutations in apparently sporadic pancreatic cancer may be at least as high as in breast or ovarian cancer. Our results suggest that some familial risks for carcinoma will be evident only through a population-based application of gene screening techniques because a low disease penetrance of the germline mutations in some families often evades clinical suspicion.
Supplementary Figure 2 from Somatic Epigenetic Silencing of <i>RIPK3</i> Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma (2023)

&lt;p&gt;Human malignant mesothelioma (MM) cell lines frequently show down regulated expression of RIPK3 protein. Western blotting illustrating RIPK3 protein expression in 20 human MM cell lines. Normal mesothelial cell line NM311A was used as a control.&lt;/p&gt;
ALITHEIA (2014)

We consider a scenario in which a data owner outsources storage of a large graph to an untrusted server; the server performs computations on this graph in response to queries from a client (whether the data owner or others), and the goal is to ensure verifiability of the returned results. Existing work on verifiable computation (VC) would compile each graph computation to a circuit or a RAM program and then use generic techniques to produce a cryptographic proof of correctness for the result. Unfortunately, such an approach will incur large overhead, especially in the proof-computation time. In this work we address the above by designing, building, and evaluating ALITHEIA, a nearly practical VC system tailored for graph queries such as computing shortest paths, longest paths, and maximum flow. The underlying principle of ALITHEIA is to minimize the use of generic VC systems by leveraging various algorithmic techniques specifically for graphs. This leads to both theoretical and practical improvements. Asymptotically, it improves the complexity of proof computation by at least a logarithmic factor. On the practical side, we show that ALITHEIA achieves significant performance improvements over current state-of-the-art (up to a 108x improvement in proof-computation time, and a 99.9% reduction in server storage), while scaling to 200,000-node graphs.
Supplementary Data from Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15<sup>+</sup> Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
The Virtual Kinect (2021)

The COVID-19 pandemic impacted researches that depended on making tests on patients and teams that had to be divided to avoid crowding in laboratories. Sharing equipment is no longer a simple strategy; the acquisition of extra equipment is beyond the means of many researchers. Research with Kinect V2 applied to body tracking suffers from sanitary restrictions, product discontinuation and limited access to newer sensors (like the Azure Kinect). Kinect V2 is an RGB-D sensor with many applications in health, ergonomics, sports, games and other areas. That is why a lot of research is still under development with it. Because of the applicability of Kinect V2 on research and the current acquisition limitations, Virtual Kinect (VK) was created. VK is an open-source solution that enables the programmer to code using Kinect SDK functions and test it without a Kinect V2 sensor or a previous recording. It simulates the behavior of a Kinect V2 sensor through MediaPipe’s Pose estimation, providing RGB image and joint tracking information, correlating the joints of the two devices. This correlation is possible due to the proximity of the devices’ joint estimates. The VK was made to be simple and practical, so that its use only depends on the DLL exchange and the use of an ordinary RGB camera.
Spatial coherence radar applied for tilted surface profilometry (2003)

A new method of spatial coherence profilometry is demon- strated. The surface profile is measured by shifting the spatial degree of coherence gradually in its own space of existence, and modulating its phase angle. In each point of the sample we analyze the change of light intensity versus the phase of a Fresnel zone pattern used as the intensity distribution of an incoherent quasimonochromatic source. The tilt of the surface is measured by gradually shifting the Fresnel zone plate on its transverse plane. This shift of the light source rotates the spatial degree of coherence around the coordinate origin until the condition of maximum interference visibility is fulfilled. The method works without any mechani- cal movement and a quasimonochromatic light illuminates the interfero- metric system. Experimental demonstration of the new method is pre- sented. © 2003 Society of Photo-Optical Instrumentation Engineers.
Inter-disciplinary characterisation of carbonate reservoirs. ALBION, a multi-scales dynamic analogue (2019)

International audience
The Primary Physiological Roles of Autoinducer 2 in Escherichia coli Are Chemotaxis and Biofilm Formation (2021)

Autoinducer 2 (AI-2) is a ubiquitous metabolite but, instead of acting as a "universal signal," relatively few phenotypes have been associated with it, and many scientists believe AI-2 is often a metabolic byproduct rather than a signal. Here, the aim is to present evidence that AI-2 influences both biofilm formation and motility (swarming and chemotaxis), using <i>Escherichia coli</i> as the model system, to establish AI-2 as a true signal with an important physiological role in this bacterium. In addition, AI-2 signaling is compared to the other primary signal of <i>E. coli</i>, indole, and it is shown that they have opposite effects on biofilm formation and virulence.
Investigation of vadose zone flow mechanisms in unsaturated chalk using cross-borehole ERT (1997)

Groundwater resources are vulnerable to surface-derived contaminants resulting from human activity. The vadose zone is a natural barrier between contaminant sources and groundwater stored in aquifers. The fate of contaminants currently in transit within the vadose zone (as determined by operative transport mechanisms) is of political, economic and social concern. Hence techniques are required to investigate solute transport mechanisms within the vadose zone.
Towards Emergent Language Symbolic Semantic Segmentation and Model Interpretability (2020)

Recent advances in methods focused on the grounding problem have resulted in techniques that can be used to construct a symbolic language associated with a specific domain. Inspired by how humans communicate complex ideas through language, we developed a generalized Symbolic Semantic ($\text{S}^2$) framework for interpretable segmentation. Unlike adversarial models (e.g., GANs), we explicitly model cooperation between two agents, a Sender and a Receiver, that must cooperate to achieve a common goal. The Sender receives information from a high layer of a segmentation network and generates a symbolic sentence derived from a categorical distribution. The Receiver obtains the symbolic sentences and co-generates the segmentation mask. In order for the model to converge, the Sender and Receiver must learn to communicate using a private language. We apply our architecture to segment tumors in the TCGA dataset. A UNet-like architecture is used to generate input to the Sender network which produces a symbolic sentence, and a Receiver network co-generates the segmentation mask based on the sentence. Our Segmentation framework achieved similar or better performance compared with state-of-the-art segmentation methods. In addition, our results suggest direct interpretation of the symbolic sentences to discriminate between normal and tumor tissue, tumor morphology, and other image characteristics.
Opportunistic flooding to improve TCP transmit performance in virtualized clouds (2011)

Virtualization is a key technology that powers cloud computing platforms such as Amazon EC2. Virtual machine (VM) consolidation, where multiple VMs share a physical host, has seen rapid adoption in practice with increasingly large number of VMs per machine and per CPU core. Our investigations, however, suggest that the increasing degree of VM consolidation has serious negative effects on the VMs' TCP transport performance. As multiple VMs share a given CPU, the scheduling latencies, which can be in the order of tens of milliseconds, substantially increase the typically sub-millisecond round-trip times (RTTs) for TCP connections in a datacenter, causing significant degradation in throughput. In this paper, we propose a light-weight solution called vFlood that (a) allows a TCP sender VM to opportunistically flood the driver domain in the same host, and (b) offloads the VM's TCP congestion control function to the driver domain in order to mask the effects of VM consolidation. Our evaluation of a vFlood prototype on Xen suggests that vFlood substantially improves TCP transmit throughput with minimal per-packet CPU overhead. Further, our application-level evaluation using Apache Olio, a web 2.0 cloud application, indicates a 33% improvement in the number of operations per second.
Adaptive optics from microscopy to nanoscopy (2014)

Adaptive optics have been introduced to compensate the effects of aberrations in high resolution microscopy. Adaptive elements, such as deformable mirrors or spatial light modulators enable the dynamic correction of aberrations in a range of applications. These methods have proved particularly useful in three dimensional imaging of tissue specimens. We review the principles behind these methods and their application to high and super resolution microscopy.
Private Lives 2: The second national survey of the health and wellbeing of gay, lesbian, bisexual and transgender (GLBT) Australians (2023)

Series: Monograph series (La Trobe University. Australian Research Centre in Sex, Health and Society) ; no. 86<br><br>Private Lives 2 (PL2) is areport on the second national survey of the health and wellbeing of gay, lesbian, bisexual, and transgender (GLBT) Australians. The first Private Lives (PL1) was released in 2006 and was, at that time, the largest survey of its kind conducted anywhere in the world. In 2011, 3,835 GLBT respondents successfully completed PL2. The project was supported by beyondblue with funds from The Movember Foundation, with additional funds provided by the Victorian Department of Health and a La Trobe University faculty grant. The project was managed jointly by Gay and Lesbian Health Victoria (GLHV) and the Australian Research Centre in Sex, Health and Society (ARCSHS) La Trobe University.<br><br>La Trobe University. Australian Research Centre in Sex, Health and Society
Secondary Metabolites from Three Florida Sponges with Antidepressant Activity (2008)

Brominated indole alkaloids are a common class of metabolites reported from sponges of the order Verongida. Herein we report the isolation, structure determination, and activity of metabolites from three Florida sponges, namely, Verongula rigida (order Verongida, family Aplysinidae), Smenospongia aurea, and S. cerebriformis (order Dictyoceratida, family Thorectidae). All three species were investigated chemically, revealing similarities in secondary metabolites. Brominated compounds, as well as sesquiterpene quinones and hydroquinones, were identified from both V. rigida and S. aurea despite their apparent taxonomic differences at the ordinal level. Similar metabolites found in these distinct sponge species of two different genera provide evidence for a microbial origin of the metabolites. Isolated compounds were evaluated in the Porsolt forced swim test (FST) and the chick anxiety-depression continuum model. Among the isolated compounds, 5,6-dibromo- N,N-dimethyltryptamine ( 1) exhibited significant antidepressant-like action in the rodent FST model, while 5-bromo- N,N-dimethyltryptamine ( 2) caused significant reduction of locomotor activity indicative of a potential sedative action. The current study provides ample evidence that marine natural products with the diversity of brominated marine alkaloids will provide potential leads for antidepressant and anxiolytic drugs.
Insertion of transition metal ions into cationic sites of high-silica zeolites by reaction in the solid phase. I. Topochemical reaction of copper compounds with mordenite and pentasils (1986)

Roasting of mechanical mixtures of copper compounds with the H forms of such zeolites as mordenite and pentasil is accompanied by migration of a part of the Cu/sup 2 +/ ions into zeolite channels and their localization at those very cationic sites that are typical for the respective samples obtained by ion exchange. In the case of pentasils, the major part of copper is localized in the channels as isolated coordination-unsaturated Cu/sup 2 +/ cations, which is confirmed by the strong influence of O/sub 2/ adsorption on the hfs of the ESR spectra. A linear relationship between the number of Cu(II) cations capable of entering the zeolite and the Al/sup 3 +/ content in the pentasil cage was found in a study of pentasils having different SiO/sub 2//Al/sub 2/O/sub 3/ ratios. Thus, the method opens up new possibilities of inserting multicharged cations into high-silica zeolites by a reaction in the solid phase.
A stereo matching algorithm: An adaptive window based on a statistical model (1992)

Abstract This paper describes a stereo matching algorithm capable of selecting an appropriate window size to achieve both objectives of precise localization and stable estimation in scene correspondence. Window size is an important parameter that depends on two local attributes: local intensity variation and scene disparity variation. A statistical model is introduced for evaluating the impact of these two types of variations on the uncertainty of disparity estimation and proposes a method of selecting an appropriate window size to minimize the uncertainty of the estimation. Experiments have been conducted for various window sizes. The experimental results demonstrate the effectiveness of the proposed model and the matching algorithm with an adaptive window.