gebhart/patrepeval huggingface dataset:
Mechanisms for directed self-assembly of heteroepitaxial Ge/Si quantum dots with deterministic placement and sub-23nm spacing on SiC nanotemplates (2011)

Artificially ordered Ge quantum dot (QD) arrays, where confined carriers can interact via exchange coupling, may create unique functionalities such as cluster qubits and spintronic bandgap systems. Development of such arrays for quantum computing requires fine control over QD size and spatial arrangement on the sub-35 nm length scale. We employ fine-probe electron-beam irradiation to locally decompose ambient hydrocarbons onto a bare Si (001) surface. These carbonaceous patterns are annealed in UHV, forming ordered arrays of nanoscale SiC precipitates that serve as templates for subsequent Ge quantum dot self-assembly during heteroepitaxy. This templating approach has so far produced interdot spacings down to 22.5 nm, and smaller spacings should be possible. We investigate the templated feature evolution during UHV processing to identify key mechanisms that must be controlled in order to preserve pattern fidelity and reduce broadening of the quantum dot size distribution. A key finding is that the presence of a small background of excess carbon reduces Ge surface diffusion, thereby suppressing coarsening to relatively high temperatures. In fact, coarsening of the carbonaceous nanodot template prior to conversion to SiC can be a more important contributor to size dispersion, and must be avoided through control of thermal budget.
Multi‐parametric Neuroimaging in a Non‐Human Primate Model of Sporadic Cerebral Amyloid Angiopathy (Saimiri boliviensis boliviensis) (2022)

Abstract Background Squirrel monkeys (SQMs) are a unique non‐human primate model (NHP), which unlike other NHPs, develops extensive age‐associated cerebral amyloid angiopathy (CAA). The growing recognition of CAA contribution to clinical decline and CAA‐related complications in current clinical trials underscore the utility of the SQM model for studying CAA pathology development. Neuroimaging can play a key role in noninvasively detecting and monitoring disease progression in conjunction with histological methods. We have previously shown the utility of quantitative R 2 * to map age‐related differences in SQM neuropathology cross‐sectionally and longitudinally. Here we aim to complement our protocol with advanced MRI approaches sensitive to brain microstructure to enable early and specific detection of alteration in tissue integrity. Our overarching goals aim to establish the in vivo and ex vivo MRI metrics profile of young and geriatric SQM cohorts. Method 2D T 2 ‐w (a) Turbo‐spin‐echo (TSE) and (b) FLAIR MRIs were acquired in vivo and ex vivo , while (c) multi‐shell diffusion‐weighted MRI (DWI) was limited to ex vivo imaging. Diffusion tensor imaging (DTI) and Diffusion kurtosis imaging (DKI) metrics were derived from comprehensive DWI datasets. Immunohistochemistry was subsequently performed to characterize the microstructural underpinnings of MRI abnormalities. Result Both in vivo and ex vivo T 2 ‐w TSE and FLAIR helped identify spontaneous asymmetric hyperintensities (ARIA‐E) in geriatric SQMs (21‐23yrs), predominantly in the parieto‐occipital WM, not seen in the young cohort (5‐yrs). Importantly, DKI‐derived mean kurtosis proved to be the most sensitive of DWI metrics for detecting lesions in the parieto‐occipital region. Widely adopted DTI metrics were far less sensitive in identifying microstructural changes. Histological assessment of region‐matched sections revealed Iba1 microgliosis, as well as immunoreactivity for both extravascular fibrinogen and decreased MBP when compared to the contralateral side. Aß immunohistochemistry (6E10/4G8) confirmed presence of CAA in the affected regions. Conclusion Advanced DWI models are sensitive and specific neuroimaging tools for identifying abnormalities associated with tissue integrity that are potentially linked to age‐associated cerebrovascular dysfunction. Ex vivo conventional MRI detected similar abnormalities observed in vivo and proved to be a useful step to validate the performance of advanced imaging strategies, which can help bridge the gap between in vivo MRI and histology.
ChemInform Abstract: A Directed Metalation of N‐tert‐Butyl‐N‐methyl‐2‐methoxybenzamide. Short Syntheses of 2‐Methoxy‐6‐methylbenzoic Acid and Lunularic Acid. (1990)

Abstract Ortho‐lithiation of the benzamide (I) mentioned in the title followed by reaction with the alkyl halides (II) yields the alkylation products (III).
Electronic precompensation of the nonlinear distortion in a 10 Gb/s 4-ary ASK directly modulated laser (2010)

The nonlinear distortion resulting from the direct modulation of a semiconductor laser using 4-ary amplitude shift keying at 10 Gb/s is mitigated by precompensation based on the use of digital signal processing to generate an appropriate modulating current.
Cutting Edge: Critical Role of NK1+ T Cells in IL-12-Induced Immune Responses In Vivo (1998)

Abstract CD1-dependent NK1+ T cells rapidly produce IL-4 upon stimulation through the TCR. These cells may therefore play an important role in the initiation of Th2 responses. Here, we show that NK1+ T cells constitutively express receptors for IL-12 and IFN-γ, and that IL-12 induces production of perforin in these cells. Moreover, while IL-12 induces high levels of IFN-γ and cytotoxic activity of hepatic or splenic mononuclear cells against tumor cells, this effect of IL-12 is significantly reduced in CD1-deficient mice with impaired NK1+ T cells development. These results indicate that NK1+ T cells play a critical role in IL-12-induced production of IFN-γ to initiate Th1 immune responses and as IL-12-induced cytotoxic effector cells to initiate antitumor immunity.
Stress Corrosion-Cracking and Corrosion Fatigue Impact of IZ-C17+ Zinc Nickel on 4340 Steel (2017)

Abstract : Sacrificial metallic coatings like cadmium and aluminum are key protective materials for high-strength steels, corrosion-resistant steels and other cathodic materials used on aircraft. The effect of these coatings on the stress-corrosion cracking and corrosion fatigue performance of the base metals is critical to understand for intended applications. Although it works well, cadmium is toxic and a carcinogen and alternatives have been sought which are similarly effective but have minimal environmental, safety, and health risks. Aluminum is effective, but is expensive to apply. The currently used application method at Navy Fleet Readiness Centers (FRCs), ion-vapor deposition (IVD), is line-of-sight limited, meaning not all parts that can be electroplated with cadmium can be effectively coated with IVD aluminum.A new coating, a zinc-nickel alloy produced from a solution supplied by Dipsol, has shown promising performance for many coating requirements including general corrosion, adhesion, and flexibility. The stress-corrosion cracking and corrosion fatigue performance of this new coating was not known. In addition, the impact of corrosion-inhibiting primer and topcoat on these degradation mechanisms was not known. This report documents the work completed to assess the stress-corrosion cracking and corrosion fatigue of the IZ-C17 zinc-nickel coating with a trivalent chromium passivation (Dipsol IZ-264) on 4340 steel, a common high-strength steel test substrate.
Channel estimation for non-ideal OFDM systems (2010)

Studies of channel estimation techniques for OFDM systems often assume idealized conditions such as a cyclic prefix (CP) long enough to absorb the entire channel delay spread, or perfect time and frequency synchronization at the receiver. This paper studies the impact of removing these assumptions. We characterize the mean square error (MSE) of various linear channel estimation methods, and we derive analytical expressions for the BER performance. The derivations are kept generic so that they apply to both time-division and frequency-division multiplexing of the pilot signal and the data subcarriers. The analysis is specialized to the BER performance characterization of OFDM-based UWB systems for different realistic channel estimation methods with residual time and frequency errors. The effect of inter-carrier interference (ICI) on channel estimation is shown to be small. However, inter-symbol interference (ISI) severely impacts the quality of the channel estimates and hence can yield a large (>2 dB) data demodulation performance degradation.
Acute Myeloid Leukemia Following Hodgkin Lymphoma: A Population-Based Study of 35 511 Patients (2006)

Treatments for Hodgkin lymphoma are associated with large relative risks of acute myeloid leukemia (AML), but there are few estimates of the excess absolute risk (EAR), a useful measure of disease burden. One-year Hodgkin lymphoma survivors (N = 35,511) were identified within 14 population-based cancer registries in Nordic countries and North America from January 1, 1970, through December 31, 2001. We used Poisson regression analysis to model the EAR of AML, per 10,000 person-years. A total of 217 Hodgkin lymphoma survivors were diagnosed with AML (10.8 expected; unadjusted EAR = 6.2; 95% confidence interval = 5.4 to 7.1). Excess absolute risk for AML was highest during the first 10 years after Hodgkin lymphoma diagnosis but remained elevated thereafter. In subsequent analyses, adjusted for time since Hodgkin lymphoma diagnosis and presented for the 5-9 year interval, the EAR was statistically significantly (P < .001) larger in patients diagnosed with Hodgkin lymphoma at age 35 years and older than in those diagnosed before 35 years of age. The EAR of AML declined statistically significantly after 1984 (7.0 to 4.2 and 16.4 to 9.9 in the < 35 and > or = 35 age groups, respectively), which may be associated with modifications in chemotherapy.
Graph transformation for keypoint trajectory coding (2016)

In contrast to still image analysis, motion information offers a powerful means to analyze video. In particular, motion trajectories determined from keypoints have become very popular in recent years for a variety of video analysis tasks, including search, retrieval and classification. Additionally, cloud-based analysis of media content has been gaining momentum, so efficient communication of salient video information to perform the necessary analysis of video at the cloud server is needed. In this paper, we propose a novel graph transformation to efficiently represent the keypoint trajectories, motivated by the fact that keypoints are distributed irregularly across the images. Compared to conventional DCT-like transformation, it is easier for graph transform to compact the energy and make the coding efficiently. Experimental results on several popular datasets including Stanford MAR, Hopkin155, KITTI, etc. demonstrate a significant rate saving between 26% and 42% with our proposed trajectory coding approaches relative to a DCT based transformation approach, provided that the coding errors are between 2 pixels to 4 pixels.
A Rapamycin-Sensitive Pathway Down-Regulates Insulin Signaling via Phosphorylation and Proteasomal Degradation of Insulin Receptor Substrate-1 (2000)

Insulin receptor substrate-1 (IRS-1) is a major substrate of the insulin receptor and acts as a docking protein for Src homology 2 domain containing signaling molecules that mediate many of the pleiotropic actions of insulin. Insulin stimulation elicits serine/threonine phosphorylation of IRS-1, which produces a mobility shift on SDS-PAGE, followed by degradation of IRS-1 after prolonged stimulation. We investigated the molecular mechanisms and the functional consequences of these phenomena in 3T3-L1 adipocytes. PI 3-kinase inhibitors or rapamycin, but not the MEK inhibitor, blocked both the insulin-induced electrophoretic mobility shift and degradation of IRS-1. Adenovirus-mediated expression of a membrane-targeted form of the p110 subunit of phosphatidylinositol (PI) 3-kinase (p110CAAX) induced a mobility shift and degradation of IRS-1, both of which were inhibited by rapamycin. Lactacystin, a specific proteasome inhibitor, inhibited insulin-induced degradation of IRS-1 without any effect on its electrophoretic mobility. Inhibition of the mobility shift did not significantly affect tyrosine phosphorylation of IRS-1 or downstream insulin signaling. In contrast, blockade of IRS-1 degradation resulted in sustained activation of Akt, p70 S6 kinase, and mitogen-activated protein (MAP) kinase during prolonged insulin treatment. These results indicate that insulin-induced serine/threonine phosphorylation and degradation of IRS-1 are mediated by a rapamycin-sensitive pathway, which is downstream of PI 3-kinase and independent of ras/MAP kinase. The pathway leads to degradation of IRS-1 by the proteasome, which plays a major role in down-regulation of certain insulin actions during prolonged stimulation.
Secreted Chaperones in Neurodegeneration (2020)

Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular - including transsynaptic - space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer's- and Parkinson's-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
Cellulose triacetate prepared from low-grade hardwood dissolving pulp and its insoluble residues in acetylation mediums (1998)

As cellulose triacetate is prepared from low-grade hardwood dissolving pulp, a considerable amount of the insoluble residue was present in the acetylation medium of the acetic acid/acetic anhydride/sulfuric acid system. The characterization of this residue indicated that the insoluble residue is composed of cellulose triacetate and xylan diacetate, retaining a fiber structure of swollen form. To reduce the insoluble residues, reaction conditions for acetylation were investigated. As one of the remedies of reducing the insoluble residues, 17 different solvents were selected to add to the acetylation medium, and among these, dichloroacetic acid was found to be very effective for its reduction. The obtained cellulose triacetate could then reveal good thermal properties similar to that from high-grade dissolving pulps. Therefore, acetylation systems with an addition of an appropriate solvent can have a potential to industrially manufacture a high-quality cellulose triacetate from even low-grade hardwood-dissolving pulps, as observed in low-grade softwood-dissolving pulps. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 67: 289–297, 1998
A new single-phase PLL structure based on second order generalized integrator (2006)

Phase, amplitude and frequency of the utility voltage are critical information for the operation of the grid-connected inverter systems. In such applications, an accurate and fast detection of the phase angle, amplotude and frequency of the utility voltage is essential to assure the correct generation of the reference signals and to cope with the new upcoming standards. This paper presents a new phase-locked-loop (PLL) method for single-phase systems. The novelty consists in generating the orthogonal voltage system using a structure based on second order generalized integrator (SOGI). The proposed structure has the following advantages: — it has a simple implementation; — the generated orthogonal system is filtered without delay by the same structure due to its resonance at the fundamental frequency, — the proposed structure is not affected by the frequency changes. The solutions for the discrete implementation of the new proposed structure are also presented. Experimental results validate the effectiveness of the proposed method.
Clinical Application of Mesenchymal Stem Cell-Derived Extracellular Vesicle-Based Therapeutics for Inflammatory Lung Diseases (2018)

It is currently thought that extracellular vesicles (EVs), such as exosomes and microvesicles, play an important autocrine/paracrine role in intercellular communication. EVs package proteins, mRNA and microRNA (miRNA), which have the ability to transfer biological information to recipient cells in the lungs. Depending on their origin, EVs fulfil different functions. EVs derived from mesenchymal stem cells (MSCs) have been found to promote therapeutic activities that are comparable to MSCs themselves. Recent animal model-based studies suggest that MSC-derived EVs have significant potential as a novel alternative to whole-cell therapies. Compared to their parent cells, EVs may have a superior safety profile and can be stored without losing function. It has been observed that MSC-derived EVs suppress pro-inflammatory processes and reduce oxidative stress, pulmonary fibrosis and remodeling in a variety of in vivo inflammatory lung disease models by transferring their components. However, there remain significant challenges to translate this therapy to the clinic. From this view point, we will summarize recent studies on EVs produced by MSCs in preclinical experimental models of inflammatory lung diseases. We will also discuss the most relevant issues in bringing MSC-derived EV-based therapeutics to the clinic for the treatment of inflammatory lung diseases.
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability (2016)

The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.
Transmembrane glucose transport in skeletal muscle of patients with non-insulin-dependent diabetes. (1993)

Insulin resistance for glucose metabolism in skeletal muscle is a key feature in non-insulin-dependent diabetes mellitus (NIDDM). Which cellular effectors of glucose metabolism are involved is still unknown. We investigated whether transmembrane glucose transport in vivo is impaired in skeletal muscle in nonobese NIDDM patients. We performed euglycemic insulin clamp studies in combination with the forearm balance technique (brachial artery and deep forearm vein catheterization) in six nonobese NIDDM patients and five age- and weight-matched controls. Unlabeled D-mannitol (a nontransportable molecule) and radioactive 3-O-methyl-D-glucose (the reference molecular probe to assess glucose transport activity) were simultaneously injected into the brachial artery, and the washout curves were measured in the deep venous effluent blood. In vivo transmembrane transport of 3-O-methyl-D-glucose in forearm muscle was determined by computerized analysis of the washout curves. At similar steady-state plasma concentrations of insulin (approximately 500 pmol/liter) and glucose (approximately 5.15 mmol/liter), transmembrane inward transport of 3-O-methyl-D-glucose in skeletal muscle was markedly reduced in the NIDDM patients (6.5 x 10(-2) +/- 0.56 x 10(-2).min-1) compared with controls (12.5 x 10(-2) +/- 1.5 x 10(-2).min-1, P < 0.005). Mean glucose uptake was also reduced in the diabetics both at the whole body level (9.25 +/- 1.84 vs. 28.3 +/- 2.44 mumol/min per kg, P < 0.02) and in the forearm tissues (5.84 +/- 1.51 vs. 37.5 +/- 7.95 mumol/min per kg, P < 0.02). When the latter rates were extrapolated to the whole body level, skeletal muscle accounted for approximately 80% of the defect in insulin action seen in NIDDM patients. We conclude that transmembrane glucose transport, when assessed in vivo in skeletal muscle, is insensitive to insulin in nonobese NIDDM patients, and plays a major role in determining whole body insulin resistance.