gebhart/patrepeval huggingface dataset:
Mass spectrometry database of lacrimal gland adenoid cystic carcinoma and normal lacrimal gland tissue identifies extracellular matrix remodeling in these tumors (2023)

Adenoid cystic carcinoma of the lacrimal gland (LGACC) is a slow-growing but aggressive orbital malignancy. Due to the rarity of LGACC, it is poorly understood, which makes diagnosing, treating, and monitoring disease progression difficult. The aim is to understand the molecular drivers of LGACC further to identify potential targets for treating this cancer. Mass spectrometry was performed on LGACC and normal lacrimal gland samples to examine the differentially expressed proteins to understand this cancer's proteomic characteristics. Downstream gene ontology and pathway analysis revealed the extracellular matrix is the most upregulated process in LGACC. This data serves as a resource for further understanding LGACC and identifying potential treatment targets. This dataset is publicly available.
Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci (2010)

Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late onset CRC. Integration of genome and transcriptome data identifies seven novel candidate genes with the potential to identify an increased risk for CRC.
ALOS PALSAR calibration and validation activities in Sweden (2008)

This paper gives an overview of activities and results from the Swedish part of the international calibration and validation efforts for ALOS PALSAR. Four large trihedral corner reflectors were deployed and the measured co-polar responses showed that the PALSAR system performed well and was stable over time. The cross-talk level was found to be lower than – 34.5 dB. Two different methods for estimation of Faraday rotation were tested and rotations of up to 3o were recorded. An evaluation of the possibilities to retrieve forest variables from PALSAR data has also been performed. The results indicate that clearcuts can be detected and under favorable conditions the stem volume estimation accuracy for a single image was 30%.
Infant B cell memory and gut bacterial colonization (2012)

Under normal conditions, the gut microbiota confers health benefits for the host. The microbiota aids in the nutrient processing and contributes to the construction of the intestinal epithelial barrier. Furthermore, animal models demonstrate the importance of stimulation from gut bacteria for a proper maturation of the immune system. In this addendum, we summarize our recent study in which we demonstrate that colonization with Escherichia coli and bifidobacteria in the first 2 months of life was related to higher numbers of CD27-positive memory B cells later in infancy. The numbers of total B cells or CD5(+) CD20(+) B cells, on the other hand, were not related to the bacterial colonization pattern. Thus, the gut microbiota might affect the B cell maturation also in humans, and our study indicates that an early colonization pattern that includes E. coli and bifidobacteria might promote this maturation early in life.
The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors (2019)

Many functions in host-microbiota interactions are potentially influenced by intestinal transit times, but little is known about the effects of altered transition times on the composition and functionality of gut microbiota. To analyze these effects, we cultivated the model community SIHUMIx in bioreactors in order to determine the effects of varying transit times (TT) on the community structure and function. After five days of continuous cultivation, we investigated the influence of different medium TT of 12 h, 24 h, and 48 h. For profiling the microbial community, we applied flow cytometric fingerprinting and revealed changes in the community structure of SIHUMIx during the change of TT, which were not associated with changes in species abundances. For pinpointing metabolic alterations, we applied metaproteomics and metabolomics and found, along with shortening the TT, a slight decrease in glycan biosynthesis, carbohydrate, and amino acid metabolism and, furthermore, a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations. Specifically, <i>B. thetaiotaomicron</i> was identified to be affected in terms of butyrate metabolism. However, communities could recover to the original state afterward. This study shows that SIHUMIx showed high structural stability when TT changed-even four-fold. Resistance values remained high, which suggests that TTs did not interfere with the structure of the community to a certain degree.
Desarrollo de patrones de frecuencia en el IR basados en láseres de diodo (2012)

espanolLos peines opticos han aumentando hasta niveles casi impensables la precision de la medida de frecuencias laser en el rango optico. Sin embargo esta tecnica requiere que los laseres a medir sean muy estrechos y muy estables para alcanzar dichos niveles. En este trabajo se presentan las primeras medidas realizadas con el peine de frecuencias del IO en el rango de 1550 nm. Estas medidas se centran en la estabilidad y anchura de linea de un laser y la medida de la frecuencia absoluta. Con estos resultados se han calibrado dos medidores de longitud de onda propios para su uso en las comunicaciones opticas. Ademas, se presenta la estabilizacion de un diodo laser en la absorcion del Rb atomico en la region espectral de 780 nm, el cual se pretende usar como patron de calibracion de medidores de longitud de onda en estas frecuencias y como laser de referencia para la comparacion de relojes opticos y de peines de frecuencia. EnglishOptical frequency combs have extremely high measurement accuracy for laser frequencies in the optics range, up to an order of approximately ~10�]11. However, this technique requires narrow linewidth and frequency stable laser sources. The first set of measurement results we carried out were with an optical frequency comb in the 1550 nm range. These measurements are focused on the frequency stability, linewidth of the laser source and the absolute value of the optical frequency. Two wavemeters for optical communications were calibrated using the previous results. Furthermore, the stabilization of a laser diode in the Rb atomic absorption at 780 nm is presented. This source is expected to be used as calibration standard for wavemeters and as reference laser for optical clocks and frequency combs comparison.
Role of Grain-to-Grain Contacts on Profiles of Retained Colloids in Porous Media in the Presence of an Energy Barrier to Deposition (2006)

Deposition of 36-microm gold-coated hollow microspheres in two porous media (glass beads and quartz sand, 710-850 microm) was examined using X-ray microtomography (XMT) in the presence of an energy barrier to deposition under fluid velocity conditions representative of engineered filtration systems. XMT allowed examination of the deposition at different locations at the grain surfaces (deposition at grain-to-grain contacts versus single-contact deposition). We demonstrate that in the presence of an energy barrier to deposition, grain-to-grain contacts strongly influence colloid deposition and the spatial distribution of retained colloids in porous media. This result contrasts drastically with observations in the absence of an energy barrier to deposition, where consistency with filtration theory was observed. In the presence of an energy barrier, colloids were dominantly retained at grain-to-grain contacts, and the concentration of retained particles varied nonmonotonically with transport distance. It is proposed that the nonmonotonic profiles resulted from translation of surface-associated microspheres and subsequent immobilization at grain-to-grain contacts. This hypothesis is demonstrated using a conceptual model. The mutability and sensitivity of retained profiles to system conditions (from hyper-exponential to nonmonotonic) may reflect the interplay of different deposition mechanisms under different conditions.
Prism-coupled excitation of multiple Tamm waves (2013)

Abstract A Tamm wave is guided by the interface of a homogeneous dielectric material and a periodically nonhomogeneous dielectric material, both isotropic. We found theoretically that multiple Tamm waves of different linear polarization states can be guided by such an interface incorporated in a prism-coupled configuration. The Tamm waves have different linear polarization states, phase speeds, and spatial profiles, but the same frequency. The narrow absorptance peaks associated with the excitation of Tamm waves in the prism-coupled configuration offer the application as chemical sensors with very high sensitivity.
Real-world driving behaviour (2001)

With increasing complexity of engine management system there is a tendency for traditional driving cyles to become further and further removed from reality. So for a sensible evaluation of emissions and fuel consumption of road vehicles in the field there is an urgent need for 'real-world' driving patterns. Existing 'standard' driving cycles can be shown to be uncharacteristic of real-world driving behaviour. A methodology is presented to characterise real-world driving patterns numerically. On the basis of this methodology an overview is given of characteristic driving behaviour of various categories or road vehicles (trucks, passenger cars and motorcycles) in different regions of the world. Where relevant, these examples are compared with the different traffic conditions in those regions. Finally some examples are given of the way in which the study of real-world driving patterns can influence a national emission inventory by taking into account off-average driving behaviour and off-average traffic conditions.
Antitumor activity of RT2 peptide derived from crocodile leukocyte peptide on human colon cancer xenografts in nude mice (2018)

RT2, derived from the leukocyte peptide of Crocodylus siamensis, can kill human cervical cancer cells via apoptosis induction, but no evidence has shown in vivo. In this study, we investigated the antitumor effect of RT2 on human colon cancer xenografts in nude mice. Twenty-four mice were injected subcutaneously with human colon cancer HCT 116 cells. Eleven days after cancer cell implantation, the mice were treated with intratumoral injections of phosphate buffered saline (PBS) or RT2 (0.01, 0.1, and 1 mg/mouse) once every 2 days for a total of 5 times. The effect of a 10-day intratumoral injection of RT2 on body weight, biochemical, and hematological parameters in BALB/c mice showed no significant difference between the groups. Tumor volume showed a significant decrease only in the treatment group with RT2 (1 mg/mouse) at day 6 (P < .05), day 8 (P < .01), and day 10 (P < .01) after the first treatment. The protein expression levels of cleaved poly (ADP-ribose) polymerase (PARP), apoptosis-inducing factor (AIF), and the p53 tumor suppressor protein (p53) in xenograft tumors increased after treatment with RT2 (1 mg/mouse) compared to those in the PBS-injected group. Moreover, RT2 increased the expression of Endo G and Bcl-2 family proteins. Therefore, the peptide RT2 can inhibit tumor growth via the induction of apoptosis in an in vivo xenograft model.
Rape and Reconciliation in Sierra Leone (2013)

Sierra Leone was engaged in a brutal civil war, which lasted from 1991 to 2002. The conflict was characterized by atrocities including amputation and systematic rape. The victims of rape in Sierra Leone endured great suffering and many continue to suffer from the effects. Exacerbating the situation, the Special Court for Sierra Leone and The Sierra Leone Truth and Reconciliation Commission proved to be inadequate for rape victims. This project will use the narratives of sexual violence in Sierra Leone as a basis from which to explore reconciliation. It will make the case that, because the victim experiences profound trauma as a result of rape, forgiveness and reconciliation are deeply needed by both the individual affected and the larger community. This article will argue that, given the nature of the crime, the victim of rape should not reconcile with her victimizer on an individual level. Nonetheless, a greater reconciliation can occur for the victim who is broken physically, spiritually, and psychologically by rape: reconciliation that is internally directed, reconciliation between the victim and the community, and reconciliation between the victim and God.
Insulin-like Growth Factor-1- and Interleukin-6-related Gene Variation and Risk of Multiple Myeloma (2009)

Insulin-like growth factor (IGF)-1 and interleukin (IL)-6 promote the proliferation and survival of multiple myeloma cells. Variation in genes related to IGF-1 and IL-6 signaling may influence susceptibility to multiple myeloma. To assess their etiologic role, we examined the association of 70 tagging single nucleotide polymorphisms (SNP) in seven IGF-1 and three IL-6 pathway genes with multiple myeloma risk in two prospective cohorts, the Nurses' Health Study and the Health Professionals Follow-up Study. Among the participants who provided DNA specimens, we identified 58 women and 24 men with multiple myeloma and matched two controls per case. We used multivariable logistic regression models to assess the association of the SNPs or tagged haplotypes with multiple myeloma risk. Several SNPs had suggestive associations with multiple myeloma based on large odds ratios (OR), although the corresponding omnibus P values were not more than nominally significant (i.e., at P < 0.05). These SNPs included rs1801278 in the gene encoding insulin receptor substrate-1 [IRS1; C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] and three IL-6 receptor SNPs: rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0), rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0), and rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0). Additional SNPs in genes encoding IGF-1, IGF binding protein-2, IRS2, and gp130 also showed suggestive associations with multiple myeloma risk. We conducted a large number of statistical tests, and the findings may be due to chance. Nonetheless, the data are consistent with the hypothesis that IGF-1- and IL-6-related gene variation influences susceptibility to multiple myeloma and warrant confirmation in larger populations.
Analytical method by high resolution liquid chromatography for the determination of carbamazepine in human plasma; Metodo analitico por cromatografia liquida de alta resolucion para la determinacion de carbamazepina en plasma humano (2007)

One of the requirements to develop the studies of bioavailability and bioequivalence is to have analytic methodologies validated for the work with samples in biological fluids. A method was developed by high resolution liquid chromatography for the determination of carbamazepine in human plasma. A mixture of hydrogen phosphate of sodium: acetonitrile (65:35) adjusted to pH= 3.3 with phosphoric acid, flow of 1.2 mL/min and ultraviolet detection at 210 nm, was used as mobile phase. Propylparabene was used as an internal standard. According to the established regulations for the validation of the methods in biological fluids, the following parameters were studied: stability of the samples, lineality, specificity, precision, accuracy and limit of detection and quantification. The method proved to be specific and sensitive with a detection and quantification limit of 0.9 and 1.0 ng, respectively. The method was lineal, precise and exact in the range of concentrations of 1. 07 at 12.67 {mu}g/mL. The mean recovery was not statistically different from 100.0 %. The analito in the proposed biological matrix remained in the studied period. The methodology described in this work is applied in our case to the study that evaluates the bioavailability and bioequivalence of a Cuban formulation of carbamazepine in healthy volunteers. (Author)
A Network-based Prototype for Interactive Telemedicine &amp; Automated Management of Distributed, Clinical Databases (1996)

A network-based prototype has been developed to automate the process of generating and maintaining distributed databases of medical images and clinical reports, and for conducting interactive consultation among disparate clinical and research sites irrespective of the architecture of interacting computers. Pathologists routinely interpret gross and microscopic specimens to tender diagnoses and to engage in a broad spectrum of research. This assessment process leads to clinical decisions often limited by time constraints and by the availability of local expertise. Consultation with peers at other institutions is typically achieved by direct transfer of slides rather than images. A network of heterogeneous computer platforms, graphical user interfaces, and operating systems was established to test the performance of the software. Clinical diagnoses rendered by pathologists using the prototypical system and software were consistent with those reported two years earlier using conventional light microscopy in more than 97% of the cases studied.
A Spectroscopic SEM: First Results (2006)

Using a circular beam separator to deflect the primary beam of an SEM through 90deg, an aberration limited final probe size of 7-8 nm has been achieved in experiments. This limit was shown to be due to magnetic leakage fields from the post-deflector lens and not due to aberrations of the beam separator. In fact, it is concluded that the beam separator aberrations are within 2 nm over a 1 mum by 1 mum field-of-view, in agreement with previous simulation predictions. The results presented in this paper therefore confirm the feasibility of the spectroscopic SEM concept, from the imaging point of view, the next step is to acquire energy spectra. To further improve on the current setup, it is clear that a post-deflector lens without significant magnetic leakage field must be used. In addition, the lens should not be a transmission type as the SPSSEM relies on scattered electrons travelling back towards the beam separator. Such a lens has been designed and manufactured and is an immersion magnetic lens design which will be useful not only for imaging but also for spectrum experiments in the future
Analyse and quantification of electrical contacts endurance under fretting loadings (2010)

La sollicitation de fretting apparait comme un processus de dégradation très pénalisant dans les multiples systèmes industriels (aéronautique, industrie automobile, industriels du nucléaire, transports ferroviaires etc. …). Ce processus d’usure engendre dans la plupart des cas soit une réparation (rechargement) des surfaces soit le remplacement des composants (situation la plus souvent observée). La sollicitation de fretting est associée à des micro-déplacements alternés entre deux surfaces en contact. On observe généralement ce type de sollicitation dans tous les contacts soumis à des vibrations ou à des cycles thermiques. La sollicitation de fretting usure dans les contacts électriques est particulièrement pénalisante. Outre l’endommagement des surfaces, ce processus induit une augmentation significative de la résistance électrique des contacts et une perte de fonctionnalité du connecteur en particulier dans les connecteurs basses tensions très sensibles aux fluctuations de la résistance électrique. Pour palier ce problème les industriels de la connectique et leurs clients (industriels de l’automobile) cherchent à mettre en place de nouveaux dépôts palliatifs pour résoudre ces problèmes tout en limitant les surcouts liés à l’utilisation de dépôts nobles tels que l’or.Le sujet de cette thèse porte sur cette problématique avec pour objectif de mettre en place une méthodologie de choix des dépôts pour optimiser la durée de vie des connecteurs. L’étude aborde essentiellement l’influence des conditions de chargements mécaniques et plus particulièrement l’amplitude de débattement
The Imaging Probe Development Center at the National Institutes of Health - Ongoing production of fluorescent imaging probes (2011)

1549 Objectives The Imaging Probe Development Center (IPDC), a core synthetic facility at the National Insitutes of Health, focuses on developing probes from all imaging modalities, including optical, radionuclide and magnetic resonance agents. IPDC is currently working with principal investigators from more than a dozen different NIH Institutes, including several from NHLBI. We can supply requested imaging probes that are already known but otherwise unavailable, or are completely novel, and probes can be intended for all types of imaging modalities. Methods New examples of fluorescent agents prepared by IPDC will be described. Results Examples of fluorescent imaging probes we have made include fluorogenic enzyme substrates, fluorescent dyes and analogs, caged derivatives which become fluorescent upon uncaging, photoactivated probes for investigation of AMPARs trafficking in neurons, fluorescent probes for lysosomal storage diseases, and indocyanine green-affibody conjugate for fluorescence imaging for potential applications during breast cancer surgery. Conclusions Fluorescent imaging probes for a variety of biomedical applications have been described to highlight the research at IPDC
Supplementary Figure 5 from Natural Killer Cells Efficiently Reject Lymphoma Silenced for the Endoplasmic Reticulum Aminopeptidase Associated with Antigen Processing (2023)

Supplementary Figure 5 from Natural Killer Cells Efficiently Reject Lymphoma Silenced for the Endoplasmic Reticulum Aminopeptidase Associated with Antigen Processing
2-Diazo-3-[[(1,1-dimethylethyl)dimethylsilyl]oxy]-3-butenoic Acid, Methyl Ester (2010)

[166392-81-0] C11H20N2O3Si (MW 256) InChI = 1S/C11H20N2O3Si/c1-8(9(13-12)10(14)15-5)16-17(6,7)11(2,3)4/h1H2,2-7H3 InChIKey = XLIWNMXKBCISIR-UHFFFAOYSA-N (precursor to highly chemoselective metal carbenoid) Physical Data: IR (neat) 2950, 2107, 1714, 1669, 1466, 1352 cm−1; 1H NMR (CDCl3) δ 4.98 (d, J = 1.8 Hz, 1H), 4.23 (d, J = 1.8 Hz, 1H), 3.78 (s, 3H), 0.90 (s, 9H), 0.21 (s, 6H). Solubility: soluble in most organic solvents including hydrocarbons. Form Supplied in: not commercially available. Preparative Methods: 1 triethylamine (2 mL, 14.3 mmol) was added to a stirring solution of methyl 2-diazo-3-oxobutanoate (3.1 g, 10.1 mmol) in dichloromethane (26 mL) at 0 °C under an inert argon atmosphere. tert-Butyldimethylsilyl trifluoromethanesulfonate (2.8 mL, 12.2 mmol) was added over 5 min and the mixture was further stirred for 30 min at 0 °C. The reaction mixture was diluted with hexane (100 mL), and the organic phase was subsequently washed with dilute aqueous sodium bicarbonate (100 mL) and brine (100 mL). The organic layer was dried (MgSO4), and the solvent was removed under reduced pressure to yield the title product as an orange oil (essentially quantitative yield), which was used without further purification. Purification: the title compound can be used without further purification, but usually it contains a trace amount of bis(tert-butyldimethylsilyl) ether as a major impurity. The compound can be quickly purified by flash chromatography in silica gel with hexane containing 1% triethylamine. Handling, Storage, and Precautions: the title compound is labile under acidic conditions. Unlike other vinyldiazoacetates, which slowly undergo electrocyclization to form pyrazoles, this diazo compound is thermally stable and can be stored in a refrigerator for several months without significant decomposition. As with all diazo compounds, caution should be emphasized in handling this compound, and excessive heating should be avoided. As a precaution, it is recommended that all procedures using this compound should be conducted behind a blast shield.