gebhart/patrepeval huggingface dataset:
Multi-target stool DNA test in the surveillance of inflammatory bowel disease: a cross-sectional cohort study (2018)

Background and aim: Colonoscopic surveillance is recommended in patients with longstanding inflammatory bowel disease (IBD) as they are at increased risk of colorectal cancer (CRC). Non-invasive surveillance may improve compliance and access. Multi-target stool DNA (MT-sDNA) has been validated for screening of sporadic CRC but has not been assessed in IBD. Our aim was to assess the performance of a MT-sDNA test in a real-life surveillance setting of patients with longstanding IBD.Material and methods: A total of 192 IBD patients enrolled from two prospective cohorts submitted an EDTA buffered stool sample and underwent chromo- or white light colonoscopy. Stools were assayed for methylated BMP3 & NDRG4, mutant KRAS and β-actin by a laboratory blinded to clinical data.Results: The multitarget-sDNA panel was positive in 2/2 CRC and 5/15 low-grade dysplasia (LGD) < 1 cm in diameter. Sensitivities were 100% (95% CI 16–100%) for CRC and 33% (95% CI 13–61%) for LGD lesions <1 cm, with specificities of 87% (95% CI 81–91%) and 93% (95% CI 88–96%), respectively. The estimated number of patients needed to screen to detect a single CRC was 96 (95% CI 93–99%) and was 28 (95% CI 22–34%) to detect any colorectal neoplasia (CRN).Conclusion: The MT-sDNA panel detected CRC in IBD. Sensitivity for sub-centimeter colorectal neoplasms in IBD patients appears similar to that observed in the general population. The test may be a valuable tool for detection of malignancy during structured surveillance of long-term IBD in a first line hospital setting.
Aragorn: Eliciting and Maintaining Secure Service Policies (2017)

Services are configured via policies that capture expected behaviors, but stakeholder requirements can change, making policy errors a surprisingly common occurrence. Aragorn applies formal argumentation to produce policies that balance stakeholder concerns.
Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals (2021)

Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.
Cross-sectional and longitudinal measures of chitinase proteins in amyotrophic lateral sclerosis and expression of CHI3L1 in activated astrocytes (2020)

CSF Chit-1 and CHI3L1 are significantly increased in ALS, and CSF Chit-1 and CHI3L1 levels correlate to the rate of disease progression. CHI3L1 is expressed by a subset of activated astrocytes predominately located in white matter.
Direct In Situ Observation of the Early‐Stage Disorder–Order Evolution of Perpendicular Lamellae in Thermally Annealed High‐χ Block Copolymer Thin Films (2019)

Abstract The evolution of well‐ordered, sub‐10 nm, perpendicular lamellae from a disordered state is documented directly using in situ atomic force microscopy, cross‐sectional scanning electron microscopy, and grazing‐incidence small angle X‐ray scattering. Since block copolymer (BCP) self‐assembly occurs on extremely fast time scales, directly imaging the growth of perpendicular lamellae remains challenging. The lack of understanding behind early‐stage self‐assembly and how metastable defects can affect the kinetic behavior near thermodynamic equilibrium prevents the realization of defect‐free thin films. By characterizing the evolution of nanostructures using a high‐χ, perpendicular lamella‐forming BCP, poly(polyhedral oligomeric silsesquioxane)‐ block ‐poly(2,2,2‐trifluoroethyl methacrylate), over a wide temperature range, three stages in the evolution of perpendicular lamellae, characterized mainly by the root‐mean‐squared (rms) roughness, is observed. At temperatures lower than the glass transition temperatures ( T g ), the film retains a smooth, disordered surface (rms roughness = 0.352 ± 0.006 nm), characteristic of spin‐coated films. Near the T g , spinodal decomposition and the appearance of lamellae are detected as the rms roughness increases at 70 °C, before peaking at 82 °C at 0.83 nm, and decaying rapidly with increasing temperatures. Above the T g , the rms roughness returns to 0.35 ± 0.03 nm, as defects are observed to annihilate sequentially.
Renaturation, activation, and practical use of recombinant duplex-specific nuclease from Kamchatka crab (2006)

We overexpressed duplex-specific nuclease (DSN) from Kamchatka crab in Escherichia coli cells and developed procedures for purification, renaturation, and activation of this protein. We demonstrated identity of the properties of the native and recombinant DSN. We also successfully applied the recombinant DSN for full-length cDNA library normalization.
Observation of nuclear modifications in W± boson production in pPb collisions at sNN=8.16TeV (2019)

The production of W bosons is studied in proton-lead (pPb) collisions at a nucleon-nucleon centreof-mass energy of s NN = 8.16 TeV. Measurements are performed in the W channel using a data sample corresponding to an integrated luminosity of 173.4 6.1 nb -1 , collected by the CMS Collaboration at the LHC. The number of positively and negatively charged W bosons is determined separately in the muon pseudorapidity region in the laboratory frame | lab | < 2.4 and transverse momentum p T > 25 GeV/c. The W boson differential cross sections, muon charge asymmetry, and the ratios of W boson yields for the proton-going over the Pb-going beam directions are reported as a function of the muon pseudorapidity in the nucleon-nucleon centre-of-mass frame. The measurements are compared to the predictions from theoretical calculations based on parton distribution functions (PDFs) at next-to-leading-order. The results favour PDF calculations that include nuclear modifications and provide constraints on the nuclear PDF global fits.
Fast Determination of Active Components in Fructus Corni by Near Infrared Spectroscopy (2013)

Today, near-infrared (NIR) has been proved to be a powerful analytical tool. It has been applied widely in agricultural, petrochemical, textile and pharmaceutical industries. In this paper, near-infrared spectroscopy (NIRS) combined with partical least square (PLS) was used as a qualitative tool to rapidly determinate two active components in Fructus Corni. The PLS calibration model of NIR Spectroscopy, the correlation coefficients (R 2 ) of Loganin and Morroniside were 0.95895 and 0.98450, the root-mean-square error of cross-validation (RMSECV), the Correction of deviation, the prediction mean square error was 0.0344,0.109;0.0625, 0.2641 and 0.0948, 0.233. The result shows that, the near-infrared Reflectance Spectroscopy could be used to determinate the content of Loganin and Morroniside, and meanwhile as a simple and rapid new method for the quality assessment of Fructus Corni. In addition, the NIRS has a unique advantage in the quality control of traditional Chinese Medicine (TCM), such as rapid, accurate, nondestructive and no pollution. It is expected to be further uses in the quality control of TCM. It is can achieve the requirement of rapid detection of large quantities of Fructus Corni.
Stem Cell-Calcium Phosphate Constructs for Bone Engineering (2010)

While human bone-marrow-derived mesenchymal stem cells (hBMSCs) have been investigated, human umbilical cord mesenchymal stem cells (hUCMSCs) are a relatively new cell source. Little has been reported on hUCMSC encapsulation in scaffolds for bone tissue engineering. The objective of this study was to encapsulate hBMSCs and hUCMSCs in calcium phosphate cement (CPC) scaffolds for dental, craniofacial, and orthopedic applications. Stem-cell-encapsulating CPC construct with chitosan and fiber reinforcement reached the strength of cancellous bone, which was much stronger than previous injectable carriers for cell delivery. hUCMSCs and hBMSCs inside the constructs showed excellent viability and osteo-differentiation. The encapsulated hUCMSCs synthesized nearly three-fold more bone minerals than the hBMSCs in vitro. Hence, stem-cell-encapsulating CPC-chitosan-fiber construct may be promising for dental and orthopedic applications. This study indicated that the hUCMSCs were a potent alternative to the gold-standard hBMSCs, which may have a broad impact on regenerative medicine and dental tissue engineering.
Characterization of an InGaAs/InP-based single-photon avalanche diode with gated-passive quenching with active reset circuit (2010)

An improved gated-mode passive quenching with active reset (gated-PQAR) circuit is utilized in conjunction with an InGaAs/InP single-photon avalanche photodiode (SPAD). Photon detection efficiency (PDE) and dark count probability (DCP) were measured at a gate repetition rate of 1 MHz. The reduced afterpulsing afforded by the gated-PQAR circuit enabled measurement of afterpulsing for hold-off times as short as 10 ns. The timing resolution (jitter) for different excess biases has also been investigated. At 230 K and an excess bias of 2.5 V, 0.3% afterpulse probability for a 10 ns hold-off time was achieved with 13% PDE, 2 × 10−6 DCP, 160 ps jitter, and 0.2 ns effective gate width. For the same hold-off time, at a higher excess bias of 3.5 V, 30% PDE, 1 × 10−5 DCP and 120 ps jitter were achieved with 7% afterpulse probability with an effective gate width of 0.7 ns.
Search for Higgs boson pair production in the $$b\bar{b}b\bar{b}$$ b b ¯ b b ¯ final state from pp collisions at $$\sqrt{s} = 8$$ s = 8 TeVwith the ATLAS detector (2015)

A search for Higgs boson pair production [Formula: see text] is performed with 19.5 fb[Formula: see text] of proton-proton collision data at [Formula: see text] TeV, which were recorded by the ATLAS detector at the Large Hadron Collider in 2012. The decay products of each Higgs boson are reconstructed as a high-momentum [Formula: see text] system with either a pair of small-radius jets or a single large-radius jet, the latter exploiting jet substructure techniques and associated <i>b</i>-tagged track-jets. No evidence for resonant or non-resonant Higgs boson pair production is observed. The data are interpreted in the context of the Randall-Sundrum model with a warped extra dimension as well as the two-Higgs-doublet model. An upper limit on the cross-section for [Formula: see text] of 3.2 (2.3) fb is set for a Kaluza-Klein graviton [Formula: see text] mass of 1.0 (1.5) TeV, at the 95 % confidence level. The search for non-resonant Standard Model <i>hh</i> production sets an observed 95 % confidence level upper limit on the production cross-section [Formula: see text] of 202 fb, compared to a Standard Model prediction of [Formula: see text] fb.
Changes in the Spatial Distribution of Visual Attention after Early Deafness (2002)

There is much anecdotal suggestion of improved visual skills in congenitally deaf individuals. However, this claim has only been met by mixed results from careful investigations of visual skills in deaf individuals. Psychophysical assessments of visual functions have failed, for the most part, to validate the view of enhanced visual skills after deafness. Only a few studies have shown an advantage for deaf individuals in visual tasks. Interestingly, all of these studies share the requirement that participants process visual information in their peripheral visual field under demanding conditions of attention. This work has led us to propose that congenital auditory deprivation alters the gradient of visual attention from central to peripheral field by enhancing peripheral processing. This hypothesis was tested by adapting a search task from Lavie and colleagues in which the interference from distracting information on the search task provides a measure of attentional resources. These authors have established that during an easy central search for a target, any surplus attention remaining will involuntarily process a peripheral distractor that the subject has been instructed to ignore. Attentional resources can be measured by adjusting the difficulty of the search task to the point at which no surplus resources are available for the distractor. Through modification of this paradigm, central and peripheral attentional resources were compared in deaf and hearing individuals. Deaf individuals possessed greater attentional resources in the periphery but less in the center when compared to hearing individuals. Furthermore, based on results from native hearing signers, it was shown that sign language alone could not be responsible for these changes. We conclude that auditory deprivation from birth leads to compensatory changes within the visual system that enhance attentional processing of the peripheral visual field.
Observation and Measurement of Forward Proton Scattering in Association with Lepton Pairs Produced via the Photon Fusion Mechanism at ATLAS (2020)

The observation of forward proton scattering in association with lepton pairs (e^{+}e^{-}+p or μ^{+}μ^{-}+p) produced via photon fusion is presented. The scattered proton is detected by the ATLAS Forward Proton spectrometer, while the leptons are reconstructed by the central ATLAS detector. Proton-proton collision data recorded in 2017 at a center-of-mass energy of sqrt[s]=13 TeV are analyzed, corresponding to an integrated luminosity of 14.6 fb^{-1}. A total of 57 (123) candidates in the ee+p (μμ+p) final state are selected, allowing the background-only hypothesis to be rejected with a significance exceeding 5 standard deviations in each channel. Proton-tagging techniques are introduced for cross-section measurements in the fiducial detector acceptance, corresponding to σ_{ee+p}=11.0±2.6(stat)±1.2(syst)±0.3(lumi) and σ_{μμ+p}=7.2±1.6(stat)±0.9(syst)±0.2(lumi) fb in the dielectron and dimuon channel, respectively.
CaMKK2 in myeloid cells is a key regulator of the immune-suppressive microenvironment in breast cancer (2019)

Tumor-associated myeloid cells regulate tumor growth and metastasis, and their accumulation is a negative prognostic factor for breast cancer. Here we find calcium/calmodulin-dependent kinase kinase (CaMKK2) to be highly expressed within intratumoral myeloid cells in mouse models of breast cancer, and demonstrate that its inhibition within myeloid cells suppresses tumor growth by increasing intratumoral accumulation of effector CD8<sup>+</sup> T cells and immune-stimulatory myeloid subsets. Tumor-associated macrophages (TAMs) isolated from Camkk2<sup>-/-</sup> mice expressed higher levels of chemokines involved in the recruitment of effector T cells compared to WT. Similarly, in vitro generated Camkk2<sup>-/-</sup> macrophages recruit more T cells, and have a reduced capability to suppress T cell proliferation, compared to WT. Treatment with CaMKK2 inhibitors blocks tumor growth in a CD8<sup>+</sup> T cell-dependent manner, and facilitates a favorable reprogramming of the immune cell microenvironment. These data, credential CaMKK2 as a myeloid-selective checkpoint, the inhibition of which may have utility in the immunotherapy of breast cancer.
Figure S2 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs (2023)

&lt;p&gt;Figure S2. Scatter-plots showing a linear relationship between expression of housekeeping genes.&lt;/p&gt;
Volatility by Design. Synthesis and Characterization of Polyether Adducts of Bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)barium and Their Implementation as Metal−Organic Chemical Vapor Deposition Precursors (1997)

The synthesis and characterization of a series of polyethers and volatile, low-melting polyether complexes of bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)barium having the general formula Ba(hfa)2·RO(CH2CH2O)nR‘ where R = R‘ = CH3, n = 3; R = CH3, R‘ = C2H5, n = 3; R = R‘ = H, n = 5, 6; R = R‘ = CH3, n = 4; R = CH3, R‘ = C2H5, n = 5; R = CH3, R‘ = n-C4H9, n = 5, 6; R = CH3, R = C5H11O, n = 3; R = CH3, R‘ = n-C6H13, n = 4, 5; R = C2H5, R‘ = n-C4H9, n = 5; R = n-C4H9, R‘ = n-C4H9, n = 4, 6; R = n-C4H9, R‘ = n-C6H13, n = 5 are reported. The complexes are conveniently synthesized by reaction of n-propylammonium+hfa- in DMF with an aqueous solution of Ba(NO3)2 and the polyether or, alternatively, by reaction of the polyether with Ba(hfa)2 in toluene. These new complexes were characterized by elemental analysis, FT-IR, 1H, 13C, and 19F NMR, MS, X-ray diffraction (Ba(hfa)2·CH3O(CH2CH2O)3CH3·H2O, Ba(hfa)2·CH3O(CH2CH2O)5C2H5), and thermogravimetric analysis. The melting points of the complexes are strongly dependent on the architecture of the polyether chain and dimensions of the terminal polyether substituent, with the lowest melting points corresponding to the longest polyethers having the largest terminal groups. The volatility of the Ba(hfa)2·polyether compounds is dependent on molecular weight and molecular structure; however, there is little direct correlation between melting point depression and enhanced volatility. The applicability of these complexes in metal−organic chemical vapor deposition is demonstrated by the successful growth of phase-pure BaTiO3 thin films using Ba(hfa)2·CH3O(CH2CH2O)5C2H5 as the Ba source. Phase composition and epitaxy in these films is analyzed by energy-dispersive X-ray spectroscopy and X-ray diffraction ϑ−2ϑ, ω, and φ scans.
Solubility Model for Ferrous Iron Hydroxide in Sodium Chloride Solutions Spike with Sodium EDTA: A Pitzer Approach. (2019)

Abstract not provided.
Reduction of Alkyl Halides and Tosylates with Sodium Cyanoborohydride in Hexamethylphosphoric Triamide ( HMPA ): A . 1‐Iododecane to n ‐Decane B . 1‐Dodecyl Tosylate to n ‐Dodecane (2003)

Abstract Reduction of alkyl halides and tosylates with sodium cyanoborohydride in hexamethylphosphoric triamide (HMPA): A. 1‐iododecane to n ‐decane B. 1‐dodecyl tosylate to n ‐dodecane product: n ‐decane reactant: 1‐dodecyl tosylate (6.80 g., 0.0201 mole) reactant: sodium cyanoborohydride (5.02 g., 0.0797 mole) product: n ‐dodecane
Precision CMB Polarization from Dome-C: the BRAIN experiment (2005)

In the current cosmological scenario, part of the linearly polarized emission of the CMB is expected to be rotational (B-modes). This component is due to tensor perturbations of the metric produced by primordial gravitational waves, which are generated a split-second after the Big Bang. The signal expected is of the order of ≲ 0.1 μK, well below the non-rotational component of the polarization signal (E-modes), and beyond the sensitivity of present generation instruments. New, more sensitive instruments are developed in several labs, with the goal to measure the B-modes. Control of systematics and foregrounds will be the key to make the results of these experiments believable. In this paper we shortly outline BRAIN, a bolometric interferometer devoted to B-modes research, and its pathfinder experiment, devoted to test the Dome-C site.
Drug Repurposing Screening Identifies Tioconazole as an ATG4 Inhibitor that Suppresses Autophagy and Sensitizes Cancer Cells to Chemotherapy (2017)

<b>Background:</b> Tumor cells require proficient autophagy to meet high metabolic demands and resist chemotherapy, which suggests that reducing autophagic flux might be an attractive route for cancer therapy. However, this theory in clinical cancer research remains controversial due to the limited number of drugs that specifically inhibit autophagy-related (ATG) proteins. <b>Methods:</b> We screened FDA-approved drugs using a novel platform that integrates computational docking and simulations as well as biochemical and cellular reporter assays to identify potential drugs that inhibit autophagy-required cysteine proteases of the ATG4 family. The effects of ATG4 inhibitors on autophagy and tumor suppression were examined using cell culture and a tumor xenograft mouse model. <b>Results:</b> Tioconazole was found to inhibit activities of ATG4A and ATG4B with an IC<sub>50</sub> of 1.3 µM and 1.8 µM, respectively. Further studies based on docking and molecular dynamics (MD) simulations supported that tioconazole can stably occupy the active site of ATG4 in its open form and transiently interact with the allosteric regulation site in LC3, which explained the experimentally observed obstruction of substrate binding and reduced autophagic flux in cells in the presence of tioconazole. Moreover, tioconazole diminished tumor cell viability and sensitized cancer cells to autophagy-inducing conditions, including starvation and treatment with chemotherapeutic agents. <b>Conclusion:</b> Tioconazole inhibited ATG4 and autophagy to enhance chemotherapeutic drug-induced cytotoxicity in cancer cell culture and tumor xenografts. These results suggest that the antifungal drug tioconazole might be repositioned as an anticancer drug or chemosensitizer.
Polarization tunable microstrip patch antenna for polarization loss compensation (2014)

Polarization loss of wireless communication system is caused by a mismatch of polarization between incident wave and receiving antenna. In order to compensate a polarization loss of circular polarization system, tunable circular polarization antenna is proposed. The polarization of the proposed antenna is tuned by using a reflection type phase shifter on sequential rotation feed (SRF) microstrip array. The axial ratio of polarization can be converted up to 3.7 dB for two orthogonal tilt angles in 9.5 GHz. Thus, polarization loss factor (PLF) is compensated by polarization matching.
Supplementary Figures 1-6 from Antitumor and Antiangiogenic Activities of BMS-690514, an Inhibitor of Human EGF and VEGF Receptor Kinase Families (2023)

Supplementary Figures 1-6 from Antitumor and Antiangiogenic Activities of BMS-690514, an Inhibitor of Human EGF and VEGF Receptor Kinase Families