gebhart/patrepeval huggingface dataset:
Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1 (2016)

High expression of the forkhead box P1 (FOXP1) transcription factor distinguishes the aggressive activated B cell (ABC) diffuse large B-cell lymphoma (DLBCL) subtype from the better prognosis germinal center B-cell (GCB)-DLBCL subtype and is highly correlated with poor outcomes. A genetic or functional role for FOXP1 in lymphomagenesis, however, remains unknown. Here, we report that sustained FOXP1 expression is vital for ABC-DLBCL cell-line survival. Genome-wide analyses revealed direct and indirect FOXP1 transcriptional enforcement of ABC-DLBCL hallmarks, including the classical NF-κB and MYD88 (myeloid differentiation primary response gene 88) pathways. FOXP1 promoted gene expression underlying transition of the GCB cell to the plasmablast--the transient B-cell stage targeted in ABC-DLBCL transformation--by antagonizing pathways distinctive of GCB-DLBCL, including that of the GCB "master regulator," BCL6 (B-cell lymphoma 6). Cell-line derived FOXP1 target genes that were highly correlated with FOXP1 expression in primary DLBCL accurately segregated the corresponding clinical subtypes of a large cohort of primary DLBCL isolates and identified conserved pathways associated with ABC-DLBCL pathology.
Enzymatic synthesis of dipeptide units of the d‐d‐configuration in aqueous media (1990)

The enzymatic synthesis of dipeptide units of the D-D-configuration in aqueous media, catalysed by muramoyl-pentapeptide carboxypeptidase (E.C.3.4.17.8), is described. Ac-L-Lys(Ac)-D-Ala-D-Lac-OH and Ac-D-Ala-OMe were used as acyl-components. Neutral, basic, and hydrophobic amino acids acting as nucleophiles were incorporated. The enzyme is stereospecific in that only the D-enantiomers of amino acids or amino acid derivatives were incorporated. As nucleophiles, the unmodified amino acids resulted in higher product yields compared with using the corresponding amino acid derivatives. Product yields ranged from 40 to 87%.
Practicing What We Preach (2014)

The rhetorical question "do we practice what we preach?" still seems to be relevant, even a decade after it appeared on the requirements engineering research landscape. New perspectives from various seasoned professionals from India address the question yet again. The Web extra at http://youtu.be/QtJcaibyetw is an audio podcast of Requirements column editor Jane Cleland-Huang speaking with Tony Gorschek, a professor of software engineering at the Blekinge Institute of Technology with more than 10 years of experience as a CTO, senior executive consultant, engineer, chief architect, and product manager, about technology transfer in the requirements engineering field.
A 67dB DR, 1.2-V, $0.18-{\mu}m$ Sigma-Delta Modulator for WCDMA Application (2007)

[ ] CMOS 1.2-V 2nd-order modulator with full-feedforward topology is designed. Using full-feedforward topology makes op-amp performance requirements much less stringent, therefore it has been adopted as a good candidate for low-voltage low-power applications throughout the world. Also, modulator is designed with top-down design approach, therefore various nonideal effects of op-amp are modeled in this paper.
Determination of Serotonin and Dopamine Metabolites in Human Brain Microdialysis and Cerebrospinal Fluid Samples by UPLC-MS/MS: Discovery of Intact Glucuronide and Sulfate Conjugates (2013)

An UPLC-MS/MS method was developed for the determination of serotonin (5-HT), dopamine (DA), their phase I metabolites 5-HIAA, DOPAC and HVA, and their sulfate and glucuronide conjugates in human brain microdialysis samples obtained from two patients with acute brain injuries, ventricular cerebrospinal fluid (CSF) samples obtained from four patients with obstructive hydrocephalus, and a lumbar CSF sample pooled mainly from patients undergoing spinal anesthesia in preparation for orthopedic surgery. The method was validated by determining the limits of detection and quantification, linearity, repeatability and specificity. The direct method enabled the analysis of the intact phase II metabolites of 5-HT and DA, without hydrolysis of the conjugates. The method also enabled the analysis of the regioisomers of the conjugates, and several intact glucuronide and sulfate conjugates were identified and quantified for the first time in the human brain microdialysis and CSF samples. We were able to show the presence of 5-HIAA sulfate, and that dopamine-3-O-sulfate predominates over dopamine-4-O-sulfate in the human brain. The quantitative results suggest that sulfonation is a more important phase II metabolism pathway than glucuronidation in the human brain.
Hydrofluoric Acid Etching of Silicon Dioxide Sacrificial Layers: II . Modeling (1994)

Modeling of sacrificial layer etching can be done by combining the diffusion rates of etchants in solution and the chemical reaction rate. Steady‐state diffusion is estimated for diffusion coefficients in water on the range of as observed from an independent experiment. Likewise, the chemical reaction rates (or initial etch rates) for each silicon dioxide/hydrofluoric acid system as a function of concentration are obtained from independent experiments. The etching kinetics of with HF are nonlinear. An analytical method is used with power law kinetic reaction rate expressions and Newton's method to linearize the problem. This allows the calculation of the surface concentration as a function of etching time. By equating the diffusive and reactive fluxes at the reaction surface, the surface HF concentration is calculated. Applying a forward Euler integrated etch rate relationship, the surface concentration can be used to plot the etch front location as a function of time.
Inuence of Ion Exchange Resin Particle Size and Size Distribution on Chromatographic Separation in Sweetener Industries (2011)

.................................................................................................................. 146 4.1 Introduction ................................................................................................... 146 4.2 Mean Particle Size ........................................................................................ 147 4.3 Operational Aspects ...................................................................................... 1484.3.1 Band Broadening .............................................................................. 149 4.3.1.1 Particle Size and Size Distribution .................................... 149 4.3.1.2 Thermodynamics ............................................................... 1504.3.2 Pressure Drop .................................................................................... 150 4.3.2.1 Particle Size Distribution ................................................... 1524.4 Inuence of Particle Size on Separation ....................................................... 152 4.4.1 Glucose-Fructose Separation for HFCS ........................................... 1534.4.1.1 Experimental Methods and Resin Properties ..................... 153 4.4.1.2 Results ................................................................................ 1554.4.2 Molasses Desugarization .................................................................. 158 4.4.2.1 Experimental Methods ....................................................... 158 4.4.2.2 Results ................................................................................ 1584.5 Inuence of Particle Size Distribution on Separation ................................... 161 4.5.1 Experimental Results ........................................................................ 161The sweetener industry is a major user of ion exchange resins for chromatographic separation. The glucose-fructose separation in the manufacture of high fructose corn syrup (HFCS) is one of the most successful applications of the simulated moving bed technology. This chapter focuses on the inuences of particle size and particle size distribution on separation efciency in low pressure systems. The effect of particle size on separation efciency is well known. The role of particle size distribution has been studied to a lesser extent. Experimental data are discussed for glucose-fructose separation and desugarization of molasses. A mathematical model for simulating chromatographic separation in the case of wide particle size distribution is presented. The productivity of a batch column for glucose-fructose separation was found to decrease almost linearly with increasing particle size. The benet of narrow particle size distribution was also demonstrated experimentally and by simulations. With large particles, the risk of viscous ngering increases with very narrow particle size distribution.
Wearable Camera Based Food Logging System (2022)

Recently, meal management apps have allowed people to record food items and calories from photos automatically. These technologies include extracting food regions from photos of served meals, identifying the name of the food in each region, and calculating nutritional data. However, what you eat is not the only indicator that should be kept in the food record. How fast you eat and the order in which you eat is also significant information for dietary management. Therefore, we aim to construct a system that automatically generates a meal log from first-person videos that users capture of their eating behavior with a wearable camera. To tackle the complex problems that the data this system assumes contains, we constructed an eating behavior record dataset: 9.9 hours of first-person video that assume the natural diets of a user. To investigate the feasibility of our proposed system, we evaluated whether the first step, the detection of the meal area in the video during the meal, could be achieved with sufficient accuracy using this dataset. Using the limited number of frames assumed to be annotated by the user as training data, 30 frames were annotated for user-specific model training and four frames for online adaptation, resulting in detection accuracy of 72% for food regions. Our next goal is to create a multi-user dataset and service the application.
Powering wearable sensors with a low-power CMOS piezoelectric energy harvesting circuit (2017)

Piezoelectric vibration based energy harvesters have been widely researched as powering modules for various types of sensor systems due to their ease of integration and high energy density. A number of piezoelectric transducer based topologies have been reported in literature. In this paper a piezoelectric transducer in parallel with a switch along with a low-power CMOS full-bridge rectifier is presented as a solution for efficient energy harvesting system for potential application in medical electronics. It consists of two NMOS and two PMOS devices comprising a full-bridge rectifier coupled with a PMOS device driven by a comparator based switch control circuit. With a load of 45KΩ, the output rectifier and the input piezoelectric transducer voltages are 694mV and 703mV, respectably, while the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OUT</sub> versus V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">IN</sub> conversion ratio is 98.7% with a power efficiency of 46%. The proposed energy harvesting circuit has been designed using a 0.13μm standard CMOS process.
Application of Polysaccharides for Surface Modification of Nanomedicines (2012)

Polysaccharides have been used in various biomedical applications due to availability and biocompatibility. In particular, polysaccharides have gained increasing interest in the development of functional nanomedicines as a component to provide a stealth function, improve interactions with target tissues or enable environment-responsive drug release. This review discusses recent advances in nanomedicine engineering based on polysaccharides with a specific emphasis on the rationale, applications and the remaining challenges.
Exploiting maleimide-functionalized hyaluronan hydrogels to test cellular responses to physical and biochemical stimuli (2021)

Current<i>in vitro</i>three-dimensional (3D) models of liver tissue have been limited by the inability to study the effects of specific extracellular matrix (ECM) components on cell phenotypes. This is in part due to limitations in the availability of chemical modifications appropriate for this purpose. For example, hyaluronic acid (HA), which is a natural ECM component within the liver, lacks key ECM motifs (e.g. arginine-glycine-aspartic acid (RGD) peptides) that support cell adhesion. However, the addition of maleimide (Mal) groups to HA could facilitate the conjugation of ECM biomimetic peptides with thiol-containing end groups. In this study, we characterized a new crosslinkable hydrogel (i.e. HA-Mal) that yielded a simplified ECM-mimicking microenvironment supportive of 3D liver cell culture. We then performed a series of experiments to assess the impact of physical and biochemical signaling in the form of RGD peptide incorporation and transforming growth factor<i>ß</i>(TGF-<i>ß</i>) supplementation, respectively, on hepatic functionality. Hepatic stellate cells (i.e. LX-2) exhibited increased cell-matrix interactions in the form of cell spreading and elongation within HA-Mal matrices containing RGD peptides, enabling physical adhesions, whereas hepatocyte-like cells (HepG2) had reduced albumin and urea production. We further exposed the encapsulated cells to soluble TGF-<i>ß</i>to elicit a fibrosis-like state. In the presence of TGF-<i>ß</i>biochemical signals, LX-2 cells became activated and HepG2 functionality significantly decreased in both RGD-containing and RGD-free hydrogels. Altogether, in this study we have developed a hydrogel biomaterial platform that allows for discrete manipulation of specific ECM motifs within the hydrogel to better understand the roles of cell-matrix interactions on cell phenotype and overall liver functionality.
Observation of fractional vortices and π phases in Josephson junctions involving periodic magnetic layers (2023)

Characteristics of $\mathrm{SN}{(\mathrm{F}/\mathrm{N})}_{n}\mathrm{IN}{(\mathrm{F}/\mathrm{N})}_{m}\mathrm{S}$ Josephson junctions with $n,m=1$ to 3 are reported. Here, S is a superconductor (Nb), F is a magnetic material (nickel), N is a nonmagnetic metal (aluminum), and I is an insulator $(\mathrm{Al}/\mathrm{Al}{\mathrm{O}}_{\mathrm{x}})$. The devices with $n=m=1$ and $n=1,m=2$ display critical current versus magnetic field $[{I}_{\mathrm{c}}(H)]$ dependences that imply the appearance of fractional magnetic vortices in the junction, corresponding to a half of the flux quantum. Stochastic switching between the two half-vortex polarities with emission of an integer vortex was observed. In the devices with $n=m=3$, a typical ${I}_{\mathrm{c}}(H)$ dependence consists of a background current with a large modulation period, and a Fraunhofer-like pattern with a small modulation period on top of the background current. The Fraunhofer-like pattern may be completely or partially inverted; in these states, there is a component of the Josephson current flowing against the bias current, indicating the presence of the $\ensuremath{\pi}$ phase in the junction. The experiments give evidence that switching between the zero and $\ensuremath{\pi}$ states can, potentially, be magnetically controlled.
Preclinical evaluation of carcinoembryonic cell adhesion molecule (CEACAM) 6 as potential therapy target for pancreatic adenocarcinoma (2009)

Despite the availability of new targeted therapies, ductal pancreatic adenocarcinoma continues to carry a poor prognosis. Carcinoembryonic antigen-related cell adhesion molecule (CEACAM)6 has been reported as a potential biomarker and therapy target for this malignancy. We have evaluated CEACAM6 as a potential therapy target, using an antibody-drug conjugate (ADC). Expression of CEACAM6 in pancreatic adenocarcinomas was determined using immunohistochemistry on tissue microarrays. The expression pattern in granulocytes and granulocytic precursors was measured by flow cytometry. Murine xenograft and non-human primate models served to evaluate efficacy and safety, respectively. Robust expression of CEACAM6 was found in > 90% of invasive pancreatic adenocarcinomas as well as in intraepithelial neoplastic lesions. In the granulocytic lineage, CEACAM6 was expressed at all stages of granulocytic maturation except for the early lineage-committed precursor cell. The anti-CEACAM6 ADC showed efficacy against established CEACAM6-expressing tumours. In non-human primates, antigen-dependent toxicity of the ADC consisted of dose-dependent and reversible depletion of granulocytes and their precursors. This was associated with preferential and rapid localization of the antibody in bone marrow, as determined by sequential in vivo PET imaging of the radiolabelled anti-CEACAM6. Localization of the radiolabelled tracer could be attenuated by predosing with unlabelled antibody confirming specific accumulation in this compartment. Based on the expression pattern in normal and malignant pancreatic tissues, efficacy against established tumours and limited and reversible bone marrow toxicity, we propose that CEACAM6 should be considered for an ADC-based therapy approach against pancreatic adenocarcinomas and possibly other CEACAM6-positive neoplasms.
Motion Editing for Time-Varying Mesh (2008)

Recently, time-varying mesh (TVM), which is composed of a sequence of mesh models, has received considerable interest due to its new and attractive functions such as free viewpoint and interactivity. TVM captures the dynamic scene of the real world from multiple synchronized cameras. However, it is expensive and time consuming to generate a TVM sequence. In this paper, an editing system is presented to reuse the original data, which reorganizes the motions to obtain a new sequence based on the user requirements. Hierarchical motion structure is observed and parsed in TVM sequences. Then, the representative motions are chosen into a motion database, where a motion graph is constructed to connect those motions with smooth transitions. After the user selects some desired motions from the motion database, the best paths are searched by a modified Dijkstra algorithm to achieve a new sequence. Our experimental results demonstrate that the edited sequences are natural and smooth.
Expression of BRI2 mRNA and protein in normal human brain and familial British dementia: its relevance to the pathogenesis of disease (2008)

These findings suggest that neurones and glia and are a major source of BRI2 protein and that in FBD, the mutated precursor protein may undergo furin cleavage within neurones to produce the amyloid peptide ABri. The failure to demonstrate BRI2 in blood vessels under the conditions tested suggests that vascular amyloid peptide production does not contribute significantly to cerebral amyloid angiopathy (CAA) in FBD and FDD, lending indirect support to the drainage hypothesis of CAA.
Influence of multiply charged cations on the properties of redox sites in mordenite (1985)

It has been shown that the introduction of various cations into H mordenite has significantly different effects on the redox sites of this zeolite. Despite their localization in sites which are inaccessible to adsorbates, Na/sup +/, Ni/sup 2 +/, Mg/sup 2 +/, and Ba/sup 2 +/ cations have a significant inhibitory action on the formation of radicals in large channels of mordenite. It has been postulated that the radical sites in H mordenite form as a result of the cleavage of the highly stressed Si-O-Si bonds in the skeleton and that the cations may have a stabilizing effect on the lattice. It has been found that Cu/sup 2 +/ ions, which are localized in the large channels and undergo a dipole-dipole interaction with adsorbed molecules, have a significantly weaker influence on the oxidation sites in H mordenite than do Na/sup +/, Ni/sup 2 +/, Mg/sup 2 +/, and Ba/sup 2 +/ ions. It has been shown that the introduction of Ce/sup 4 +/ and Be/sup 2 +/ ions into H mordenite does not influence the redox sites in H mordenite.
Sub-20-fs, kilohertz-repetition-rate Ti:sapphire amplifier (1995)

A simple four-pass Ti:sapphire amplifier is seeded by sub-10-fs pulses generated from a mirror-dispersion-controlled Ti:sapphire laser. Pulses of 17-18-fs duration with energies up to 50 and 100 microJ have been produced at repetition rates of 2 and 1 kHz, respectively. Because of the absence of a pulse stretcher, this performance is achieved from an extremely compact system.
Three-dimensional simulation of fluid flow around oscillating cylinders (2002)

Three-dimensional fluid flows around a single cylinder in forced oscillations or two tandem circular cylinders in free oscillations is computed by finite difference method without any turbulence model. The overlapped grid technique is employed in order to solve the flow around many bodies which are respectively oscillating by fluid forces. The unsteady lift forces of a single cylinder in forced oscillation can be predicted quantitatively. It is shown that the different behaviors of flow-induced oscillations of tandem circular cylinders appear according to the degree of freedom of the upstream cylinder.
Macrophages/microglia and the pathophysiology of CNS injuries in AIDS (1994)

Abstract How HIV-1 penetrates the central nervous system (CNS) and induces neurological disease remains poorly understood. Clinical and pathological consequences of HIV-1 associated CNS infections are the subjects of a relatively new field comprising a spectrum of many brain diseases including those that are HIV-1 associated or secondary to bacterial, fungal, protozoal, or tumor infiltration of brain. The molecular and biological approaches used to study HIV-1-mediated brain disease are interdisciplinary. A wide variety of expertise and cooperative research efforts is required between molecular virologists, cellular immunologists, and neurobiologists. Indeed, specialists studying microglial maturation, astrocyte function, neurotoxicity, HIV-1 neurovirulence, and apoptosis all play pivotal roles in examining facets of this disease complex.
Syntheses of 1-[2-(Phosphonomethoxy)Alkyl]Thymine Monophosphates and an Evaluation of their Inhibitory Activity Toward Human Thymidine Phosphorylase (2012)

A series of new monophosphates of 1-[2-(phosphonomethoxy)alkyl]thymines, such as PMPTp(,) 3-MeO-PMPTp, HPMPTp, and FPMPTp, were synthesized and tested for their ability to inhibit human thymidine phosphorylase. Kinetic measurements of enzyme activity were performed using thymidine and inorganic phosphate as the substrates. The data show that some monophosphates provide a considerable increase of the multisubstrate inhibitory effect. The highest inhibitory potency was found with (R)-FPMPTp 4c (K (i) (dT) = 4.09 ± 0.47 μM, K (i)(P(i)) = 2.13 ± 0.29 μM) and (R) 3-MeO-PMPTp 4d (K (i) (dT) = 5.78 ± 0.71 μM, K (i)(P(i)) = 2.71 ± 0.37 μM).
Plasmon–exciton systems with high quantum yield using deterministic aluminium nanostructures with rotational symmetries (2019)

The abundance and corrosion-resistant properties of aluminium, coupled with its compatibility to silicon processing make aluminium an excellent plasmonic material for light-matter interaction in the ultraviolet-visible spectrum. We investigate the interplay of the excitation and emission enhancements of quantum dots coupled with ultra-small aluminium nanoantennae with varying rotational symmetries, where emission enhancements of ∼8 and ∼6 times have been directly measured for gammadion and star-shaped structures. We observed spontaneous emission modification in the Al antenna with a C<sub>6</sub> symmetry and deduce a Purcell factor in the range of 68.01 < F<sub>P</sub> < 118.25 at plasmonic hotspots, corresponding to a modified quantum yield of >89% in the single antenna and near-unity quantum yield at the plasmonic hotspots. This finding brings us a step closer towards the realization of circularly polarized nanoemitters.