gebhart/patrepeval huggingface dataset:
Interdot spin transfer dynamics in laterally coupled excited spin ensemble of high-density InGaAs quantum dots (2018)

Interdot spin transfer dynamics is studied in a laterally coupled excited spin ensemble of high-density InGaAs quantum dots (QDs). We observe a rise time of the photoluminescence intensity of ∼100 ps and a simultaneous increase in the spin polarization of the excited spin ensemble, indicating spin injection from higher-energy levels in smaller QDs. Moreover, this coupled ensemble exhibits decay properties of the spin polarization that vary with the excited spin density. This phenomenon can be quantitatively understood by considering interdot spin transfer into lower-energy levels of the surrounding QDs, where the transfer rate depends on the degree of state filling of each QD level.
Enhancer Trap Method Using a Green Fluorescent Protein Reporter Plasmid for Cloning Tissue-Specific Enhancers Active in Prostate Cells (2003)

Understanding the development and function of the prostate requires elucidation of the mechanisms through which genes are specifically activated in the prostate and the means by which they are regulated. Studies of development in many systems has led to a model showing that control of gene expression is exerted through three types of sequence region. The area immediately upstream or overlapping with the start site of transcription, the promoter, is important in defining the point(s) where transcription starts and, through the binding of specific transcription factors, may be involved in basal levels of transcription, responses to hormones or other regulatory factors, or in the tissue specificity of the gene’s expression. Enhancers are sequence regions separate from the promoter that act to increase the level of transcription from a promoter. They may be located upstream or downstream of a gene or within an intron, and characteristically their action is independent of their orientation and position relative to the promoter and is relatively independent of distance. In many cases, enhancers confer strongly tissue-specific expression, and they may exhibit significant selectivity in the promoters they activate. A third class of regulatory sequence is the locus control region (LCR). LCRs control the activation of sets of genes and are typically located at a significant distance from them (e.g., 50 kb). Their role is believed to be in the opening up of regions or domains of chromatin.
DNA-encoded bispecific T cell engagers and antibodies present long-term antitumor activity (2019)

Specific antibody therapy, including mAbs and bispecific T cell engagers (BiTEs), are important new tools for cancer immunotherapy. However, these approaches are slow to develop and may be limited in their production, thus restricting the patients who can access these treatments. BiTEs exhibit a particularly short half-life and difficult production. The development of an approach allowing simplified development, delivery, and in vivo production would be an important advance. Here we describe the development of a designed synthetic DNA plasmid, which we optimized to permit high expression of an anti-HER2 antibody (HER2dMAb) and delivered it into animals through adaptive electroporation. HER2dMAb was efficiently expressed in vitro and in vivo, reaching levels of 50 μg/ml in mouse sera. Mechanistically, HER2dMAb blocked HER2 signaling and induced antibody-dependent cytotoxicity. HER2dMAb delayed tumor progression for HER2-expressing ovarian and breast cancer models. We next used the HER2dMAb single-chain variable fragment portion to engineer a DNA-encoded BiTE (DBiTE). This HER2DBiTE was expressed in vivo for approximately 4 months after a single administration. The HER2DBiTE was highly cytolytic and delayed cancer progression in mice. These studies illustrate an approach to generate DBiTEs in vivo, which represent promising immunotherapies for HER2+ tumors, including ovarian and potentially other cancers.
snRNA interactions at 5' and 3' splice sites monitored by photoactivated crosslinking in yeast spliceosomes. (1995)

Splice site recognition and catalysis of the transesterification reactions in the spliceosome are accompanied by a dynamic series of interactions involving conserved or invariant sequences in the spliceosomal snRNAs. We have used site-specific photoactivated crosslinking in yeast spliceosomes to monitor interactions between snRNAs and exon sequences near the 5' and 3' splice sites. The last nucleotide of the 5' exon can be crosslinked to an invariant loop sequence in U5 SnRNA before and after 5' splice site cleavage. The first nucleotide of the 3' exon can also be crosslinked to the same U5 loop sequence, but this contact is only detectable after the first transesterification. These results are in close agreement with earlier data from mammalian splicing extracts, and they are consistent with a model in which U5 snRNA aligns the 5' and 3' exons for the second transesterification. After the first catalytic step of splicing, the first nucleotide of the 3' exon can also crosslink to nt U23 in U2 snRNA. This is one of a cluster of residues in U2-U6 helix I implicated by mutational analysis in the second catalytic step of splicing. The crosslinking data suggest that these residues in U2-U6 helix I are in close proximity to the scissile phosphodiester bond at the 3' splice site prior to the second transesterification. These results constitute the first biochemical evidence for a direct interaction between the 3' splice site and U2 snRNA.
Direct oxidative amidation of aromatic aldehydes using aqueous hydrogen peroxide in continuous flow microreactor systems (2012)

A practical and economical protocol has been developed for the direct oxidative amidation of aromatic aldehydes with secondary amines to synthesize amides in a single operation under mild conditions within 15–40 min. The utilization of aqueous hydrogen peroxide affords a clean synthetic route. No catalysts or promoting reagents are required.
Perlecan Domain V Inhibits Amyloid-β Induced Brain Endothelial Cell Toxicity and Restores Angiogenic Function (2013)

In Alzheimer's disease (AD), amyloid-β (Aβ) deposits in the cerebrovasculature can result in neurovascular dysfunction and/or cerebral amyloid angiopathy. The accumulation of Aβ in blood vessels can cause endothelial cell damage, resulting in impaired Aβ clearance by the blood-brain barrier. Additionally, impaired endothelial cell function can result in decreased angiogenesis in the brains of AD patients, affecting cognitive function. VEGF is a crucial mediator of angiogenesis and is deficient in AD brains thus promoting angiogenesis could be an important component of successful AD treatment. The C-terminal portion of the extracellular matrix proteoglycan perlecan, Domain V (DV), promotes brain-derived endothelial cell proliferation and is proangiogenic in that it increases VEGFR2 expression and production of VEGF. In this study, we show that Aβ25-35 reduces proliferation of a mouse brain microvascular endothelial cell line (MBEC) in vitro and that DV and mouse LG3 (C-terminal fragment of DV) block these effects of Aβ25-35. Additionally, we show that DV restores the ability of MBECs to form tube-like structures on Matrigel in the presence of Aβ25-35 and that this is α5β1 dependent. Interestingly, the reduction in tube-like structure formation by Aβ25-35 was not due to endothelial cell death, suggesting that Aβ25-35 induces the downregulation of a cell surface molecule required for adhesion events critical to the angiogenic process. We propose a model suggesting that DV works through both the α5β1 integrin receptor and VEGFR2 to increase VEGF production, causing competition with Aβ25-35 for VEGFR2 binding, thus ultimately increasing VEGF expression and restoring angiogenesis. This supports DV as a potential anti-amyloid therapy.
Alginate–antacid combinations: raft formation and gastric retention studies (2009)

the in vitro and in vivo performance is maintained in the new GDAL formulation even with higher antacid levels and the product is as good as, or better than, previous formulations.
Modeling a leaky glottis. (1992)

During the last decade, awareness has grown that the glottis does not necessarily close completely during normal phonation. To what extent a glottal leak affects the glottal flow waveform, however, is still poorly understood. A speech production model is implemented that is capable of simulating source/tract interaction using a time-varying glottal impedance analogous to that in the two-mass glottal model of Ishizaka and Flanagan. The original formulas are extended to incorporate two different types of glottal leakage: (1) a leak that is in open connection with the membranous part of the glottis, and (2) a leak formed by a separate duct (e.g., in the posterior commissure). However, instead of letting the glottal geometry be defined by a self-oscillating mechanical model of the vocal folds, the glottal inlet and outlet areas are prescribed by the authors. In the present simulations it is found that for a moderate leak area the flow through a type 2 leak and the flow through the membranous part may be in opposite directions during the interval that the folds close, thus enhancing the excitation of the vocal tract. Another interesting consequence of this result is that a physical explanation might be given for some of the waveform details sometimes observed in inverse filtered speech that are often considered as artifacts of the inverse filtering method.
Continuous flow vortex fluidic synthesis of silica xerogel as a delivery vehicle for curcumin (2014)

Sol–gel synthesis of silica xerogel using a continuous flow vortex fluidic device at room temperature is effective in direct incorporation of preformed curcumin particles, which has antimicrobial activity against <italic>Staphylococcus aureus</italic>.
WYSIWYT testing in the spreadsheet paradigm: an empirical evaluation (2002)

Is it possible to achieve some of the benefits of formal testing within the informal programming conventions of the spreadsheet paradigm? We have been working on an approach that attempts to do so via the development of a testing methodology for this paradigm. Our "What You See Is What You Test" (WYSIWYT) methodology supplements the convention by which spreadsheets provide automatic immediate visual feedback about values by providing automatic immediate visual feedback about "testedness". In previous work we described this methodology (G. Rothermal et al., 1998). We present empirical data about the methodology's effectiveness. Our results show that the use of the methodology was associated with significant improvement in testing effectiveness and efficiency, even with no training on the theory of testing or test adequacy that the model implements. These results may be due at least in part to the fact that use of the methodology was associated with a significant reduction in overconfidence.
Advances in Grating‐Based Photoacoustic Spectroscopy for the Study of Protein Dynamics (1998)

Abstract Recent advances in transient grating spectroscopy are described in relation to extracting photoacoustic parameters. The time resolution for measurement of dynamically driven acoustics has been extended to the picosecond level. This improvement was achieved by adopting counter‐propagating beam geometries and resolving the acoustic phase shift in analogy to phase modulation spectroscopy. At the other extreme, the dynamic range of this technique has been extended to milliseconds in order to follow dynamical processes central to biological functions. In addition, diffractive optics were used for generating the necessary excitation and probe beam geometries. A novel optical setup was developed which permits both the rapid exploration of fringe spacing dependencies in separating thermal from nonthermal contributions to the observed signal as well as heterodyne detection without active feedback. The latter capability significantly increases the signal‐to‐noise ratio and permits separation of the real and imaginary components from the nonlinear four‐wave‐mixing signal. Applications of these new methods are demonstrated by following the functionally relevant structural relaxation processes of heme proteins over 10 decades in time.
Variation in Antithrombotic Therapy and Clinical Outcomes in Patients With Preexisting Atrial Fibrillation Undergoing Transcatheter Aortic Valve Replacement (2021)

There was significant variability in discharge medication patterns across US sites in patients with atrial fibrillation undergoing transcatheter aortic valve replacement, including significant underuse of OAC in this high-risk cohort. The use of OAC+APT (versus OAC alone or APT alone) was not associated with a lower risk of stroke or mortality but was associated with increased risk of bleeding complications at 1 year compared with APT alone.
Smart3DGuides: Making Unconstrained Immersive 3D Drawing More Accurate (2019)

Most current commercial Virtual Reality (VR) drawing applications for creativity rely on freehand 3D drawing as their main interaction paradigm. However, the presence of the additional third dimension makes accurate freehand drawing challenging. Some systems address this problem by constraining or beautifying user strokes, which can be intrusive and can limit the expressivity of freehand drawing. In this paper, we evaluate the effectiveness of relying solely on visual guidance to increase overall drawing shape-likeness. We identified a set of common mistakes that users make while creating freehand strokes in VR and then designed a set of visual guides, the Smart3DGuides, which help users avoid these mistakes. We evaluated Smart3DGuides in two user studies, and our results show that non-constraining visual guides help users draw more accurately.
P.157: NK and B Cell Subset Assessment in Type I Diabetes Patients on Waitlist for Pancreas Transplantation (2021)

Introduction: Type 1 Diabetes (T1D) is an immune mediated disease with near complete destruction of beta cells. About 40 % patients with T1D develop End Stage Renal disease (ESRD) during their lifetime and require kidney and/or kidney pancreas transplantation. Recent genetic studies have described differences in genomic regions associated with immune responses and types of cells infiltrating islets between patients with early onset of diabetes (< 7 yrs.) and later onset of diabetes (≥ 7 yrs.). Limited data are available regarding immune profiles of these subsets of patients especially when evaluated for transplantation. Therefore, we studied flow cytometric profiles of immune subsets in these patients with the long-term vision of developing personalized immunosuppression. Methods: After IRB approval, we prospectively performed quantitative B cell and Natural Killer (NK) cell subset immunophenotyping by flow cytometry, and measured Immunoglobulin (IgA, IgM and IgG) levels by Nephelometry on 18 T1D subjects with ESRD waitlisted for Simultaneous Pancreas and Kidney Transplantation (SPK) in two age and gender matched groups of patients: a) onset < 7 yrs. (Group 1, n=9), and b) onset > 7 yrs. (Group 2, n=9). Results: Detailed baseline demographics of the two groups are shown under Table 1, both groups were comparable. B cells, NK cells and their subsets are shown in Table 2. Group 1 showed a significantly lower number of CD 16 + 56- cells (p-value 0.027) as compared to group 2; other cells count, and percentages were not significantly different.Conclusion: While previous work has shown a link between altered NK cells and the early onset of type I diabetes, our data do not show a significant difference in the major NK cell subsets between the two groups of patients. Additional studies with a larger sample size could help resolve this disparity.
Polymacromonomers:  Dynamics of Dilute and Nondilute Solutions (2005)

Polymacromonomers (PMs) are a class of branched polymers whose global shape depends strongly on the degree of polymerization of the backbone and the length of the side chain. As opposed to their equivalent linear chains, PMs can indeed adopt spherical, cylindrical, or wormlike shapes. Other parameters such as the rigidity of the side chain, the distance between branches and the interactions (incompatibility) between the backbone and the branches can also contribute to the global morphology of the PMs. In this work we describe the dynamical behavior of several poly(ω-norbornenyl polystyrene) differing by their backbone and their side chain lengths, in dilute and nondilute ranges of concentration, using dynamic light scattering and viscosity experiments. The results obtained, using both techniques, suggest dense and nonentangled particles as revealed by the low viscosity values and the scaling laws observed for the variation of the diffusion coefficient as a function of the molar mass and the concentration c. The transition from dilute to nondilute regime is characterized by an abrupt increase of the diffusion coefficient with the concentration, as opposed to the case of linear and flexible polymer coils. Above this concentration, the diffusion coefficient is independent of the molar mass and hardly varies with the concentration. It is identified as reflecting the overall collective motion of the branches. This transition is also observed in the variation of the reduced viscosity ηsp/c as a function of c. Similar studies have been carried out on star polymers of roughly same molar mass where no such an abrupt transition was observed.
Preparation and Characterization of Novel Mixed Periodic Mesoporous Organosilica Nanoparticles (2020)

We report herein the preparation of mixed periodic mesoporous organosilica nanoparticles (<b>E-Pn 75/25</b> and <b>90/10 PMO NPs</b>) by sol-gel co-condensation of <i>E</i>-1,2-bis(triethoxysilyl)ethylene ((<i>E</i>)-BTSE or <b>E</b>) with previously synthesized disilylated <i>tert</i>-butyl 3,5-dialkoxybenzoates bearing either sulfide (precursor <b>P1</b>) or carbamate (precursor <b>P2</b>) functionalities in the linker. The syntheses were performed with cetyltrimethylammonium bromide (CTAB) as template in the presence of sodium hydroxide in water at 80 °C. The nanomaterials have been characterized by Transmission Electron Microscopy (TEM), nitrogen-sorption measurements (BET), Dynamic Light Scattering (DLS), zeta-potential, Thermogravimetric Analysis (TGA), FTIR, <sup>13</sup>C CP MAS NMR and small angle X-ray diffraction (p-XRD). All the nanomaterials were obtained as mesoporous rodlike-shape nanoparticles. Remarkably, <b>E-Pn 90/10 PMO NPs</b> presented high specific surface areas ranging from 700 to 970 m<sup>2</sup>g<sup>-1</sup>, comparable or even higher than pure <b>E PMO</b> nanorods. Moreover, XRD analyses showed an organized porosity for <b>E-P1 90/10 PMO NPs</b> typical for a hexagonal 2D symmetry. The other materials showed a worm-like mesoporosity.
Speech Recognition technology from the ICSI Realization Group (1998)

Summary of potential applications of the International Computer Science Institute's speech recognition work to scalable and mobile networking.
Frontal Interaction with Isolated Orography (1994)

The interaction of a three-dimensional cold front and an isolated orographic ridge is examined by means of primitive equation model simulations. The front evolves as part of a developing nonlinear baroclinic wave and propagates southward toward the ridge. Many of the features in this interaction, such as the anticyclonic distortion of the front, divergence and frontolysis on the windward slope, convergence and frontogenesis in the lee, and the frontogenetical forcing associated with tilting, have previously been captured by simulations of a passive scalar traversing a ridge. It is shown that the ridge decelerates the cold postfrontal air and creates a high pressure anomaly on the windward slope. If this anomaly is strong enough, it accelerates air over the ridge peak in a shallow ageostrophic flow that possesses many features found in a gravity current. This current provides relatively strong surface frontogenesis through the convergence term, but cannot transport enough mass across the peak to weaken the anomalous high pressure. The cold air and pressure anomaly propagate eastward in a manner similar to a topographic Rossby wave. When the east ridge end is reached, the anomalous pressure gradient accelerates the flow into the lee, where frontogenesis occurs from shearing. The motion behind the front as it propagates over and around the ridge is distinctly unbalanced. Blocking, as measured by the ratio of the mass flux around the ridge end to that over the peak, is determined by a Froude number that depends on the propagation speed of the front (i.e., the strength of the baroclinic wave) and the mountain height. Higher mountains or weaker waves tend to produce total blocking of the front, resulting in flow only around the east ridge end. Lower mountains and stronger waves produce frontogenesis patterns and frontal distortions that more closely resemble the passive scalar simulations.
Electroactive Inverse Opal: A Single Material for All Colors (2008)

Das ganze Spektrum: Elektrochemische Oxidation und Reduktion führen dazu, dass das inverse Opalgitter eines elektroaktiven Polymergels quellt bzw. schrumpft. Dabei lässt sich die Wellenlänge des Streulichts von Ultraviolett über den gesamten sichtbaren Bereich bis hin zum Nahinfrarot einstellen (siehe Bild).
Time-Series Data Clustering (2018)

This chapter addresses the case of multivariate time-series clustering and utilizes spatiotemporal data as specific application domain of interest. Time-series data is one of the most common forms of data encountered in a wide variety of scenarios such as the stock markets, sensor data, fault monitoring, machine state monitoring, environmental applications, or medical data. Time-series data allow diverse formulations for the clustering process, depending upon whether the series are clustered on the basis of their online correlations, or whether they are clustered on the basis of their shapes. Online correlation-based clustering methods are closely related to the problem of forecasting. Such methods are typically based on clustering the streams on the basis of their correlations with one another in their past window of history. Sensor selection algorithms are naturally related to correlation clustering. This is because such methods typically pick a representative set of streams which can be used in order to predict the other streams in the data.