gebhart/patrepeval huggingface dataset:
Rational Modification of a Candidate Cancer Drug for Use Against Chagas Disease (2009)

Chagas disease is one of the major neglected diseases of the world. Existing drug therapies are limited, ineffective, and highly toxic. We describe a novel strategy of drug discovery of adapting an existing clinical compound with excellent pharmaceutical properties to target a pathogenic organism. The protein farnesyltransferase (PFT) inhibitor tipifarnib, now in phase III anticancer clinical trials, was previously found to kill Trypanosoma cruzi by blocking sterol 14 alpha-demethylase (14DM). We rationally developed tipifarnib analogues that display reduced affinity for human PFT to reduce toxicity while increasing affinity for parasite 14DM. The lead compound has picomolar activity against cultured T. cruzi and is efficacious in a mouse model of acute Chagas disease.
Layer-by-layer Adaptively Optimized ECC of NAND flash-based SSD Storing Convolutional Neural Network Weight for Scene Recognition (2018)

Layer-by-layer Adaptively Optimized Error Correcting Code (ECC) is proposed to improve the reliability of triple-level cell (TLC) NAND flash-based SSD for the scene recognition using convolutional neural network (CNN) of IoT edge devices. Layer-by-layer Adaptively Optimized ECC is composed of Layer-by-layer Iteration-Optimized Low Density Parity-Check (LBL-LDPC) and Layer-by-layer Code-length Adjusted Asymmetric Coding (LBL-AC). The conventional techniques like LDPC ECC and Asymmetric Coding (AC) improve the reliability. However, they require large overheads of the ECC decoding time and the flag/parity cell. Proposed LBL-LDPC and LBL-AC decrease the ECC decoding time by 14% and the data overhead by 26%, respectively, without recognition accuracy degradation. In addition, the data-retention time extends by 230%.
Airway involvement in hypersensitivity pneumonitis (1998)

Exposure to organic particles causes, in a susceptible host, diffuse inflammation of the lung acinus. However, immunopathologic response may not be confined to the alveoli and may also involve the large and peripheral airways. Therefore, after allergen inhalation a clinical spectrum of respiratory disorders may be observed, including hypersensitivity pneumonitis, asthma, chronic airway obstruction, and simple chronic bronchitis. Hypersensitivity pneumonitis is not a uniform disease but a complex syndrome, and the involvement of the airways may occur alone, simultaneously with, or after the parenchymal disease.
X-Ray Photoemission Spectroscopic Study of Ce-Based Amorphous Alloys (1997)

Valence band and core level XPS spectra have been measured for the amorphous Ce x Ru 100- x ( x =18, 58, 81), Ce x Cu 100- x ( x =14, 33, 50) and Ce 66 Si 34 alloys produced by sputtering. The coupling constant between the 4f and conduction electron levels, Δ, and the number of 4f electrons, n f , are estimated from the Ce-3d core level spectra. The amorphous Ce x Cu 100- x ( x =14, 33, 50) and Ce 66 Si 34 alloys are heavy fermion systems with small Δ, while the amorphous Ce x Ru 100- x ( x =18, 58, 81) alloys are intermediate valence systems with large Δ. We also derive the zero temperature magnetic susceptibility, χ(0), and Kondo temperature, T K , from these spectroscopic data and compare with those estimated from several low temperature physical properties.
Monolithic silicon‐micromachined free‐space optical interferometers onchip (2014)

Abstract The integration of microactuators within a silicon photonic chip gave rise to the field of optical micro‐electro‐mechanical systems (MEMS) that was originally driven by the telecommunication market. Following the latter's bubble collapse in the beginning of the third millennium, new directions of research with considerable momentum appeared focusing on the realization and applications of miniaturized instrumentation in biology, chemistry, physics and materials science. At the heart of these applications light interferometry is a key optical phenomenon, in which miniaturized scanning interferometers are the manipulating optical devices. Monolithic free‐space optical interferometers realized on a silicon chip take advantage of the recent progress in the microfabrication technology that is enabling accurate control of the etching depth, the aspect ratio, the verticality and the curvature of the etched surfaces. The fabrication technology, the library of micro‐optical and mechanical components, the realized architectures and their characterization are described in detail in this review, followed by a discussion of the foreseen challenges. image
Supplementary Figures from A Designer Cross-reactive DNA Immunotherapeutic Vaccine that Targets Multiple MAGE-A Family Members Simultaneously for Cancer Therapy (2023)

&lt;p&gt;Supplementary Figure 1: Expression of human and mouse consensus MAGE-A plasmids in vitro. Supplementary Figure 2: Consensus mouse MAGE-A vaccine induces low CD4+ T cells in C57Bl/6 mice. Supplementary Figure 3: Consensus mouse MAGE-A vaccine induces immune responses to one dominant epitope. Supplementary Figure 4: MAGE-A vaccine induced memory T cell responses. Supplementary Figure 5: Evaluation of organ toxicity after MAGE-A immunization. Supplementary Figure 6: Expression of mouse MAGE-A in a panel of mouse tumor cell lines and in autochthonous melanomas. Supplementary Figure 7: Immune responses in spleen and tumor of autochthonous tumor bearing mice. Supplementary Figure 8: Impact of MAGE-A vaccine in YUMM1.7 subcutaneous tumor model.&lt;/p&gt;
Large-Scale Community Detection on YouTube for Topic Discovery and Exploration (2021)

Detecting coherent, well-connected communities in large graphs provides insight into the graph structure and can serve as the basis for content discovery. Clustering is a popular technique for community detection but global algorithms that examine the entire graph do not scale. Local algorithms are highly parallelizable but perform sub-optimally, especially in applications where we need to optimize multiple metrics. We present a multi-stage algorithm based on local-clustering that is highly scalable, combining a pre-processing stage, a lo- cal clustering stage, and a post-processing stage. We apply it to the YouTube video graph to generate named clusters of videos with coherent content. We formalize coverage, co- herence, and connectivity metrics and evaluate the quality of the algorithm for large YouTube graphs. Our use of local algorithms for global clustering, and its implementation and practical evaluation on such a large scale is a ﬁrst of its kind.
The Role of Nanoparticle Layer Separation in the Finite Deformation Response of Layered Polyurethane-Clay Nanocomposites (2009)

Nanoscale control of structure in polymer nanocomposites is critical for their performance but has been difficult to investigate systematically due to the lack of a suitable experimental model. In this work, we investigated the role of nanoparticle layer separation in the finite deformation response of layered polyurethane− (PU−) montmorillonite (MTM) nanocomposites. A series of multilayered nanocomposites was manufactured, with alternating PU and MTM nanolayers, using a layer-by-layer manufacturing technique. The systematic variation in MTM nanoparticle volume fraction was achieved by varying the thickness of the PU nanolayer and therefore the MTM layer separation. Traditional polymer nanocomposite blending techniques result in a wide variation in nanoparticle separation for a given nanocomposite. In this investigation, we controlled the MTM nanoparticle layer separation, which allowed us to examine its effect on the nanocomposite response over a broad range in nanoparticle volume fraction. The PU−MTM nanocomposites demonstrated an increasing yield strength and stiffness with increased MTM volume fraction or reduced nanoparticle layer separation. A transition from ductile to brittle behavior in the stress−strain constitutive response was observed at a high volume fraction of MTM nanoparticles. We demonstrate that a critical nanoparticle separation exists, below which brittle behavior dominates the response of PU−MTM nanocomposites.
Molecular Cloning and Characterization of Lysosomal Sialic Acid O-Acetylesterase (1996)

O-Acetylation and de-O-acetylation of sialic acids have been implicated in the regulation of a variety of biological phenomena, including endogenous lectin recognition, tumor antigenicity, virus binding, and complement activation. Applying a strategy designed to identify genes preferentially expressed in active sites of embryonic hematopoiesis, we isolated a novel cDNA from the pluripotent hematopoietic cell line FDCPmixA4 whose open reading frame contained sequences homologous to peptide fragments of a lysosomal sialic acid O-acetylesterase (Lse) previously purified from rat liver, but with no evident similarity to endoplasmic reticulum-derived acetylesterases. The expressed Lse protein exhibits sialic-acid O-acetylesterase activity that is not attributable to a typical serine esterase active site. lse expression is spatially and temporally restricted during embryogenesis, and its mRNA levels correlate with differences in O-acetylesterase activity described in adult tissues and blood cell types. Using interspecific backcross analysis, we further mapped the lse gene to the central region of mouse chromosome 9. This constitutes the first report on the molecular cloning of a sialic acid-specific O-acetylesterase in vertebrates and suggests novel roles for the 9-O-acetyl modification of sialic acids during the development and differentiation of mammalian organisms.
3D packaging technique on liquid crystal polymer (LCP) for miniature wireless biomedical sensor (2010)

This paper presents a novel 3D packaging technique for a miniature wireless biomedical sensor. The application makes the packaging of the sensor and control of IC a difficult challenge. It is demonstrated that the thickness requirement can be met using novel epoxy interconnects and that micro-vias can be implemented in the package to distribute signals vertically. First, the layer-to-layer interconnection between silicon and liquid crystal polymer (LCP) layers is demonstrated using a magnetically aligned Z-axis anisotropic conductive adhesive (ACA). The resistance through Z-axis ACA represented 1.15 Ω on average for 75 micron pads. Second, 3D transitions through LCP via holes of 20 µm are demonstrated, which are suitable to distribute signals through the small form factor unit. These miniature 3D packaging techniques could make it possible to integrate all components in the small area (500 µm × 500 µm) to implement an implanted wireless biomedical micro-sensor.
Implementation of a Wireless Mesh Network Testbed for Traffic Control (2007)

Wireless mesh networks (WMN) have attracted considerable interest in years as a convenient, flexible and low-cost alternative to wired communication infrastructures in many contexts. However, the great majority of research on metropolitan-scale WMN has been centered around maximization of available bandwidth, suitable for non-real-time applications such as Internet access for the general public. On the other hand, the suitability of WMN for mission-critical infrastructure applications remains by and large unknown, as protocols typically employed in WMN are, for the most part, not designed for real-time communications. In this paper, we describe the smart transport and roads communications (STaRComm) project at National ICT Australia (NICTA), which sets a goal of designing a wireless mesh network architecture to solve the communication needs of the traffic control system in Sydney, Australia. This system, known as SCATS (Sydney coordinated adaptive traffic system) and used in over 100 cities around the world, connects a hierarchy of several thousand devices - from individual traffic light controllers to regional computers and the central traffic management centre (TMC) - and places stringent requirements on the reliability and latency of the data exchanges. We discuss our experience in the deployment of an initial testbed consisting of 7 mesh nodes placed at intersections with traffic lights, and share the results and insights learned from our measurements and initial trials in the process.
High-Performance Nanostructured Supercapacitor on an Engineered Nonwoven (2014)

Abstract : The goal of this research was to investigate the feasibility of engineered nonwovens for forming supercapacitor electrode scaffolds. A further objective was to develop and demonstrate a scalable method for coating a nonwoven with conductive carbon nanotubes (CNT) and an active redox species such as MnO2. CNT provide the low electrical resistivity required of an electrode conductive pathway, as well as increased surface roughness. Surface-adsorbed MnO2 contributes to energy storage when it undergoes reversible reduction from Mn(IV) to Mn(III). Based on recently reported studies of CNT/MnO2 electrodes, a specific pseudocapacitance greater than 1,000 F/g (based on the mass of MnO2) was sought.
Plasma tau predicts cerebral vulnerability in aging (2020)

Identifying cerebral vulnerability in late life may help prevent or slow the progression of aging-related chronic diseases. However, non-invasive biomarkers aimed at detecting subclinical cerebral changes in the elderly are lacking. Here, we have examined the potential of plasma total tau (t-tau) for identifying cerebral and cognitive deficits in normal elderly subjects. Patterns of cortical thickness and cortical glucose metabolism were used as outcomes of cerebral vulnerability. We found that increased plasma t-tau levels were associated with widespread reductions of cortical glucose uptake, thinning of the temporal lobe, and memory deficits. Importantly, tau-related reductions of glucose consumption in the orbitofrontal cortex emerged as a determining factor of the relationship between cortical thinning and memory loss. Together, these results support the view that plasma t-tau may serve to identify subclinical cerebral and cognitive deficits in normal aging, allowing detection of individuals at risk for developing aging-related neurodegenerative conditions.
Using Sunyaev‐Zeldovich Infrared Experiment (SuZIE) Arcminute‐Scale Cosmic Microwave Background Anisotropy Data to Probe Open and Flat Λ Cold Dark Matter Cosmogonies (1997)

We use arcminute-scale data from the Sunyaev-Zeldovich Infrared Experiment to set limits on anisotropies in cosmic microwave background radiation in open and spatially flat Λ cold dark matter cosmogonies. There are no 2 σ detections for the models tested. The upper limits obtained are consistent with the amplitude of anisotropy detected by the COBE Differential Microwave Radiometer experiment.
An efficient oxygen reduction electrocatalyst from graphene by simultaneously generating pores and nitrogen doped active sites (2012)

A simple way to simultaneously create pores and nitrogen doped active sites on graphene for the electrochemical oxygen reduction reaction (ORR) is developed. The key aspect of the process is the in-situ generation of Fe2O3 nanoparticles and their concomitant dispersion on graphene by pyrolyzing graphene oxide (GO) with the iron phenanthroline complex. Thus the deposited Fe2O3 nanoparticles act as the seeds for pore generation by etching the carbon layer along the graphene–Fe2O3 interface. Detection of the presence of Fe3C along with Fe2O3 confirms carbon spill-over from graphene as a plausible step involved in the pore engraving process. Since the process offers a good control on the size and dispersion of the Fe2O3 nanoparticles, the pore size and distribution also could be managed very effectively in this process. As the phenanthroline complex decomposes and gives Fe2O3 nanoparticles and subsequently the pores on graphene, the unsaturated carbons along the pore openings simultaneously capture nitrogen of the phenanthroline complex and provide very efficient active sites for ORR under alkaline conditions. The degree of nitrogen doping and hence the ORR activity could be further improved by subjecting the porous material for a second round of nitrogen doping using iron-free phenanthroline. This porous graphene enriched with the N-doped active sites effectively reduces oxygen molecule through a 3e− pathway, suggesting a preferential shift towards the more favourable 4e− route compared to the 2e− reaction as reported for many N-doped carbon nano-morphologies. The 90 mV onset potential difference for oxygen reduction as compared to the state-of-the art 20 wt% Pt/C catalyst is significantly low compared to the overpotentials in the range of 120–200 mV reported in the literature for few N-doped graphenes.
Supplementary Video 1 from Protein Kinase A Effects of an Expressed <i>PRKAR1A</i> Mutation Associated with Aggressive Tumors (2023)

Supplementary Video 1 from Protein Kinase A Effects of an Expressed &lt;i&gt;PRKAR1A&lt;/i&gt; Mutation Associated with Aggressive Tumors
Sodium cobalt bronze batteries and a method for making same (2023)

A solid state secondary battery utilizing a low cost, environmentally sound, sodium cobalt bronze electrode. A method is provided for producing same.
ChemInform Abstract: Synthesis and Characterization of Amino Protected Peptides Derived from Amino‐α‐hydroxyiminophosphonates. (1991)

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.
A dataset of multiresolution functional brain parcellations in an elderly population with no or mild cognitive impairment (2016)

We present group eight resolutions of brain parcellations for clusters generated from resting-state functional magnetic resonance images for 99 cognitively normal elderly persons and 129 patients with mild cognitive impairment, pooled from four independent datasets. This dataset was generated as part of the following study: <i>Common Effects of Amnestic Mild Cognitive Impairment on Resting-State Connectivity Across Four Independent Studies</i> (Tam et al., 2015) [1]. The brain parcellations have been registered to both symmetric and asymmetric MNI brain templates and generated using a method called bootstrap analysis of stable clusters (BASC) (Bellec et al., 2010) [2]. We present two variants of these parcellations. One variant contains bihemisphereic parcels (4, 6, 12, 22, 33, 65, 111, and 208 total parcels across eight resolutions). The second variant contains spatially connected regions of interest (ROIs) that span only one hemisphere (10, 17, 30, 51, 77, 199, and 322 total ROIs across eight resolutions). We also present maps illustrating functional connectivity differences between patients and controls for four regions of interest (striatum, dorsal prefrontal cortex, middle temporal lobe, and medial frontal cortex). The brain parcels and associated statistical maps have been publicly released as 3D volumes, available in .mnc and .nii file formats on figshare and on Neurovault. Finally, the code used to generate this dataset is available on Github.
Synthesis and Properties of Hydroxyl-Containing Ionic Liquids (2018)

Hydroxyl-containing ionic liquids were synthesized by quaternization of 1,2-dimethyl-1H-imidazole, N-methylpyrrolidine, and pyridine with 2-chloroethanol or 6-chlorohexan-1-ol, followed by exchange of chloride ion for bis(trifluoromethanesulfonyl)azanide, and their properties were studied.
Hetero-Supramolecular Modification of Nanocrystalline TiO₂-Film Electrodes: Photoassisted Electrocatalysis at B₁₂-on-TiO₂ (1996)

Nanocrystalline TiO2-film electrodes exhibit a unique set of intrinsic properties (transparency for visible light, electric conductivity in the doped state, semiconductor properties, large surface area, surface affinity towards organic anchoring groups). These can be combined with those of TiO2-surface-anchored molecular subunits such as light emitters or absorbers, redoxactive–possibly electrochromic–compounds, and electroactive molecular hosts or catalysts. The number of macroscopic devices resulting from such a hetero-supramolecular architecture includes photovoltaic cells, erasable photochromic devices, electrochromic displays and filters, and electrocatalytically active surfaces. The principals behind these applications are reviewed with special emphasis on a new type of photo assisted electrocatalysis using vitamin B12-modified TiO2.
Supplementary Table 1 from Loss of Keap1 Function Activates Nrf2 and Provides Advantages for Lung Cancer Cell Growth (2023)

Supplementary Table 1 from Loss of Keap1 Function Activates Nrf2 and Provides Advantages for Lung Cancer Cell Growth
Sulforaphane alleviates cadmium-induced toxicity in human mesenchymal stem cells through POR and TNFSF10 genes expression (2019)

Sulforaphane is a dietary compound possessing anti-inflammatory, antioxidant, anti-diabetic, anti-carcinogenic, and anti-aging properties. The role of sulforaphane in the context of cadmium (Cd)-induced toxicity through the alteration of nuclear morphology, mitochondrial membrane potential, and gene expression patterns, however, remains unclear. Thus, we assessed the protective role of sulforaphane against Cd-induced nuclear and mitochondrial damage in human mesenchymal stem cells (hMSCs). Cells were exposed to Cd and sulforaphane, either alone or in combination, for 48 h. The cell viability was assessed by adopting MTT assay. The nuclear morphology was investigated using Acridine orange/Ethidium bromide (AO/EB) dual staining and Hoechst staining. The mitochondrial membrane potential loss and lysosomal staining were analyzed using JC-1 staining and LysoRed staining respectively. The gene expression was studied using quantitative real-time PCR analysis. After 48 h of exposure to Cd, the viability of hMSCs decreased in a dose-dependent manner. In contrast, a single treatment with the phytochemical sulforaphane did not cause any remarkable reduction in hMSC viability. Combined treatment with Cd and sulforaphane resulted in a marked recovery in cell viability compared to that observed in cells treated with Cd alone. Analysis of nuclear morphology indicated that Cd induced necrotic cell death, while combined Cd and sulforaphane treatment prevented nuclear morphology changes. Cd ions also significantly attenuate the mitochondrial membrane potential (MMP) and alter gene expression in hMSCs; however, we observed that sulforaphane improves MMP under conditions of Cd-sulforaphane co-treatment of hMSCs. The gene expression results indicate that POR, TNFRSF1A and TNFSF10 genes expression are significantly upregulated by Cd-sulforaphane co-treatment than Cd or sulforaphane treatment alone. Our study results clearly indicate that sulforaphane can protect hMSCs against Cd-induced changes in nuclear morphology, attenuation of MMP, and alteration of gene expression patterns. Thus, intake of sulforaphane-enriched vegetables and fruits will be helpful to overcome Cd-induced toxicity in humans.
Improved approach for anchoring Nα‐9‐fluorenylmethyloxycarbonylamino acids as p‐alkoxybenzyl esters in solid‐phase peptide synthesis (1985)

Several Fmoc-amino acids have been esterified by use of N,N-dimethylformamide dineopentyl acetal to 2,4,5-trichlorophenyl 3'-(4''-hydroxymethyl-phenoxy)propionate, and the resultant handle derivatives were purified and then quantitatively coupled onto aminomethyl supports. Compared to literature methodology, the present procedure is preferred because: (i) extra steps to selectively protect and liberate the carboxyl of the handle are circumvented; and (ii) the additional methylene group spacer reflecting substitution of a propionyl group for an acetyl group in the handle changes the electronic parameters of the resultant p-alkoxybenzyl ester sufficiently so that the rates of acidolytic cleavage of the anchoring linkage are 2- to 3-fold increased and useful improvements in yields can be achieved.