gebhart/patrepeval huggingface dataset:
Abstract 4708: Hes6 as a glioma biomarker with functional significance for cancer growth (2010)

Abstract Malignant gliomas are the most common type of primary brain tumors affecting 16,000 new patients every year in the United States. In this study, we undertook a large-scale transcriptomics mining study of Affymetrix data from 9,783 samples from the genesapiens database (www.genesapiens.org) focusing on glioma biomarkers. We searched for genes that were specifically expressed in Glioblastoma Multiforme (GBM) and anaplastic astrocytoma using gene expression data from 475 different types of glioma samples (including 322 GBM, 66 anaplastic astrocytomas) and 425 samples from different normal anatomical locations of central nervous system. One of the prominent biomarkers arising from this bioinformatic search was the transcription cofactor HES6 (Hairy and enhancer of split 6), which was highly expressed in gliomas compared to normal brain. Since the role of HES6 in glioma pathogenesis is poorly understood, we chose to validate its expression by immunostaining and functional role by siRNA knockdown studies in glioma cell lines. HES6 protein levels were studied in a glioma tissue microarray material that consisted of 414 samples as well as in normal brain tissue controls. Positive HES6 immunoreactivity was present in 99 % of available gliomas. Recurrent tumors of grade 2 astrocytomas and grade 2-3 oligodenrogliomas showed higher levels of HES6 immunoreactivity than the primary tumors of these classes. Endothelial cells that aligned the blood vessels within the tumors were also stained in 75 % of gliomas. HES6 immunoreactivity was also present in glial and endothelial cell nuclei in non-neoplastic cerebral white matter and cortex. Cell viability was reduced by 60 % after HES6 silencing in A172 and LN405 cells and by ∼20-25 % in the U87MG and SVG p12 cell lines. HES6 silencing also increased apoptosis 2-3 fold in two cell lines as measured by Apo-ONE Homogeneous Caspase-3/7 Assay. We then studied the biological consequences of HES6 silencing by genome-wide gene expression studies. Gene ontology analysis implicated genes involved in cellular movement, development and RNA post-transcriptional modification. Also, aberrant expression around key regulator genes, such as p53, c-myc and SP1 was seen. In conclusion, these results suggest that HES6 is a possible glioma marker that also has critical functional role in glioma growth. This work was supported by funding under the 6th FP of the European Union, Project RIGHT (LSHB-CT-2004-005276), and the Academy of Finland. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. 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 4708.
Blind and reference-free fluorescence lifetime estimation via consumer time-of-flight sensors (2015)

Fluorescence lifetime imaging (FLI) is a popular method for extracting useful information that is otherwise unavailable from a conventional intensity image. Usually, however, it requires expensive equipment, is often limited to either distinctly frequency- or time-domain modalities, and demands calibration measurements and precise knowledge of the illumination signal. Here, we present a generalized time-based, cost-effective method for estimating lifetimes by repurposing a consumer-grade time-of-flight sensor. By developing mathematical theory that unifies time- and frequency-domain approaches, we can interpret a time-based signal as a combination of multiple frequency measurements. We show that we can estimate lifetimes without knowledge of the illumination signal and without any calibration. We experimentally demonstrate this blind, reference-free method using a quantum dot solution and discuss the method’s implementation in FLI applications.
Towards synchronous deterministic channels for the Internet of Things (2014)

Embedded systems are omnipresent in our daily lives and rapidly gaining more and more importance, with performance improvements and technological evolutions in several directions. One of the most promising directions of evolution is in their interconnection. Already today there is a broad variety of use cases for interconnected embedded systems (automobiles, airplanes, automated production halls, etc.) and the most cutting edge examples demand the distributed embedded systems to tightly couple their operation. As a direct result of this tight coupling, stringent requirements on the underlying communication network immediately arise. The Internet-of-Things (IoT) as a discipline and movement to systematically connect distributed embedded systems on large or even Internet-like scales, promises a new generation of systems and system-of-systems. In order to also enable tight coupling of embedded systems in the IoT, there is a need for deterministic communication channels with predictable and low communication latency and jitter. In this paper we discuss how synchronous deterministic channels can be developed for the IoT by application of the time-triggered communication paradigm and other technology standards currently under development.
Effects of cross host species inoculation of nitrogen‐fixing endophytes on growth and leaf physiology of maize (2012)

Abstract Plants that grow and thrive under abiotic stress often do so with the help of endophytic microorganisms. Although nitrogen‐fixing (diazotrophic) endophytes colonize many wild plants, these natural relationships may be disrupted in cultivated crop species where breeding and genotype selection often occur under conditions of intensive fertilization and irrigation. Many energy crops including corn may still benefit from diazotrophic endophyte inoculations allowing for more efficient biomass production with less input of petroleum‐derived fertilizer. A selection of diazotrophic endophytes isolated from willow ( S alix sitchensis , S itka willow) and poplar ( P opulus trichocarpa , black cottonwood) growing in nutrient‐poor river sides were used as inoculum in three experiments testing the effect on plant growth and leaf level physiology of a sweet corn variety under various levels of applied nitrogen fertilizer. We report substantial growth promotion with improved leaf physiology of corn plants in response to diazotrophic endophyte inoculations. Significant gains of early biomass with a greater root : shoot ratio were found for plants receiving endophytic inocula over the uninoculated control groups regardless of the nitrogen level. Furthermore, inoculated plants exhibited consistently higher rates of net CO 2 assimilation than did those without endophytic inoculation. These results have beneficial implications for enhanced plant growth in a low‐input system on nutrient‐poor sites. The immediate increase of root mass observed in endophyte inoculated plants has the potential to provide better establishment and early growth in resource‐limited environments. The initial results of this study also indicate that the beneficial effect from endophytes isolated from poplar and willow species is not restricted to the species from which they were initially isolated.
Is Grade or Stage of Primary Importance in Determining the Outcome after Radical Prostatectomy for Disease Clinically Confined to the Prostate? (1989)

A series of 145 patients with T1-2NOMO prostatic carcinoma underwent radical prostatectomy. Specimens were analysed by Gleason sum and categorised according to whether the disease was organ-confined, specimen-confined or margin-positive. The failure of treatment was indicated by elevation of acid phosphatase, by the appearance of biopsy proven local disease or distant nodal disease, or by parenchymal or nodal disease by any imaging modality. Analysis of the data demonstrated that the outcome of surgical intervention was related to the anatomical extent of disease. The Gleason sum was related to the extent of disease and predicted the probability of disease outside the organ of origin.
Immunogenicity of Novel Consensus-Based DNA Vaccines Against Chikungunya Virus (2008)

CHIKV is an emerging arbovirus and is an important human pathogen that causes a syndrome characterized by fever, headache, rash, nausea, vomiting, myalgia, arthralgia and occasionally neurological manifestations such as acute limb weakness. It is also associated with a fatal haemorrhagic condition. CHIKV is geographically distributed from Africa through Southeast Asia and South America, and its transmission to humans is mainly through Aedes species mosquitoes. The frequency of recent epidemics in the Indian Ocean islands suggests that something else was carrying the virus, as Aedes aegypti are not found there. In fact, the relative Asian tiger mosquito, Aedes albopictus, was present and has raised concern in the world health community regarding the potential for a CHIK virus pandemic. Efforts to monitor the disease will only provide minimal warning in a global society, and steps must be taken to prevent the morbidity and mortality associated with a possible pandemic. There is no specific treatment for Chikungunya virus and there is no vaccine currently available. We propose a novel consensus-based approach to vaccine development, employing a DNA vaccine strategy that can provide more highly cross-reactive cellular immunity against CHIK virus. The vaccine cassette was designed based on Capsid (Cap) and Envelope (E1) specific consensus sequences with several modifications, including codon optimization, RNA optimization, the addition of a Kozak sequence, and a substituted immunoglobulin E leader sequence. The expression of Cap and envelope E1 was evaluated using T7-coupled transcription/translation and immuno blot analysis. A recently developed, adaptive constant-current electroporation technique was used to immunize mice (both Balb/C & C57BL/6 mice strain) with an intramuscular injection of plasmid coding for the CHICK-Cap and E1. We show such constructs can induce strong cellular immunity against CHIK-Cap and E1 antigens. The analysis of specific antibody responses suggested that CHIK-E1 could induce a strong E1 specific antibody response. Epitope mapping results indicated that there is an increase in the breadth and magnitude of cross-reactive cellular responses induced by both the Capsid and Envelope immunogen. These properties suggest that such a consensus immunogen deserves further examination for its potential to serve as a component antigen in a CHIK vaccine cocktail. 13th International Congress on Infectious Diseases Abstracts (Oral Presentations)International Journal of Infectious DiseasesVol. 12Preview Full-Text PDF Open Archive
Antiretroviral Monocyte Efficacy Score Linked to Cognitive Impairment in Hiv (2012)

ARV efficacy against monocytes/macrophages correlates with cognitive function in HIV-infected individuals on ARV therapy within this cohort. If validated, efficacy against monocytes/macrophages may provide a new target to improve HIV NCI.
VizieR Online Data Catalog: Gaia-ESO Survey: Cha I members (Sacco+, 2017) (2017)

VizieR On-line Data Catalog: J/A+A/601/A97. Originally published in: 2017A&A...601A..97S
Mechanical behaviour of leg extensor muscles in male and female sprinters (2002)

Leg extensor muscle characteristics, running speed and serum testosterone were studied in sixteen males and twelve female sprinters. The rise of center of gravity was measured during squat jumps executed without (SJ) and with extra loads (SJbm), counter movement jump (CMJ) and continuous jumping (CJ) for 5 s. Nine females and nine males performed also half-squat exercises with extra loads ranging from 50% to 200% of the subject's body mass (bm). Average mechanical power (P), force (F) and velocity (v) were calculated and measured during half-squat exercises using the ErgopowerÂ®. Total serum testosterone (TT) was determined in venous blood. In women, 60 m dash, SJ, CMJ and CJ performances were significantly lower (P<0.001) than men. Gender differences were not found in F during half-squat exercises and in SJbm. Women demonstrated significantly higher ratios CMJ:SJ and CJ:SJ than men. With loads 50-100 % of bm men demonstrated greater v and P than women. It was suggested that high testosterone level in men might be a factor ensured superiority in explosive power and speed, but not in muscle strength adjusted to body mass.
Can We Rely on AGNP Therapeutic Targets Also For LAI Antipsychotics? (2017)

The updated AGNP Consensus Guidelines for Therapeutic Drug Monitoring (TDM) in Neuropsychopharmacology recently published in the journal have reinforced the key role of TDM to individualize psychoparmacological therapies in clinical practice. However, we believe, that these guidelines have missed the important opportunity to face with, and to provide useful information on, the emerging issue of long-acting injectable formulations of atypical antipsychotics. Specific therapeutic ranges also for these formulations should be included in the next AGNP guidelines.
Outcome of Open Reduction and Internal Fixation of Surgical Neck Nonunions of the Humerus (2004)

Open reduction and internal fixation with autogenous bone graft results in excellent outcomes even in patients >65 years old and patients with significant medical problems. This treatment method offers predictable fracture healing and has a low complication rate.
Synthesis of a Carboxylate Functionalized Bis-Amino Acid Monomer (2009)

The synthesis of the first functionalized bis-amino acid monomer proAc(2S3S4R) 1 that carries an acetyl side chain is presented. This monomer was incorporated into oligomer 3 and the solution phase structure was determined by using two-dimensional nuclear magnetic resonance. The solution structure confirmed the intended connectivity and stereochemistry of the oligomer. This first functionalized bis-amino acid represents a milestone toward functionalized bis-peptide nanostructures for catalytic, molecular recognition, and nanotechnology applications.
The NMR toolbox 2.0 : expansion to different nano- and micrometre sized particles (2014)

Nuclear Magnetic Resonance spectroscopy (NMR) has proven to be a powerful technique to explore the surface chemistry of colloidal semi-conductor nanocrystals (NCs) from the ligand’s point of view. By exploiting chemical shift perturbations, the resonance’s line-width and the molecular diffusion coefficient, interacting species may be distinguished from non-interacting ones in the dispersion. Information regarding the identity and quantity of the interacting ligands at the NC surface can be obtained. Monitoring the impact of concentration changes on the spectral properties allows the chemical exchange regime to be established. Ligand exchange processes may be characterized either using ex-situ exchange procedures or directly in the NMR tube. [1]\nIn this presentation, we propose a further expansion of our NMR toolbox. Additional techniques are introduced in response to our desire to extend the application scope beyond colloidal NCs. We illustrate the NMR toolbox 2.0 using three distinct systems. First, the study of Aluminium doped Zinc Oxide NCs with oleic acid or oleylamine ligands will be presented. This system demonstrates how the existing methods in the NMR toolbox can be fine-tuned to address the questions raised in specific systems. Second, the extension of the toolbox to high temperatures (up to 120°C) is shown to afford improved understanding of the surface chemistry and ligand exchange procedures in Copper Indium Sulfide NCs capped with oleylamine ligands. Finally, the approaches developed to study the interaction of lysine with hydroxyapatite, a biocompatible vehicle for drug delivery, are presented. These micrometre sized, water soluble particles required the introduction of high-resolution Magic Angle Spinning (hr-MAS) and Saturation Transfer Difference (STD) NMR spectroscopy. In this fashion, the potential applicability of our NMR tools beyond the nanoscopic dimensions is demonstrated.
Myocardial T1 measurement in patients with thalassemia major (2009)

Cardiac complications secondary to iron overload are the leading cause of death in thalassemia major (TM). Cardiovascular magnetic resonance (CMR) can provide a noninvasive means of measuring the amount of tissue iron. With CMR, tissue iron is detected indirectly by the effect on relaxation times of hydrogen nuclei in the presence of ferritin and hemosiderin iron. The iron results in shortening of proton relaxation times and both CMR T2* and T2 have been validated as non-invasive means for assessment of myocardial iron overload. [1–4]. We have demonstrated a linear correlation between T2 and T2* in patients with iron overload [5]. However, there is currently little data on myocardial iron assessment using the longitudinal relaxation time T1 mainly due to the cardiac and respiratory problems in CMR.

A modified Look-Locker Inversion recovery (MOLLI) has been recently proposed for myocardial T1 quantification [6]. It is of interest, therefore, to investigate whether T1 measurement is affected by iron overload in TM patients. For quantitatively analysis, it is important to further investigate the relationship between T1 and the more established T2* measurements in TM patient population.

In this study therefore, we aimed to compare myocardial T1 [6] and T2* measurements [3]in vivo in order to establish the relationship between them. We hypothesised that T1 would correlate with T2* linearly when iron becomes dominant in the myocardium.
Preferentially oriented epitaxial Y-Ba-Cu-O films prepared by the ion beam sputtering method (1988)

Preferentially oriented epitaxial Y-Ba-Cu-O films were prepared on (100) SrTiO3 substrates by oxygen reactive ion beam sputtering. The epitaxial orientations were varied by controlling both substrate temperature and oxygen parital pressure. c-axis oriented films tended to be formed at higher substrate temperatures (&amp;gt;620 °C) and lower oxygen pressures (&amp;lt;3×10−3 Torr). In contrast, a/c- and a-axis oriented films were formed at lower substrate temperatures (&amp;lt;600 °C) and higher oxygen pressures (&amp;gt;3×10−3 Torr). The best Tc (end) of 82 K was observed in one of the c-axis oriented film without post-annealing. The tendency for preferential orientation can be well understood in terms of the lattice mismatch between the substrate and the film, the lattice constants of which depend on oxygen deficiency.
H7, a protein kinase C inhibitor, increases the glutathione content of neuroblastoma cells (1992)

It is shown that the intracellular glutathione (GSH) concentration of neuroblastoma-2a cells in culture increases with a maximum at 24 h after starting treatment with 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H7), an inhibitor of protein kinase C (PKC). Other inhibitors of this and other protein kinases, e.g. sphingosine, staurosporine, and HA 1004, at the concentrations tested, had a less marked or negligible effect on intracellular GSH concentration. 12-O-Tetradecanoylphorbol-13-acetate (TPA) was also tested and showed no significant effect 24 h after addition.
Novel Fine-Grain Back-Bias Assist Techniques for 14nm FDSOI Top-Tier SRAMs integrated in 3D-Monolithic (2019)

For the first time, we propose a 3D-monolithic SRAM architecture with a local back-plane for top-tier transistors enabling local back-bias assist techniques without area penalty as well as the capability to route two additional row-wise signals on individual back-planes. Experimental data are extracted from a 14nm planar Fully-Depleted-Silicon-on-Insulator (FDSOI) <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$0.078\mu \mathrm{m}^{2}$</tex> SRAM in order to properly model 3D top-tier cells. Simulations show this technique yields a 7% bitline capacitance reduction, a 12%/16% read/write access time improvement at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$V_{DD}=0.8\mathrm{V}$</tex> and a reduction of minimum operating voltage <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$V_{min}$</tex> by 60mV at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$6\sigma$</tex> w.r.t. planar SRAMs.
Practical Synthesis of 1-Aryl-6-(hydroxymethyl)-2-ketopiperazines via a 6-exo Amide−Epoxide Cyclization (2004)

[reaction: see text] Chiral 1-aryl-6-(hydroxymethyl)-2-ketopiperazines can be prepared via an operationally simple, 6-exo epoxide ring-opening cyclization to form the ketopiperazine C6-N1 bond in high yields and with excellent enantiomeric purity.
Wireless-powered cooperative multi-relay networks with relay selection (2017)

In this paper, we consider wireless information and power transfer in a cooperative multi-relay network (MRN) with relay selection. The off-grid relay terminals, which are randomly deployed within a certain cooperating area, help forward the source information to the destination following a decode-and-forward protocol. Adaptive power splitting is employed at each relay that attempts to decode the source information first and stores any remaining energy. Then according to different criteria, a single best relay is selected to forward the decoded source signal to the destination. Considering the spatial randomness of the intermediate relays and energy causality, the end-to-end outage probability of this wireless-powered MRN is analytically obtained under different relay selection schemes. Simulation results demonstrate that with more knowledge available for relay selection, a significantly better outage performance can be achieved, albeit at a higher implementation complexity.
Supplementary Figures S1-S15 from First-in-Human Study of the Radioligand <sup>68</sup>Ga-N188 Targeting Nectin-4 for PET/CT Imaging of Advanced Urothelial Carcinoma (2023)

&lt;p&gt;Figure S1. Synthesis of N188. Figure S2. Mass spectrometry characterization of N188.Figure S3. SPR characterization of N188.Figure S4. Radio-HPLC characterization of 68Ga-N188.Figure S5. Stability of 68Ga-N188 in serum and normal saline. Figure S6. Synthesis of FITC-N188. Figure S7. Mass spectrometry characterization of FITC-N188. Figure S8. Blood routine safety test. Figure S9. Toxicity test of 68Ga-N188. Figure S10. Results of PET/CT dynamic imaging studies in one healthy subject. Figure S11. Pharmacokinetics of 68Ga-N188 in mouse blood. Figure. S12 68Ga-N188 PET/CT imaging with maximum intensity projection (MIP) reconstruction of 12 advanced UC patients with obtained pathological sections. Figure S13. Representative PET/CT images of a patient (No. 3) with advanced urothelial carcinoma. Figure. S14 Comparison of brain metastasis imaging of patient No. 4 using 68Ga-N188, 18F-FDG PET/CT and MRI. Figure. S15 Nectin-4 IHC staining in 12 mUC patients with pathological sections of primary focus.&lt;/p&gt;
Encapsulation of gold nanoclusters: stabilization and more (2021)

Gold nanoparticles with only a few atoms, known as gold nanoclusters (AuNCs), have dimensions below 2 nm and feature singular properties such as size dependent luminescence. AuNCs are also highly photostable and have catalytic activity, low toxicity and good biocompatibility. With these properties, they are extremely promising candidates for application in bioimaging, sensing and catalysis. However, when stabilized only with small capping ligands, their use is hindered by lack of colloidal stability. Encapsulation of the AuNCs can contribute to provide a more robust protection and even to improve their properties. Here, we review the encapsulation of AuNCs in polymers, silica and metal organic frameworks (MOFs) for applications in bioimaging, sensing and catalysis.