gebhart/patrepeval huggingface dataset:
Thermochromic Properties of Double-Doped VO2 Thin Films Prepared by a Wet Coating Method Using Polyvanadate-Based Sols Containing W and Mo or W and Ti (2001)

A mixture of metallic vanadium, tungsten and molybdenum powder was dissolved in a hydrogen peroxide solution, to yield a polyvanadate sol containing W and Mo. A thin film of V 1- x - y W x Mo y O 2 was fabricated on a fused silica substrate by spin-coating using such a sol followed by reduction in hydrogen and successive annealing in a nitrogen atmosphere. Thin films in the system V 1- x - z W x Ti z O 2 were similarly prepared using a sol containing W and Ti. All the films obtained in this study showed a clear thermochromic switching performance with a large transmittance change in the infrared region. For V 1- x - y W x Mo y O 2 , the switching temperature ( T t ) was lowered by doping at approximately T t = T t0 (=67°C)- ax - by , where a and b are the decrease rates of each individual dopant (about 1920 and 870°C, respectively, for 0≦ x , y ≦0.03). Doping of Ti had little effect on T t , but markedly reduced hysteresis of the transition. We demonstrated that a double-doped film of V 1- x - z W x Ti z O 2 ( x =0.018 and y =0.10) showed thermochromic switching almost without any hysteresis at a temperature as low as 45°C.
Deubiquitinases A20 and CYLD modulate costimulatory signaling via CD137 (4–1BB) (2017)

TRAF2 dependent K63-polyubiquitinations have been recently shown to connect CD137 (4-1BB) stimulation to NF-κB activation. In a search of deubiquitinase enzymes (DUBs) that could regulate such a signaling route, A20 and CYLD were found to coimmunoprecipitate with CD137 and TRAF2 complexes. Indeed, overexpression of A20 or CYLD downregulated CD137-elicited ubiquitination of TRAF2 and TAK1 upon stimulation with agonist monoclonal antibodies. Moreover, overexpression of A20 or CYLD downregulated CD137-induced NF-κB activation in cultured cells and in gene-transferred hepatocytes <i>in vivo</i>, while silencing these deubiquitinases enhanced CD137 costimulation of primary human CD8 T cells. Therefore A20 and CYLD directly downregulate the signaling from a T and NK-cell costimulatory receptor under exploitation for cancer immunotherapy in clinical trials.
Identification of Two Widely Separated Loci Conferring Nicotinic Acid Dependence on Wild-Type Shigella flexneri 2a (1971)

Two widely separated loci causing the nicotinic acid dependence of wild-type Shigella flexneri 2a were identified by intergeneric mating procedures and found to be closely linked to the gal and fuc chromosomal determinants.
Prognostic Value of Sst2 and Galectin-3 for Death Relative to Renal Function in Patients Hospitalized for Heart Failure (2015)

In patients with HF, sST2 improved prediction for death beyond risk factors without being influenced by renal function, however, the prognostic value of galectin-3 is less clear below an eGFR of 60 ml/min/1.73 m(2).
The Escherichia coli aquaporin‐Z water channel (2000)

The membrane pathway of the rapid fluxes of water by which microorganisms adapt promptly to abrupt changes in environmental osmolality have begun to be understood since the discovery of the Escherichia coli aquaporin-Z water channel, AqpZ. As in animals and plants, aquaporins are variously represented among microorganisms, in which 31 homologous genes have already been identified in eubacteria, Archaea, fungi and protozoa. The AqpZ channel is selectively permeable to water, although other functions are not excluded. Consistent with a conservation over the course of evolution, AqpZ and AQP1, a human counterpart, share similar structures. The aqpZ gene is growth phase and osmotically regulated. AqpZ has a role in both the short- and the long-term osmoregulatory response and is required by rapidly growing cells. AqpZ-like proteins seem to be necessary for the virulence expressed by some pathogenic bacteria. Microbial aquaporins are also likely to be involved in spore formation and/or germination. Additional roles may still be unknown. The use of AqpZ as a model system will continue to provide insight into the understanding of the importance of aquaporins.
An efficient Chinese remainder theorem based node capture resilience scheme for Mobile WSNs (2010)

Node capture attack is a critical issue in Mobile WSNs where attacker-controlled replicas may act maliciously. In this paper, we present a novel Chinese remainder theorem based node capture resilience scheme that can be utilized to discover and revoke captured nodes. Moreover, our scheme can limit the ability of captured nodes to further compromise forward security, backward security, and launch collusion attacks. Detailed analysis shows that our scheme indeed achieves the expected design goals.
Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases (2021)

The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are likely PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions and that PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a focused peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated interactor recognition across the Nedd4 family.
Contextual Online Dictionary Learning for Hyperspectral Image Classification (2017)

Sparse representation (SR) has been successfully used in the classification of hyperspectral images (HSIs) by representing HSI pixels over a dictionary and yielding discriminative sparse coefficients. Most of SR-based classification methods construct the dictionary by directly using some labeled pixels as atoms. Such dictionary can lead to inefficient SR for large-sized HSIs, and may be incomplete when the number of labeled pixels is less than the number of spectral bands. This paper proposes a contextual online dictionary learning (DL) method for HSIs classification, which learns a dictionary over the whole image rather than few labeled pixels. The proposed method can effectively and efficiently improve the adaptive representation capability of different pixels with an online learning mechanism. Specifically, the contextual characteristics of the HSI are integrated with discriminative spectral information for online DL, i.e., pushing similar pixels in neighborhood to share similar sparse coefficients with respect to the well-learned dictionary. By this way, the obtained sparse coefficients are structured and discriminative. Finally, a traditional classifier, i.e., the linear support vector machine, is applied to the sparse coefficients, and the final classification results are obtained. Experimental results on real HSIs show the effectiveness of the proposed method.
Endovascular options in the treatment of delayed ischemic neurological deficits due to cerebral vasospasm (2009)

The second leading cause of death and disability in patients with aneurysmal subarachnoid hemorrhage (SAH) is delayed cerebral ischemia due to vasospasm. Although up to 70% of patients have been shown to have angiographic evidence of vasospasm, only 20-30% will present with clinical changes, including mental status changes and neurological deficits that necessitate acute management. Endovascular capabilities have progressed to become viable options in the treatment of cerebral vasospasm. The rationale for intraarterial therapy includes the fact that morbidity and mortality rates have not changed in recent years despite optimized noninvasive medical care. In this report, the authors discuss the most common endovascular options-namely intraarterial vasodilators and transluminal balloon angioplasty-from the standpoint of mechanism, efficacy, limitations, and complications as well as the treatment algorithms for cerebral vasospasm used at our institution.
The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis (2016)

In Arabidopsis, the C-repeat binding factors (CBFs) have been extensively studied as key transcription factors in the cold stress response. However, their exact functions in the cold response remains unclear due to the lack of a null cbf triple mutant. In this study, we used CRISPR/Cas9 technology to mutate CBF1 or CBF1/CBF2 in a cbf3 T-DNA insertion mutant to generate cbf1,3 double and cbf1 cbf2 cbf3 (cbfs) triple mutants. The response of the cbfs triple mutants to chilling stress is impaired. Furthermore, no significant difference in freezing tolerance was observed between the wild-type and the cbf1,3 and cbfs mutants without cold acclimation. However, the cbfs mutants were extremely sensitive to freezing stress after cold acclimation, and freezing sensitivity ranking was cbfs > cbf1,3 > cbf3. RNA-Seq analysis showed that 134 genes were CBF regulated, of which 112 were regulated positively and 22 negatively by CBFs. Our study reveals the essential functions of CBFs in chilling stress response and cold acclimation, as well as defines a set of genes as CBF regulon. It also provides materials for the genetic dissection of components in CBF-dependent cold signaling.
Studies of Adaptive Systems (1975)

Abstract : This report is organized as five separate reports covering the five tasks of the contract. Four of these reports are included in the present document plus a separate report written by Prof. C. W. Merriam, III. The first section of this report provides the asymptotic theory and geometric procedure for determining the amplitude of the crosscorrelation function for FM signals whose instantaneous frequency curves overlap at one point in time. In addition, the geometric procedure can be used to upperbound the crosscorrelation function for multiple intersecting cases, where absolute phase of the signal components is not generally known.
Abstract 2946: Gene expression profiling in circulating cells (CTCs) of breast carcinoma patients - a tool for early metastasis detection and therapy individualization (2010)

Abstract Background: Tumor cell dissemination is an early process in breast cancer (BC) and circulating tumor cells (CTCs) are considered potential surrogate marker for the detection and characterization of minimal residual disease. Here we monitored hematogenous micrometastasis in BC patients by gene expression profiling of CTCs based on CTC-abundance in blood and expression of 35 oncomarkers on the mRNA level by multimarker quantitative PCR (qPCR). Characteristics of the early dissemination process and gene expression profile changes were studied by analyzing tumor tissue and CTCs of primary and metastatic BC patients. Methods: In primary BC five ml blood was collected before and after chemotherapy (n=87 patients). In metastatic BC 5 ml blood of 72 patients was studied either at the time of relapse of BC or at a documented progressive BC before receiving new therapy. All samples were analyzed for CTCs using the AdnaTest BreastCancer (AdnaGen AG, Langenhagen, Germany). CTCs were immunomagnetically enriched using the AdnaTest BreastCancerSelect followed by RNA isolation, subsequent gene expression analysis by reverse transcription and multiplex-PCR for the detection of EpCAM, MUC-1 and HER-2 transcripts. RNA from formalin fixed paraffin embedded (FFPE)-tumor tissue (n=46) was isolated with RecoverAll® (Ambion). After reverse transcription the cDNA was gene-specifically pre-amplified for multimarker qPCR analysis on the Biomark® (Fludigm, USA) microfluidic chip for 48 genes in each of 48 samples (2034 rxn in total). qPCR data were analyzed with GenEx ver. 5.0 (MultiD, SE) and correlated to available clinical data. Results: 286 CTC samples were analyzed in total. Blood sample was considered positive in the AdnaTest if at least one marker was measured above the cut-off level in the sample. CTCs were found in 29/87 (33,3%) of primary BC patients before chemotherapy and in 10/87 (11,5 %) patients after chemotherapeutical treatment. Among metastatic BC patients 48/72 (67%) were CTC positive. Gene expression analysis of the CTCs in metastatic BC patients and FFPE samples revealed 20 genes that were differentially expressed (p&amp;lt;0.05) Interestingly, gene expression profiles of CTCs in primary BC patients correlated to those measured on the primary tumor, while CTCs of metastatic BC patients had significantly different gene expression profiles. Conclusion: Gene expression profiling of CTCs is a potential discriminator of patients with therapy sensitive and therapy resistant tumor cell populations and therefore with good and inferior prognosis. The predictive value of expression profiles in CTCs for therapeutic interventions will be prospectively evaluated. Study has been supported by IGA NS 9776-3 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2946.
Clinical and Immunological Correlates of Pre-Co-Seasonal Sublingual Immunotherapy with Birch Monomeric Allergoid in Patients with Allergic Rhinoconjunctivitis (2009)

Sublingual immunotherapy is safe and efficacious in the treatment of patients with allergic rhinitis. The clinical and biological efficacy of modified allergens (allergoids) has not been fully clarified. We investigated in birch allergic patients the effect of a pre-co-seasonal sublingual immunotherapy regimen with a modified allergen extract on clinical parameters and on T cell proliferation and regulatory cytokine production (IL-10, TGF-beta). We found that during the birch pollen season symptoms and drug usage scores were 30 and 40 percent improved, respectively, in treated versus control subjects (p<0.0001 for both comparisons) whereas well days were 23.5 (33 percent) versus 16.9 (23 percent) (p=0.0024), respectively. Bet v 1 allergen specific proliferation decreased (p = 0.0010), whereas IL-10 transcription increased (p=0.0010) in treated, but not in control patients. Moreover, TGF-beta transcription was increased, although not significantly (p=0.066), following immunotherapy. Thus, sublingual immunotherapy with modified allergen in birch-allergic subjects was safe, clinically efficacious and associated with the reduction of allergen-specific proliferation and with the increased production of the IL-10 regulatory cytokine.
Effect of Carprofen Treatment Following Experimentally Induced Escherichia coli Mastitis in Primiparous Cows (2005)

Acute Escherichia coli mastitis is one of the major sources of economic loss in the dairy industry due to reduced milk production, treatment costs, discarded milk, and occasional fatal disease. Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used as adjunctive therapy to antibiotics. The objective of the current study was to evaluate the effect of carprofen treatment following infusion of Escherichia coli into the mammary glands of primiparous cows during the periparturient period. Severity of mastitis was scored based on the average milk production in the uninfected quarters on d +2 postinoculation and a clinical severity score. Carprofen was administered intravenously at 9 h postchallenge, when clinical signs of mastitis appeared. In previous work, efficacy of NSAIDs was mainly evaluated using clinical symptoms. In the present study, the effect of carprofen on innate immune response was also assessed by quantification of inflammatory mediators. All primiparous cows reacted as moderate responders throughout the experimental period. Primiparous cows were intramammarily inoculated with 1 x 10(4) cfu of E. coli P4:O32 in 2 left quarters. Analysis of blood and milk parameters, including IL-8, complement component C5a, lipopolysaccharide-binding protein (LBP), soluble CD14, prostaglandin E2, and thromboxane B2 was performed from d 0 to d +6 relative to intramammary inoculation. Rectal temperature in carprofen-treated animals was lower than in control animals at 3 and 6 h posttreatment. Treatment also restored the decreased reticulorumen motility that occurs during E. coli mastitis to preinfection levels faster than in control animals. Carprofen treatment resulted in an earlier normalization of the clinical severity score. Eicosanoid (prostaglandin E2 and thromboxane B2) production in milk tended to be inhibited by carprofen. No significant differences in the kinetic patterns of somatic cell count, IL-8, complement component C5a, LBP, and soluble CD14 were observed. In conclusion, carprofen treatment improved general clinical condition by effective antipyrexia and restoration of reticulorumen motility but did not significantly inhibit eicosanoid production. Carprofen treatment did not result in a significant decrease of chemotactic inflammatory mediators, IL-8 and C5a, and early innate immune molecules, sCD14 and LBP. Therefore, major modulatory effects from NSAID administration were not observed in this mastitis model, although a larger study might confirm some apparent trends obtained in the present results.
Tumor-targeted delivery of polyethylene glycol-conjugated D-amino acid oxidase for antitumor therapy via enzymatic generation of hydrogen peroxide. (2002)

Hydrogen peroxide (H(2)O(2)) is a strong oxidant that induces apoptosis of tumor cells in vitro. Here, we investigated the antitumor activity of an H(2)O(2)-generating enzyme, D-amino acid oxidase (DAO), and its conjugate with polyethylene glycol (PEG; PEG-DAO). Compared with DAO, PEG-DAO showed improved pharmacokinetic parameters in mice after i.v. injection. PEG-DAO administered i.v. accumulated selectively in tumor tissue with insignificant accumulation in normal organs and tissues. To generate cytotoxic H(2)O(2) at the tumor site, PEG-DAO was first administrated i.v. to tumor-bearing mice. After an adequate lag time, the substrate of DAO, D-proline, was injected i.p. This treatment resulted in significant suppression of tumor growth compared with tumor growth in control animals (not given treatment; P < 0.001). Similar treatment with native DAO showed no effect under the same conditions. Oxidative metabolites were significantly increased in solid tumors by administration of PEG-DAO followed by D-proline (P < 0.002, compared with the group receiving no treatment), as evidenced by thiobarbituric acid-reactive substance assay. This treatment did not affect results from the metabolites in the liver and kidney. These findings suggest that tumor-targeted delivery of DAO is accomplished by using pegylated enzyme and thereby taking advantage of the enhanced permeability and retention effect in solid tumor. PEG-DAO thus delivered together with D-proline produces remarkable antitumor activity via extensive generation of H(2)O(2).
A High-Frequency Three-Level Buck Converter With Real-Time Calibration and Wide Output Range for Fast-DVS (2017)

This paper presents a 50-MHz 5-V-input 3-Woutput three-level buck converter. A real-time flying capacitor (C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> ) calibration is proposed to ensure a constant voltage of V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> /2 across C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> , which is highly dependent on various practical conditions, such as parasitic capacitance, time mismatches, or any loading circuits from C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> . The calibration is essential to ensure the reliability and minimize the inductor current and output voltage ripple, thus maintaining the advantages of the three-level operation and further extending the system bandwidth without encountering sub-harmonic oscillation. The converter is fabricated in a UMC 65-nm process using standard 2.5-V I/O devices, and is able to handle a 5-V input voltage and provide a 0.6-4.2-V-wide output range. In the measurement, the voltage across C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> is always calibrated to Vg/2 under various conditions to release the voltage stress on the highand low-side power transistors and C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> , and to ensure reliability with up to 69% output voltage ripple reduction. A 90% peak efficiency and a 23-29-ns/V reference-tracking response are also observed.
Nature of epigenetic aging from a single-cell perspective (2022)

Abstract Age-related changes in DNA methylation (DNAm) form the basis for the development of most robust predictors of age, epigenetic clocks, but a clear mechanistic basis for exactly what part of the aging process they quantify is lacking. Here, to clarify the nature of epigenetic aging, we juxtapose the aging dynamics of tissue and single-cell DNAm (scDNAm) with scDNAm changes during early development, and corroborate our analyses with a single-cell RNAseq analysis within the same multi-omics dataset. We show that epigenetic aging involves co-regulated changes, but it is dominated by the stochastic component, and this agrees with transcriptional coordination patterns. We further support the finding of stochastic epigenetic aging by direct tissue and single-cell DNAm analyses and modeling of aging DNAm trajectories with a stochastic process akin to radiocarbon decay. Finally, we describe a single-cell algorithm for the identification of co-regulated and stochastic CpG clusters showing consistent transcriptomic coordination patterns, providing new opportunities for targeting aging and evaluating longevity interventions.
Determination of the Functional Groups in Algae Parachlorella Kessleri by Potentiometric Titrations (2012)

The acidic functional groups of the cell wall of native algae Parachlorella kessleri were evaluated by potentiometric titrations. The Gran´s method was applied to determination of the total, strong, weak and very weak acidities. The total organic acidity obtained for biomass was 3.93 mmol g-1, the largest content belonged to the strong acidic groups (2.13 mmol g-1) together with the weak acidic carboxylic groups (1.28 mmol g-1). Very weak acidities represented by the amine groups (0.52 mmol g-1) did not exceed 14% and they formed the lowest numerous part of all acidic functional groups.
Figure S5 from Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes (2023)

&lt;p&gt;RCAS-KrasG12D can induce tumors from KRT6A+ cells in K6a-tva/MMTV-Wnt1 mouse precancerous lesions.&lt;/p&gt;