gebhart/patrepeval huggingface dataset:
Molecular beam study on interaction dynamics in a reactive system: NO on bare Ru(0001) (2000)

The interaction dynamics of NO with the reactive Ru(0001) surface has been investigated with the use of supersonic molecular beam techniques. Helium scattering, King and Wells sticking measurements and time-of-flight (TOF) experiments are performed. The initial sticking coefficient is remarkably high with incident energy, varying from unity at thermal energies to ∽90% for 0.25⩽Ei⩽2.4 eV and does not seem to depend on surface temperature for 400⩽Ts⩽850 K. Counter intuitively, the non-sticking ∽10% of the incident flux has only about 12% translational energy transfer in the specular scattering direction. Molecular sticking is observed at low surface temperatures for above thermal incident energies, up to at least 0.45 eV.
Structural study of α-filamin repeats 14-16 (2006)

Cellular processes like motility, chemotaxis, phagocytosis and morphogenesis are dependent on the dynamic regulation of the actin cytoskeleton. This cytoskeleton system is tightly controlled by a number of diverse actin-binding proteins (ABPs) by various mechanisms described as nucleation, polymerization, capping, severing, depolymerization and sequestration. The ABPs are grouped based on sequence identity as in the Wiskott-Aldrich Syndrome protein homology domain 2 (WH2), and the calponin homology domain (CH) containing proteins.In this work, we elucidate the crystal structures of hybrids of gelsolin domain 1 with thymosin β4, ciboulot domain 2, and the second WH2 domain of N-WASP each bound to actin. We show that the single WH2 motif containing protein thymosin β4 in part sequesters actin by binding its pointed end via a C-terminal helix. This interaction prevents the addition of bound actin protomers to the barbed end of the filament. We propose that sequence variations in some WH2 motifs conferred F-actin binding ability to multiple repeat-containing proteins. These F-actin binding domains interact with the barbed end of a filament and the adjacent WH2 motifs are then freed to add their bound actin to the growing filament end. We demonstrate the binding of ciboulot domains 2 and 3 to both G- and F-actin and that full length ciboulot is capable of binding two actin monomers simultaneously. We have also cloned, expressed, purified and crystallized rod domains 14-16 from the actin crosslinking protein a-filamin. Preliminary X-ray crystallography data gives us hope that we shall be able to solve the structure of this triple domain repeat.
A Proposal for the Deterrence of Information Leakage Using Anti-virus Software (2013)

In recent years, the leakage of confidential files through the P2P (peer-to-peer) file sharing software has become a problem. Once sensitive files have been leaked to a P2P network, they are distributed rapidly and at random to a great many computers, bringing the danger of far-reaching damage. To deal with this, we propose a method to control the diffusion of sensitive file leakage on P2P networks by deleting the leaked sensitive files in the destination PC of the P2P user. In this method, we focus on the characteristic of anti-virus software that reacts to the unique patterns of a virus, automatically isolating and deleting a file concerned. By using the unique pattern of a virus to make the leaked sensitive file appear as a viral infection file, the anti-virus software installed on the destination PC will automatically delete the file. This is the concept of our method.
Fitting Gaussian copulae for efficient visual codebooks generation (2012)

The Bag of Words model is probably one of the most effective ways to represent images based on the aggregation of locally extracted descriptors. It uses clustering techniques to build visual dictionaries that map each image into a fixed length signature. Despite its effectiveness, one major drawback of this model is the codebook informativeness and its computational complexity. In this paper we propose Copula-BoW (C-BoW), namely an efficient local feature aggregator inspired by the Copula theory. In C-BoW, we build in a quadratic time an efficient codebook for vector quantization, based on the correlation of the marginal distributions of the local features. Our experimental results prove that the C-BoW signature is much more efficient and as discriminative as traditional BoW for scene recognition and video retrieval (TRECVID [14] data). Moreover, we also show that our new model provides complementary information when combined to existing local features aggregators, substantially improving the final retrieval performance.
Polymer-Pen Chemical Lift-Off Lithography (2017)

We designed and fabricated large arrays of polymer pens having sub-20 nm tips to perform chemical lift-off lithography (CLL). As such, we developed a hybrid patterning strategy called polymer-pen chemical lift-off lithography (PPCLL). We demonstrated PPCLL patterning using pyramidal and v-shaped polymer-pen arrays. Associated simulations revealed a nanometer-scale quadratic relationship between contact line widths of the polymer pens and two other variables: polymer-pen base line widths and vertical compression distances. We devised a stamp support system consisting of interspersed arrays of flat-tipped polymer pens that are taller than all other sharp-tipped polymer pens. These supports partially or fully offset stamp weights thereby also serving as a leveling system. We investigated a series of v-shaped polymer pens with known height differences to control relative vertical positions of each polymer pen precisely at the sub-20 nm scale mimicking a high-precision scanning stage. In doing so, we obtained linear-array patterns of alkanethiols with sub-50 nm to sub-500 nm line widths and minimum sub-20 nm line width tunable increments. The CLL pattern line widths were in agreement with those predicted by simulations. Our results suggest that through informed design of a stamp support system and tuning of polymer-pen base widths, throughput can be increased by eliminating the need for a scanning stage system in PPCLL without sacrificing precision. To demonstrate functional microarrays patterned by PPCLL, we inserted probe DNA into PPCLL patterns and observed hybridization by complementary target sequences.
Fluxionality in (cycloheptatriene)iron tricarbonyl complexes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluxionality in (cycloheptatriene)iron tricarbonyl complexesKarin J. Karel, Thomas A. Albright, and Maurice BrookhartCite this: Organometallics 1982, 1, 3, 419–430Publication Date (Print):March 1, 1982Publication History Published online1 May 2002Published inissue 1 March 1982https://pubs.acs.org/doi/10.1021/om00063a001https://doi.org/10.1021/om00063a001research-articleACS PublicationsRequest reuse permissionsArticle Views218Altmetric-Citations30LEARN 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
<title>Statistical characterization of fracture of brittle MEMS materials</title> (1999)

The fracture of brittle MEMS materials is often characterized by ultimate strength measures such as the maximum stress or strain in an element at failure. It has been known for many decades that a better way to characterize the strength of a brittle material on the macro-scale is to make use of statistical measures. This is due to the nature of brittle materials in which failure occurs when a critically sized flaw exists in the region that is under tensile stress. The distribution of flaws is often random, so the strength of a brittle material can only be properly characterized by statistical measures. Working with MEMS devices, where the site scale is small, it becomes even more important to use a statistical approach. Doing so can explain two observed effects. First, there is an apparent size effect on the strength of the material. The larger the structure that is under a given stress, the larger the region where a critically sized flaw may exist, resulting a higher probability of failure. Second, two identical beams with different stress states, loaded to the same maximum stress can have dramatically different average strengths. In this paper, Weibull statistics are used to characterize the strength of one MEMS material-- polycrystalline silicon. The relevant statistical measures are obtained from the fracture of a large number of cantilever beams. It is shown that, for this material, the average failure strength of a beam loaded in uniaxial tension should be on the order of 40% lower than the average strength of identical beams loaded in cantilever bending.
Tafazzin regulates the function of lipopolysaccharide activated B lymphocytes in mice (2021)

Abstract B lymphocytes are responsible for humoral immunity and play a key role in the immune response. Optimal mitochondrial function is required to support B cell activity during activation. We examined how deficiency of tafazzin, a cardiolipin remodeling enzyme required for mitochondrial function, alters the metabolic activity of B cells and their response to activation by lipopolysaccharide in mice. B cells were isolated from 3 month old wild type or tafazzin knockdown mice and incubated for up to 72 h with lipopolysaccharide and cell proliferation, expression of cell surface markers, secretion of antibodies and chemokines, proteasome and immunoproteasome activities, and metabolic function determined. In addition, proteomic analysis was performed to identify altered levels of proteins involved in survival, immunogenic, proteasomal and mitochondrial processes. Compared to wild type lipopolysaccharide activated B cells, lipopolysaccharide activated tafazzin knockdown B cells exhibited significantly reduced proliferation, lowered expression of cluster of differentiation 86 and cluster of differentiation 69 surface markers, reduced secretion of immunoglobulin M antibody, reduced secretion of keratinocytes-derived chemokine and macrophage-inflammatory protein-2, reduced proteasome and immunoproteasome activities, and reduced mitochondrial respiration and glycolysis. Proteomic analysis revealed significant alterations in key protein targets that regulate cell survival, immunogenicity, proteasomal processing and mitochondrial function consistent with the findings of the above functional studies. The results indicate that the cardiolipin transacylase enzyme tafazzin plays a key role in regulating mouse B cell function and metabolic activity during activation.
Role of Epidermal Growth Factor Receptor and the HER-2 Gene in Hormone Refractory Prostate Cancer (2008)

PURPOSE: Amplification and mutation of the epidermal growth factor receptor(EGFR) and HER-2 genes were analyzed in the tissues of hormone refractory prostate cancer(HRPC) patients. MATERIALS AND METHODS: Gene amplifications of the EGFR and HER-2 gene were analyzed by fluorescence in situ hybridization(FISH) with direct sequencing. Studies were performed on 10 patients; tissues were sampled at the time of initial diagnosis and after the conversion to HRPC(a total of 20 tissue samples). Direct sequencing was performed on exons 18-24 of the EGFR gene and exons 19 and 20 of the HER-2 gene. The amplifications and mutations were compared with the clinicopathologic features. RESULTS: Gene amplification of the EGFR gene was observed in 6(30%) out of 20 samples. A total of six EGFR mutations in exons 18 and 19 were detected in three pairs of tissues(three patients). One patient with a hormone refractory status had a novel deletion mutation in EGFR exon 19. EGFR mutations were associated with the acinar type of prostate cancer, but they were not associated with the ductal type. No significant correlation was found between mutation change and the hormone sensitive or refractory status. However, the time to convert to HRPC was significantly shorter in the patients with a mutation in the EGFR gene (p=0.017). There were no HER-2 gene amplifications or mutations found in any of the samples. CONCLUSONS: EGFR gene mutation and amplification occurred frequently in these advanced prostate cancer cases, but EGFR mutations do not appear to play a significant role in the hormone refractory pathway. However, EGFR gene mutation is closely associated with the time to convert to HRPC.
Towards Explainable Graph Representations in Digital Pathology (2020)

Explainability of machine learning (ML) techniques in digital pathology (DP) is of great significance to facilitate their wide adoption in clinics. Recently, graph techniques encoding relevant biological entities have been employed to represent and assess DP images. Such paradigm shift from pixel-wise to entity-wise analysis provides more control over concept representation. In this paper, we introduce a post-hoc explainer to derive compact per-instance explanations emphasizing diagnostically important entities in the graph. Although we focus our analyses to cells and cellular interactions in breast cancer subtyping, the proposed explainer is generic enough to be extended to other topological representations in DP. Qualitative and quantitative analyses demonstrate the efficacy of the explainer in generating comprehensive and compact explanations.
Neuronavigation Using Three-Dimensional Proton Magnetic Resonance Spectroscopy Data (2014)

The proposed methods improve upon the current state of the art in neuronavigation through the use of detailed 3D (1)H-MRSI data. Specifically, 3D MRSI-based overlays provide comprehensive, quantitative visual cues and location information during neurosurgery, enabling a progressive new form of online spectroscopy-guided neuronavigation.
Anisotropic second-harmonic generation from chromophoric self-assembled monolayers upon oxide overlayers of Si(111) surfaces (1997)

The nonlinear optical response of stilbazolium-based organic monolayers self-assembled upon silicon(111) substrates, which have oxide layers 4–860 nm thick, is studied by reflection second-harmonic generation at an input wavelength of 1.053 µm. All samples, irrespective of oxide thickness, display clear threefold symmetry about the azimuth, which is shown to arise from interference between an isotropic component generated by the chromophoric monolayer, and an anisotropic component of sixfold symmetry, which originates from the Si(111) substrate. Maximum second-harmonic intensity and orientation relative to the silicon lattice vary with different oxide thicknesses as a consequence of multiple internal reflections within the oxide layer, which can be expressed as thickness-dependent local field corrections. Evaluation of the principal tensor components permits estimation of the molecular tilt angle from the surface normal as ∼25° for monolayers self-assembled upon thick oxide overlayers (&gt;30 nm).
Pre‐Clinical Safety Evaluation of Pyrrolidine Dithiocarbamate (2010)

Pyrrolidine dithiocarbamate (PDTC) was examined for its potential in the intranasal treatment of human rhinovirus infections. Prior to clinical testing, a comprehensive non-clinical programme was performed to evaluate the general toxicity of PDTC. The animal experiments included investigations in rodents with study durations ranging from single dose to repeated dosing over a period of 28 days. The routes of administration were intranasal, inhalative, oral and intravenous for single-dose toxicity and pharmacokinetic studies, and intranasal for repeated dose studies. Blood and tissue samples were obtained from PDTC-treated rats to analyse pharmacokinetics and tissue distribution. Accumulation of selected metals due to PDTC treatment was examined in liver, brain, nerves and fat tissues.
A High Frequency Self-Reconfigurable Battery for Arbitrary Waveform Generation (2021)

This article presents an innovative self-reconfigurable battery (SRB) architecture, which is able to generate directly at its output any waveform signals. Thanks to that specific characteristic of the proposed system, it is even possible to dispense with any AC charger. Although the individual ability of each cell in the battery pack to perform an efficient active cell balancing has been already studied in the literature, the system presented in this article is the first of its kind. This article describes a real prototype of a high frequency SRB of 128 cells and demonstrates that it can be charged without any dedicated charger directly on the electrical grid, by generating a sinusoidal waveform voltage, while perfectly balancing the cells in real time.
Multimodal Biomarkers to Discriminate Cognitive State (2017)

Multimodal biomarkers based on behavioral, neurophysiological, and cognitive measurements have recently increased in popularity for the detection of cognitive stress and neurologically based disorders. Such conditions significantly and adversely affect human performance and quality of life in a large fraction of the world’s population. Example modalities used in detection of these conditions include speech, facial expression, physiology, eye tracking, gait, and electroencephalography (EEG). Toward the goal of finding simple, noninvasive means to detect, predict, and monitor cognitive stress and neurological conditions, MIT Lincoln Laboratory is developing biomarkers that satisfy three criteria. First, we seek biomarkers that reflect core components of cognitive status, such as work­ing memory capacity, processing speed, attention, and arousal. Second, and as importantly, we seek biomarkers that reflect timing and coordination relations both within components of each modality and across different modalities. This is based on the hypothesis that neural coordination across different parts of the brain is essential in cognition. An example of timing and coordination within a modality is the set of finely timed and synchronized physiological components of speech production, whereas an example of coordination across modalities is the timing and synchrony that occur between speech and facial expression during speaking. Third, we seek multimodal biomarkers that contribute in a complementary fashion under various channel and background conditions. In this chapter, as an illustration of the biomarker approach, we focus on cognitive stress and the particular case of detecting different cognitive load levels. We also briefly show how similar feature-extraction principles can be applied to a neurological condition through the example of major depressive disorder (MDD). MDD is one of several neuropsychiatric disorders where multimodal biomarkers based on principles of timing and coordination are important for detection (Cummins et al., 2015; Helfer et al., 2014; Quatieri &amp; Malyska, 2012; Trevino, Quatieri, &amp; Malyska, 2011; Williamson, Quatieri, Helfer, Ciccarelli, &amp; Mehta, 2014; Williamson et al., 2013, 2015; Yu, Quatieri, Williamson, &amp; Mundt, 2014).
Complex Trainable ISTA for Linear and Nonlinear Inverse Problems (2019)

Complex-field signal recovery problems from noisy linear/nonlinear measurements appear in many areas of signal processing and wireless communications. In this paper, we propose a trainable iterative signal recovery algorithm named complex-field TISTA (C-TISTA) which treats complex-field nonlinear inverse problems. C-TISTA is based on the concept of deep unfolding and consists of a gradient descent step with the Wirtinger derivatives followed by a shrinkage step with a trainable complex-valued shrinkage function. Importantly, it contains a small number of trainable parameters so that its training process can be executed efficiently. Numerical results indicate that C-TISTA shows remarkable signal recovery performance compared with existing algorithms.
Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses. (2012)

Abstract not provided.
Adaptive Resistance to the “Last Hope” Antibiotics Polymyxin B and Colistin in Pseudomonas aeruginosa Is Mediated by the Novel Two-Component Regulatory System ParR-ParS (2010)

As multidrug resistance increases alarmingly, polymyxin B and colistin are increasingly being used in the clinic to treat serious Pseudomonas aeruginosa infections. In this opportunistic pathogen, subinhibitory levels of polymyxins and certain antimicrobial peptides induce resistance toward higher, otherwise lethal, levels of these antimicrobial agents. It is known that the modification of lipid A of lipopolysaccharide (LPS) is a key component of this adaptive peptide resistance, but to date, the regulatory mechanism underlying peptide regulation in P. aeruginosa has remained elusive. The PhoP-PhoQ and PmrA-PmrB two-component systems, which control this modification under low-Mg2+ conditions, do not appear to play a major role in peptide-mediated adaptive resistance, unlike in Salmonella where PhoQ is a peptide sensor. Here we describe the identification and characterization of a novel P. aeruginosa two-component regulator affecting polymyxin-adaptive resistance, ParR-ParS (PA1799-PA1798). This system was required for activation of the arnBCADTEF LPS modification operon in the presence of subinhibitory concentrations of polymyxin, colistin, or the bovine peptide indolicidin, leading to increased resistance to various polycationic antibiotics, including aminoglycosides. This study highlights the complexity of the regulatory network controlling resistance to cationic antibiotics and host peptides in P. aeruginosa, which has major relevance in the development and deployment of cationic antimicrobials.
Human Ocular Mucus (1982)

Twenty biopsy specimens of the human conjunctival epithelial surface with its associated mucus from normal subjects and contact lens wearers with biomicroscopic evidence of excess mucus were studied by scanning electron microscopy. Mucus existed in strands, sheets, and granules; each morphologic type of mucus was observed in all samples. No qualitative difference in morphologic features of mucus was found between normal subjects and those with excess mucus. Mucous forms observed by scanning electron microscopy closely resembled structures previously shown by biomicroscopic and light microscopic techniques, providing evidence that careful scanning electron microscopic preparation of biopsy specimens containing mucus may not greatly alter in situ morphologic characteristics of mucus.
Gastrointestinal polypoid lesions: a poorly known endoscopic feature of portal hypertension (2014)

Portal hypertension-associated gastric or small intestine polypoid lesions may be associated with a significant risk of bleeding and are responsive to adequate treatment of portal hypertension.