gebhart/patrepeval huggingface dataset:
Characterisation of Immune Cell Subsets of Tumour Infiltrating Lymphocytes in Brain Metastases (2021)

The heterogeneity of tumor infiltrating lymphocytes is not well characterized in brain metastasis. To address this, we performed a targeted analysis of immune cell subsets in brain metastasis tissues to test which immunosuppressive routes are involved in brain metastasis. We performed multiplex immunofluorescence (mIF), using commercially available validated antibodies on twenty formalin-fixed paraffin embedded whole sections. We quantitated the subsets of immune cells utilizing a targeted panel of proteins including PanCK, CD8, CD4, VISTA and Iba1, and analyzed an average of 15000 cells per sample. We classified tumours as either high (&amp;gt;30%) or low (&amp;lt;30%) tumour infiltrating lymphocytes (TILs) and found that increased TILs density correlated with survival. We next sought out to phenotype these TILs using mIF. The tumours with low TILs (n=9) had significantly higher expression of the immune-checkpoint molecule VISTA in tumor cells (p&amp;lt;0.01) as well as in their microenvironment (p&amp;lt;0.001). Contrastingly, the brain metastatic tumours with high TILs (n=8) displayed higher levels of activated microglia, as measured by Iba1 expression. Low TILs-tumours displayed CD8+ T-cells that co-express VISTA (p&amp;lt;0.01) significantly more compared to high TILs group, where CD8+ T-cells significantly co-express Iba1 (p&amp;lt;0.05). Interestingly, no definite phenotypes of CD4+ subsets were observed. These results were supported by RNA analysis of a publicly available, independent cohort. In conclusion, our work contributes to a growing understanding of the immune surveillance escape routes active in brain metastasis.
Discrete Energy Electron Capture Negative Ion Mass Spectrometry (2000)

Abstract Standard electron capture negative ion mass spectrometry (ECNIMS) has long been known as a sensitive and selective method for the analysis of molecules with positive electron affinities. Applications of this technique for the analysis of environmental contaminants, particularly of halogenated compounds such as polychlorobiphenyls (PCBs), are common. However, the requirement for a moderating gas in the ion source to lower the energy of the electrons into the range required for resonance electron capture generates new experimental variables that are difficult to control. Differences in the moderating gas pressure cause changes in the electron energy distribution and in the resulting ion abundances, whereas small fluctuations in temperature often cause major differences in ion abundance ratios. Even more serious are the uncontrollable reactions between ions, molecules, and radicals within the high‐pressure ion source region that give unpredictable spurious product ions, making spectral interpretation difficult and leading to wide variations of negative ion spectra from different instruments. Because of these difficulties, the advantages in sensitivity and specificity of ECNIMS for analysis of electronegative compounds often have been unrealized. Better results can be obtained by having direct control over the electron energies. Control over electron energies can be achieved using a trochoidal electron monochromator, which allows the operator to tune to or scan a range of electron energies necessary for resonance electron capture. With this device some of the inherent difficulties encountered with ECNIMS can be avoided and reliable spectra for a broader range of compounds becomes possible. The ability to tune to a desired electron energy or to scan over a range of electron energies makes another dimension of analytical information available for identifying compounds. Quadrupole and sector instruments have been equipped with electron monochromators and the results are very promising. A clear advantage of these units is the reproducibility of the data they produce, the potential for three‐dimensional spectra for easier interpretation of the results, and the availability of a new dimension of analytical information. These instruments have not shown the sensitivity inherent in the ECNIMS method. Improvements of about two or three orders of magnitude in sensitivity will be required before these instruments can compete with existing technology for trace analysis of environmental residues or other electron‐capturing compounds. An improvement in the sensitivity of this magnitude is well within reasonable expectations and it should not be long before gas chromatography/electron monochromator mass spectrometry (GC/EMMS) becomes a standard technique for detecting environmental compounds, explosives and substances of abuse.
Synthesis and Characterization of Random and Block Copolypeptides Derived from γ-Methylglutamate and Leucine N-Carboxyanhydrides (2005)

The synthesis of random and block copolypolyeptides derived from gamma-methylglutamate and leucine N-carboxyanhydrides using Al-Schiff's base complexes and allylamine as initiators is here reported. The copolymer structures were confirmed by (1)H and (13)C NMR. The calculation of the statistical average block lengths reveals the presence of longer methylglutamate units in the copolymer. The determination of the reactivity ratios indicated a slightly higher reactivity of gamma-methylglutamateNCA as compared to leucineNCA. Block copolypeptides containing glutamate and leucine units were obtained by sequential polymerization of the two NCAs using Al-Schiff's base complexes or allylamine in dioxane as solvent. Based on (13)C NMR spectra of copolymers exhibiting two signals corresponding to peptide linkages, we confirmed the block structure and concluded that the copolymerization proceeds by attack of an amino group present on a glutamate chain end onto a LeuNCA. The copolymerization with allylamine was also shown, from calculation of the average block lengths of sequences, to exhibit living behavior. Viscometry analysis further showed that molar masses of the copolypeptides obtained with Al-Schiff's base were quite close to those derived from allylamine, supporting the proposed mechanism of copolymerization.
ANALYSIS OF LIQUID BREAKUP REGIMES IN FUEL SLINGER ATOMIZATION (2006)

Results are presented from analyses of liquid breakup regimes in which fuel slingers have recently been found to operate. A result is obtained for the liquid film thickness t that provides the proper length scale for correlating the atomization performance of slingers operating in the supercritical film-mode breakup regime. A corresponding result is also found for the subcritical ligament diameter d' that correlates the atomization performance of slingers operating in the subcritical film-mode regime. The transition between these modes is shown to scale as Wet1/2. Corresponding results are also presented for noncircular channel shapes. An analysis of in-channel Coriolis effects indicates how such liquid accumulation can be avoided. Slinger atomization performance is shown to correlate with a Weber number based on the appropriate length scale that governs the liquid breakup regime in which the slinger operates, with only a weak residual Ohnesorge number effect. Available data on slinger atomization performance are found to correlate well with the present results.
Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees (2010)

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and `generalizability' of these summaries. This paper provides an implementation of the geometric distance between trees developed by Billera, Holmes and Vogtmann (2001) [BHV] equally applicable to phylogenetic trees and hieirarchical clustering trees, and shows some of the applications in statistical inference for which this distance can be useful. In particular, since BHV have shown that the space of trees is negatively curved (a CAT(0) space), a natural representation of a collection of trees is a tree. We compare this representation to the Euclidean approximations of treespace made available through Multidimensional Scaling of the matrix of distances between trees. We also provide applications of the distances between trees to hierarchical clustering trees constructed from microarrays. Our method gives a new way of evaluating the influence both of certain columns (positions, variables or genes) and of certain rows (whether species, observations or arrays).
Low-power fanout optimization using multiple threshold voltage inverters (2005)

This paper addresses the problem of low-power fanout optimization with multiple threshold voltage inverters. Introducing splitting and merging conversions that preserve delay, power, and input capacitance, the fanout tree is converted to a set of inverter chains and for each chain the optimal sizes and threshold voltages are determined. Experimental results show that using this technique, the power dissipation of fanout tree is reduced by an average of 33% for a state-of-the-art CMOS technology.
Power Theft Detection in Microgrids (2015)

Theft of electricity amounts to 1.5% GDP, of most of the developing nations like India. Hence there is a great need to detect power thefts in developing nations. In this paper, we have proposed a wireless network based infrastructure for power theft detection which caters to other functional requirements of the microgrid such as renewable energy integration, automatic meter reading etc. Algorithm for power theft detection (PTDA) which is proposed in this paper, works in the distributed intelligent devices of the microgrid infrastructure for power theft detection. The coordinated action of intelligent devices with PTDA in the microgrid infrastructure enables not only the detection of power theft, but the localization of power theft in the micro-grid. PTDA increases the 1) cost of communication 2) energy consumption of intelligent devices 3) packet latency, if any critical data is piggy backed with power theft data in micro-grid. To solve these issues, we have proposed EPTDNA (Efficient Power Theft Data Networking Algorithm) which uses the frequency of power theft detection and average power draw for power theft, for the efficient routing of power theft. The performance analysis and results given in this paper shows how EPTDNA solves the major issues with PTDA.
Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel activities (2012)

Abstract Artemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin. Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC) of 1 mg/mL compared to artemisinin whose MIC was &gt;2 mg/mL.
Architecture and Configuration of Broadband Access Networks Supporting Multimedia Applications (2005)

Recent Internet access speeds have made it possible even for home users to reach and use previously unavailable bandwidth consuming (e.g. video on demand) services. However, the rapid spread of these applications is hindered by the lack of QoS guarantees in packet networks. In this article a QoS architecture is presented which have been designed for access networks and applies a logical overlay network to make network management tasks easier. The novelty of the architecture lies in the application of two key procedures adopted for dimensioning logical channels between edge nodes and mapping them to the physical routes. The upper load thresholds of the applied logical channels are also determined, which may form the basis of a more sophisticated call admission control policy.
Impact of main branch stenting on endothelial shear stress: role of side branch diameter, angle and lesion (2011)

In-stent restenosis and stent thrombosis remain clinically significant problems for bifurcation lesions. The objective of this study is to determine the haemodynamic effect of the side branch (SB) on main branch (MB) stenting. We hypothesize that the presence of a SB has a negative effect on MB wall shear stress (WSS), wall shear stress gradient (WSSG) and oscillatory shear index (OSI); and that the bifurcation diameter ratio (SB diameter/MB diameter) and angle are important contributors. We further hypothesized that stent undersizing exaggerates the negative effects on WSS, WSSG and OSI. To test these hypotheses, we developed computational models of stents and non-Newtonian blood. The models were then interfaced, meshed and solved in a validated finite-element package. Stents at bifurcation models were created with 30° and 70° bifurcation angles and bifurcations with diameter ratios of SB/MB = 1/2 and 3/4. It was found that stents placed in the MB at a bifurcation lowered WSS dramatically, while elevating WSSG and OSI. Undersizing the stent exaggerated the decrease in WSS, increase in WSSG and OSI, and disturbed the flow between the struts and the vessel wall. Stenting the MB at bifurcations with larger SB/MB ratios or smaller SB angles (30°) resulted in lower WSS, higher WSSG and OSI. Stenosis at the SB lowered WSS and elevated WSSG and OSI. These findings highlight the effects of major biomechanical factors in MB stenting on endothelial WSS, WSSG, OSI and suggests potential mechanisms for the potentially higher adverse clinical events associated with bifurcation stenting.
Tau pathology reduction with SM07883, a novel, potent, and selective oral DYRK1A inhibitor: A potential therapeutic for Alzheimer's disease (2019)

Dual-specificity tyrosine phosphorylation-regulated kinase-1A (DYRK1A) is known to phosphorylate the microtubule-associated tau protein. Overexpression is correlated with tau hyperphosphorylation and neurofibrillary tangle (NFT) formation in Alzheimer's disease (AD). This study assessed the potential of SM07883, an oral DYRK1A inhibitor, to inhibit tau hyperphosphorylation, aggregation, NFT formation, and associated phenotypes in mouse models. Exploratory neuroinflammatory effects were also studied. SM07883 specificity was tested in a kinase panel screen and showed potent inhibition of DYRK1A (IC<sub>50</sub> = 1.6 nM) and GSK-3β (IC<sub>50</sub> = 10.8 nM) kinase activity. Tau phosphorylation measured in cell-based assays showed a reduction in phosphorylation of multiple tau epitopes, especially the threonine 212 site (EC<sub>50</sub> = 16 nM). SM07883 showed good oral bioavailability in multiple species and demonstrated a dose-dependent reduction of transient hypothermia-induced phosphorylated tau in the brains of wild-type mice compared to vehicle (47%, p < 0.001). Long-term efficacy assessed in aged JNPL3 mice overexpressing the P301L human tau mutation (3 mg/kg, QD, for 3 months) exhibited significant reductions in tau hyperphosphorylation, oligomeric and aggregated tau, and tau-positive inclusions compared to vehicle in brainstem and spinal cord samples. Reduced gliosis compared to vehicle was further confirmed by ELISA. SM07883 was well tolerated with improved general health, weight gain, and functional improvement in a wire-hang test compared to vehicle-treated mice (p = 0.048). SM07883, a potent, orally bioavailable, brain-penetrant DYRK1A inhibitor, significantly reduced effects of pathological tau overexpression and neuroinflammation, while functional endpoints were improved compared to vehicle in animal models. This small molecule has potential as a treatment for AD.
Pentamidine congeners 1: Synthesis of Cis- and Trans-butamidine analogues as anti-Pneumocystis carinii pneumonia agents. (2020)

Butamidine analogues possessing unsaturation in the ether bridge between the bisamidinophenyl or bisimidazolinophenyl functionalities have been synthesized as semirigid congeners of pentamidine. These compounds demonstrated good anti-P. carinii pueumonia activity in a rat model of the disease.
Influence of the consumption pattern of magnesium from magnesium-rich mineral water on magnesium bioavailability (2011)

It is generally considered that the absorption of Mg is inversely related to the ingested dose. The objective of the present study was to determine if the mode of administration (bolus v. consumption throughout the day) could influence Mg bioavailability from Mg-rich natural mineral water comparing the same nutritional Mg amount (126 mg). Using a 2 d cross-over design, twelve healthy men were asked to drink 1·5 litres Mg-rich mineral water either as 2 × 750 ml or 7 × 212 ml throughout the day. Two stable isotopes ((25)Mg and (26)Mg) were used to label the water in order to distinguish both regimens. Fractional apparent Mg absorption was determined by faecal monitoring and Mg retention was determined by measuring urinary excretion of Mg isotopes. Higher Mg absorption (50·7 (SD 12·7) v. 32·4 (SD 8·1) %; P = 0·0007) and retention (47·5 (SD 12·9) v. 29·0 (SD 7·5) %; P = 0·0008) from Mg-rich mineral water were observed when it was consumed in seven servings compared with larger servings. Thus, regular water consumption throughout the day is an effective way to increase Mg bioavailability from Mg-rich mineral water.
An Evaluation of Parallel Grid Construction for Ray Tracing Dynamic Scenes (2006)

We describe and analyze several ways to parallelize the rebuild of a grid acceleration structure used for interactive ray tracing of dynamic scenes. While doing so, we also analyze memory system performance on a multi-core multi-processor system. In particular, we present a scalable sort-middle approach that uses a minimum amount of synchronization, scales to many CPUs, and becomes performance limited only by memory bandwidth. This algorithm is capable of rebuilding grids within a fraction of a second, enabling interactive ray tracing of large multi-million triangle scenes
Supplementary Fig. 1 from Antitumor Activity of a Kinesin Inhibitor (2023)

Supplementary Fig. 1 from Antitumor Activity of a Kinesin Inhibitor
Magnification of photonic crystal fluorescence enhancement via TM resonance excitation and TE resonance extraction on a dielectric nanorod surface (2010)

Using a one-dimensional grating surface photonic crystal (PC), we experimentally demonstrate that the detection of fluorescent molecules on a PC surface can be substantially magnified through the combined effects of resonance-enhanced excitation of the fluorescent dye, resonance-enhanced extraction of the fluorescence emission and a dielectric nanorod surface coating increasing the surface area available for fluorophore-PC interaction. Enhanced excitation is obtained by engineering a high-Q TM resonant mode to efficiently couple with an incident TM-polarized lambda = 633 nm laser for exciting Cyanine-5 (Cy5). Enhanced extraction results from a low-Q TE resonance designed to spectrally overlap the Cy5 emission spectrum for channeling TE-polarized emission towards the detection instrument. The entire PC surface is coated with a porous film of TiO(2) nanorods that allows more fluorophores to penetrate into the region of enhanced near-electric fields. Experimental results reveal a 588-fold enhancement in fluorescence intensity relative to an unpatterned glass surface.
Scheduling for Device-to-Device Communication Considering Spatial Reuse and User Fairness in Public Safety LTE (2016)

Public safety networks are desired to meet increasing demands for sharing images or videos among first responders and incident commanders. Long term evolution (LTE) is considered a candidate to achieve such broadband services. However, in the case of a disaster or a big sporting event, the traffic suddenly increases sharply as the number of active public safety users increases. This paper reports methods for allocating radio resources for device-to-device (D2D) communication as a means to enhance system capacity of the public safety LTE (PS-LTE). The methods allow spatial reuse of the resources among D2D communicating public safety users satisfying certain sharing conditions. Two practical scheduling algorithms that take into account both spatial reuse of the resources and fairness between the D2D communicating users are described. System level simulation results reveal that the methods can increase the number of users that satisfy the throughput requirement for video transmission.
6.1: Invited Paper : All‐Polymer Thin Film Transistors Fabricated by High‐Resolution Ink‐jet Printing (2001)

Abstract All‐polymer thin film transistors (TFTs) are fabricated by ink‐jet printing for the first time. Source/drain electrodes are printed using a conducting polymer (PEDOT) solution on substrates with patterned wetting‐and‐dewetting regions. A channel length down to 5 μm has been achieved without short‐circuits. The TFTs show a high mobility of 0.02 cm 2 /V·s and on/off ratio of more than 10 5 . These characteristics are equal or better than reference devices with gold electrodes. The fabrication of printed inverters is also demonstrated, in which components such as gate electrodes, interconnections, via‐holes or resistors, are patterned with the ink‐jet technique.
TB-IRIS, T-cell activation, and remodeling of the T-cell compartment in highly immunosuppressed HIV-infected patients with TB (2014)

A distinct pattern of pre-ART T-cell and cytokine markers appear to poise the immune response of certain patients to develop TB-IRIS. Experience of TB-IRIS is then associated with long-term remodeling of the CD4 T-cell memory compartment towards an effector memory-dominated phenotype. We speculate that these pre and post-ART TB-IRIS-associated immune parameters may contribute to superior immune control of TB/HIV co-infection and better clinical outcome.
Content Delivery Networks (2021)

This chapter provides an overview on the recent advances and perspectives on content delivery networks (CDNs). After a reminder on the definition and core features of CDNs, the first section highlights their importance with quantitative illustrations. The second section identifies the various types of CDNs which have been deployed to address different markets. The growth of the CDNs has been driven primarily by video streaming. Next to media content, CDNs have evolved to deliver always more demanding social networks and applications. Security solutions are now fully integrated into CDNs and marketed as flagship products. The third, fourth, and fifth sections outline the challenges and technical evolutions of the CDNs to keep up with their customers' hunger for media content, web performance, and security. The sixth section focuses on the convergence of CDNs and clouds. The seventh section reviews the status and perspectives of different approaches for using multiple CDNs. The last section presents the current positioning and future perspectives of the CDNs in the mobile domain.
Efficient charge collection in hybrid polymer/TiO2 solar cells using poly(ethylenedioxythiophene)/polystyrene sulphonate as hole collector (2005)

We report a study of the optimization of power conversion efficiency in hybrid solar cells based on nanostructured titanium dioxide and a poly[2-(2-ethylhexyloxy)-5-methoxy-1,4-phenylenevinylene] (MEH-PPV) based conjugated polymer. Charge collection efficiency is enhanced by introducing a poly(ethylenedioxythiophene)/polystyrene sulphonate (PEDOT) layer (under the gold electrode) as the hole collector. Device performance is maximized for a device with a net active layer thickness of 100 nm. The optimized device has peak external quantum efficiencies ≈40% at the polymer’s maximum absorption wavelength and yield short circuit current density ⩾2mAcm−2 for air mass (AM) 1.5 conditions (100mWcm−2, 1 sun). The AM 1.5 open circuit voltage for this device is 0.64 V and the fill factor is 0.43, resulting in an overall power conversion efficiency of 0.58%.