gebhart/patrepeval huggingface dataset:
Microtubule depolymerization contributes to spontaneous neurotransmitter release in vitro (2023)

Microtubules are key to multiple neuronal functions involving the transport of organelles, however, their relationship to neurotransmitter release is still unresolved. Here, we show that microtubules present in the presynaptic compartment of cholinergic autaptic synapses are dynamic. To investigate how the balance between microtubule growth and shrinkage affects neurotransmission we induced synchronous microtubule depolymerization by photoactivation of the chemical inhibitor SBTub3. The consequence was an increase in spontaneous neurotransmitter release. An analogous effect was obtained by dialyzing the cytosol with Kif18A, a plus-end-directed kinesin with microtubule depolymerizing activity. Kif18A also inhibited the refilling of the readily releasable pool of synaptic vesicles during high frequency stimulation. The action of Kif18A was associated to one order of magnitude increases in the numbers of exo-endocytic pits and endosomes present in the presynaptic terminal. An enhancement of spontaneous neurotransmitter release was also observed when neurons were dialyzed with stathmin-1, a protein with a widespread presence in the nervous system that induces microtubule depolymerization. Taken together, these results support that microtubules restrict spontaneous neurotransmitter release as well as promote the replenishment of the readily releasable pool of synaptic vesicles.
Simian Virus 40 Sequences in Human Lymphoblastoid B-Cell Lines (2002)

Human Epstein-Barr virus-immortalized lymphoblastoid B-cell lines tested positive by PCR for simian virus 40 (SV40) DNA (22 of 42 cell lines, 52.3%). B lymphocytes or tissues from which B-cell lines derived were also SV40 positive. In situ hybridization showed that SV40 DNA was present in the nucleus of a small fraction (1/250) of cells. SV40 T-antigen mRNA was detected by reverse transcription-PCR. Lymphoblastoid B-cell lines (n = 4) infected with SV40 remained SV40 positive for 4 to 6 months. SV40-positive B-cell lines were more tumorigenic in SCID mice than were SV40-negative cell lines (4 of 5 [80%] SV40-positive cell lines versus 2 of 4 [50%] SV40-negative cell lines). These results suggest that SV40 may play a role in the early phases of human lymphomagenesis.
Optimal and efficient decoding of concatenated quantum block codes (2006)

We consider the problem of optimally decoding a quantum error correction code---that is, to find the optimal recovery procedure given the outcomes of partial ``check'' measurements on the system. In general, this problem is NP hard. However, we demonstrate that for concatenated block codes, the optimal decoding can be efficiently computed using a message-passing algorithm. We compare the performance of the message-passing algorithm to that of the widespread blockwise hard decoding technique. Our Monte Carlo results using the five-qubit and Steane's code on a depolarizing channel demonstrate significant advantages of the message-passing algorithms in two respects: (i) Optimal decoding increases by as much as 94$%$ the error threshold below which the error correction procedure can be used to reliably send information over a noisy channel; and (ii) for noise levels below these thresholds, the probability of error after optimal decoding is suppressed at a significantly higher rate, leading to a substantial reduction of the error correction overhead.
Data from MAGE-A Inhibits Apoptosis in Proliferating Myeloma Cells through Repression of Bax and Maintenance of Survivin (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The type I Melanoma Antigen GEnes (MAGEs) are commonly expressed in cancers, fueling speculation that they may be therapeutic targets with oncogenic potential. They form complexes with RING domain proteins that have E3 ubiquitin ligase activity and promote p53 degradation. MAGE-A3 was detected in tumor specimens from patients with multiple myeloma and its expression correlated with higher frequencies of Ki-67&lt;sup&gt;+&lt;/sup&gt; malignant cells. In this report, we examine the mechanistic role of MAGE-A in promoting survival of proliferating multiple myeloma cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The impact of MAGE-A3 expression on survival and proliferation &lt;i&gt;in vivo&lt;/i&gt; was examined by immunohistochemical analysis in an independent set of tumor specimens segregated into two groups: newly diagnosed, untreated patients and patients who had relapsed after chemotherapy. The mechanisms of MAGE-A3 activity were investigated &lt;i&gt;in vitro&lt;/i&gt; by silencing its expression by short hairpin RNA interference in myeloma cell lines and primary cells and assessing the resultant effects on proliferation and apoptosis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; MAGE-A3 was detected in a significantly higher percentage of relapsed patients compared with newly diagnosed, establishing a novel correlation with progression of disease. Silencing of MAGE-A showed that it was dispensable for cell cycling, but was required for survival of proliferating myeloma cells. Loss of MAGE-A led to apoptosis mediated by p53-dependent activation of proapoptotic Bax expression and by reduction of survivin expression through both p53-dependent and -independent mechanisms.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These data support a role for MAGE-A in the pathogenesis and progression of multiple myeloma by inhibiting apoptosis in proliferating myeloma cells through two novel mechanisms. &lt;i&gt;Clin Cancer Res; 17(13); 4309–19. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Sharp‐Cornered Liquid Drops by Wetting of Nanoscale Features (2008)

Serrated-edge droplets: The wetting of metallic microstructures with nanoscale features, used as substrates for surface-enhanced Raman scattering, can result in sharp bending of the droplet edges. Tethering of the liquid/air/substrate contact line induces flows of analyte to particular locations as the droplet recedes during evaporation (see SEM image). Molecules are preferentially deposited in the pyramidal pits on these structures.
Measurement of the average very forward energy as a function of the track multiplicity at central pseudorapidities in proton-proton collisions at $$\sqrt{s}=13\,\text {TeV} $$ (2019)

The average total energy as well as its hadronic and electromagnetic components are measured with the CMS detector at pseudorapidities <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>-</mml:mo> <mml:mn>6.6</mml:mn> <mml:mo><</mml:mo> <mml:mi>η</mml:mi> <mml:mo><</mml:mo> <mml:mo>-</mml:mo> <mml:mn>5.2</mml:mn></mml:mrow> </mml:math> in proton-proton collisions at a centre-of-mass energy <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> <mml:mspace></mml:mspace> <mml:mtext>TeV</mml:mtext></mml:mrow> </mml:math> . The results are presented as a function of the charged particle multiplicity in the region <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>|</mml:mo> <mml:mi>η</mml:mi> <mml:mo>|</mml:mo> <mml:mo><</mml:mo> <mml:mn>2</mml:mn></mml:mrow> </mml:math> . This measurement is sensitive to correlations induced by the underlying event structure over a very wide pseudorapidity region. The predictions of Monte Carlo event generators commonly used in collider experiments and ultra-high energy cosmic ray physics are compared to the data. All generators considered overestimate the fraction of energy going into hadrons.
MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases (2013)

MicroRNAs (miRNAs) play a key role in regulating mRNA expression, and individual miRNAs have been proposed as diagnostic and therapeutic candidates. The identification of such candidates is complicated by the involvement of multiple miRNAs and mRNAs as well as unknown disease topology of the miRNAs. Here, we investigated if disease-associated miRNAs regulate modules of disease-associated mRNAs, if those miRNAs act complementarily or synergistically, and if single or combinations of miRNAs can be targeted to alter module functions. We first analyzed publicly available miRNA and mRNA expression data for five different diseases. Integrated target prediction and network-based analysis showed that the miRNAs regulated modules of disease-relevant genes. Most of the miRNAs acted complementarily to regulate multiple mRNAs. To functionally test these findings, we repeated the analysis using our own miRNA and mRNA expression data from CD4+ T cells from patients with seasonal allergic rhinitis. This is a good model of complex diseases because of its well-defined phenotype and pathogenesis. Combined computational and functional studies confirmed that miRNAs mainly acted complementarily and that a combination of two complementary miRNAs, miR-223 and miR-139-3p, could be targeted to alter disease-relevant module functions, namely, the release of type 2 helper T-cell (Th2) cytokines. Taken together, our findings indicate that miRNAs act complementarily to regulate modules of disease-related mRNAs and can be targeted to alter disease-relevant functions.
A Validation Study of Multicenter Diffusion Tensor Imaging: Reliability of Fractional Anisotropy and Diffusivity Values (2011)

We found that a 3T magnet and high-angular-resolution pulse sequence yielded comparable DTI measurements across different MR imaging magnets and platforms. Our results indicate that FA is the most comparable measure across magnets, followed by individual diffusivities. The comparability of DTI measures between different magnets supports the feasibility of multicentered clinical trials by using DTI as an outcome measure.
ChemInform Abstract: Farnesyl Chain Modification of Squalene Synthase Inhibitor Benzylfarnesylamine: Conversion to the Terminal Bis(trifluoromethyl) Derivative. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Computational Analysis of 1,2‐dialkynylpyrroles (2018)

Computational chemistry can be used to quickly predict the properties of molecules. We are interested in studying the potential of 1,2‐dialkynylpyrroles to undergo a thermal Bergan cyclization‐triggered rearrangement to reactive diradical intermediates that display cytotoxic activity. These diradical intermediates have garnered much interest in the scientific community as a potential tumor suppressing compound. In order to analyze these diradicals, a B3LYP hybrid functional with a 6–31G** basis set was used to predict the electronic energy of each intermediate and transition state in the reaction. The electronic energy values for each step in the reaction were used to construct an energy diagram that quantified the energy gap between the intermediates and transition states. The goal of this experiment was to create an analogue of a dialkynylpyrrole that maximized the energy gap between the diradical singlet and the Retro Bergman transition state, and minimized the energy gap between the diradical singlet and the diradical triplet. An analogue that produced a diradical with these properties would be long lived and reactive. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Comparative Efficacy Between the Glycoprotein IIb/IIIa Antagonists Roxifiban and Orbofiban in Inhibiting Platelet Responses in Flow Models of Thrombosis (2002)

This study was undertaken to compare the platelet binding characteristics and anti-platelet efficacy of a nonpeptide glycoprotein IIb/IIIa antagonist roxifiban with orbofiban in static and dynamic adhesion and aggregation assays. The results indicate that roxifiban binds with higher affinity to glycoprotein IIb/IIIa receptors and exhibits slower dissociation rates than orbofiban. Furthermore, the platelet inhibitory effects of roxifiban, but not orbofiban, were unaffected by changes in plasma calcium concentrations. Both agents reduced, in a concentration-dependent manner, the size of platelet thrombi deposited onto collagen I upon perfusion of heparinized blood at a shear rate of 1,500/s. At a clinically achievable concentration of 60 nM, roxifiban abrogated the formation of thrombi containing > 20 platelets per thrombus, thereby displaying comparable in vitro efficacy to that achieved by the theoretical maximal abciximab blood concentration (3.5 microg/ml) produced after standard treatment. In contrast, orbofiban, even at 500 nM, was only effective in inhibiting the formation of larger platelet thrombi (> or =150 platelets per thrombus). Pretreatment of surface-anchored platelets with roxifiban (100 nM), but not orbofiban (500 nM), inhibited monocytic THP-1 cell attachment under flow. However, this heterotypic adhesion process was also suppressed when orbofiban (500 nM) was maintained in the perfusion buffer during the entire course of flow experiment. These findings demonstrate roxifiban (unlike orbofiban) is a potent glycoprotein IIb/IIIa antagonist with a long receptor-bound lifetime and prolonged anti-platelet efficacy and may thus be beneficial for the treatment and prevention of acute ischemic syndromes.
2-(p-Hydroxybenzyl)indoles - Side Products Formed Upon Cleavage of Indole Derivatives from Carboxylated Wang Polymer - an NMR Study (2003)

Treatment of carboxylated Wang polymer attached to a 2-unsubstituted indole derivative with a trifluoroacetic acid based mixture resulted in a side reaction: p-hydroxybenzylation at the 2-position of the indole ring. The structure of the resulting N-3-aminopropyl)-N-benzyl-4-[2-(4-hydroxybenzyl)-1H-indol-3-yl]-butyramide trifluoroacetate was ascertained by a full assignment of its 1H- and 13C-NMR spectra. The side reaction could be suppressed by the use of 1,2-ethanedithiol in high concentrations (16 %).
Data services for E-tailers leveraging web search engine assets (2013)

Retail is increasingly moving online. There are only a few big e-tailers but there is a long tail of small-sized e-tailers. The big e-tailers are able to collect significant data on user activities at their websites. They use these assets to derive insights about their products and to provide superior experiences for their users. On the other hand, small e-tailers do not possess such user data and hence cannot match the rich user experiences offered by big e-tailers. Our key insight is that web search engines possess significant data on user behaviors that can be used to help smaller e-tailers mine the same signals that big e-tailers derive from their proprietary user data assets. These signals can be exposed as data services in the cloud; e-tailers can leverage them to enable similar user experiences as the big e-tailers. We present three such data services in the paper: entity synonym data service, query-to-entity data service and entity tagging data service. The entity synonym service is an in-production data service that is currently available while the other two are data services currently in development at Microsoft. Our experiments on product datasets show (i) these data services have high quality and (ii) they have significant impact on user experiences on e-tailer websites. To the best of our knowledge, this is the first paper to explore the potential of using search engine data assets for e-tailers.
Performance of OFDM system with Fractional Sampling and delay diversity (2009)

This paper presents the performance of a Fractional Sampling OFDM receiver with delay diversity. Delay diversity achieves transmit diversity by intentionally ingenerating paths which have different delays at a transmitter side. However, the correlations between subcarriers are not always low. The proposed scheme which combines the delay diversity and the FS offers diversity gain by reducing the correlation between the sub-carriers. The proposed scheme improves the BER performance by about 2dB and the improvement depends on the amount of the delay.
Regulation of the Integration-Excision Reaction by Bacteriophage (1981)

Bacteriophage λ regulates the integration-excision reaction as a crucial aspect of controlled development along the two viral pathways, lysogenic and productive. The events essential for the lysogenic response are complete repression of productive functions and integration of the viral DNA. The events essential for the productive response are an ordered expression of replication and maturation functions and, for an induced prophage, excision of the viral DNA. The choice between the two pathways available to the phage can be considered in terms of an initial regulatory partition toward one pathway or the other, stabilized in turn by subsequent regulatory events. The cII- and cIII-gene products (cII and cIII proteins) of λ provide for the first stage of the lysogenic response, turning on production of the maintenance repressor cI and the integration protein Int and delaying the expression of late lytic functions. The cI protein stabilizes the lysogenic pathway by a switch-off...
What our ICT graduates really need from us: a perspective from the workplace (2009)

A national Discipline-Based Initiative (DBI) project for Information and Communications Technology (ICT), funded by the Australian Learning and Teaching Council, has sought the opinions of recent graduates of ICT in the workplace to help inform the curriculum. An online survey was devised to question graduates on workplace requirements and university preparation for abilities categorized as: personal/interpersonal; cognitive; business and technical. The graduates in employment have highlighted broad mismatches between the requirements of their professional work in these categories and the preparation for employment they received from university. A regression analysis was used to determine influences on graduates' opinions of the preparation they received at university. The quantitative and qualitative results from this survey could have far-reaching consequences for ICT education and this initiative will enable the development of curricula that ensures graduates are equipped with the skills required by the ICT industry.
LUMPED-ELEMENT ANALYSIS OF AN ELECTROSTATIC SQUEEZE-FILM MEMS DROPLET EJECTOR (2010)

We present a theoretical model of an electrostatica squeeze-film dominated, MEMS droplet ejector. Th consists of a microfluidic chamber filled with fluid to be orifice plate, and a piston positioned a few microns b orifice. Drop ejection occurs when a high-frequency drive applied between the orifice plate and the pis lumped-element model of the ejector takes into account t electrical-structural-fluidic interactions that occur du ejection. The model is used to study effect of fluid prop drive waveform on key performance parameters such displacement and ejected fluid volume.
RF Lens-Embedded Antenna Array for mmWave MIMO: Design and Performance (2018)

The requirement of high data rate in 5G calls for utilization of the mmWave frequency band. Researchers seeking to compensate for mmWave's high path loss have proposed that mmWave MIMO systems make use of beamforming. Hybrid beamforming systems demonstrate promising performance in achieving high gain and directivity by using phase shifters. The actual implementation, however, is costly and complex. To reduce such cost and complexity, this article presents actual prototypes of the lens antenna to be used in 5G mmWave beamforming systems. Using a lens as a passive phase shifter enables beamforming without the heavy network of phase shifters, while gain and directivity are achieved by the energy-focusing property of the lens. Proposed in this article are two types of lens antennas, one for static and the other for mobile usage. The lens antennas' sizes are varied to also discuss the lens design. Their performance is evaluated using measurements and simulation data along with link- and system-level analysis. Results show the lens antenna yields high gain, directivity, and improved beam-switching feasibility compared to when a lens is not used.
Automated human induced pluripotent stem cell colony segmentation for use in cell culture automation applications (2023)

Human induced pluripotent stem cells (hiPSCs) have demonstrated great promise for a variety of applications that include cell therapy and regenerative medicine. Production of clinical grade hiPSCs requires reproducible manufacturing methods with stringent quality-controls such as those provided by image-controlled robotic processing systems. In this paper we present an automated image analysis method for identifying and picking hiPSC colonies for clonal expansion using the CellX<sup>TM</sup> robotic cell processing system. This method couples a light weight deep learning segmentation approach based on the U-Net architecture to automatically segment the hiPSC colonies in full field of view (FOV) high resolution phase contrast images with a standardized approach for suggesting pick locations. The utility of this method is demonstrated using images and data obtained from the CellX<sup>TM</sup> system where clinical grade hiPSCs were reprogrammed, clonally expanded, and differentiated into retinal organoids for use in treatment of patients with inherited retinal degenerative blindness.
4H-SiC bipolar junction transistors for UHF and L-band long-pulse radar applications (2010)

This paper reviews the current status of 4H-SiC RF npn bipolar junction transistors (BJT's). Process developments including precise and uniform SiC etch and low resistance p-type ohmic contact formation on a two inch SiC wafer will be presented. The high temperature operation up to 500°C and radiation hardness up to 1.6 Mrad, as well as RF performance promising for long-pulse UHF and L-band radar applications will be reported. Rationale and approaches to the further improvement to S-band will be discussed.
Low Temperature Growth of High Purity, Low Resistivity Copper Films by Atomic Layer Deposition (2011)

The atomic layer deposition of copper metal thin films was achieved using a three precursor sequence entailing Cu(OCHMeCH2NMe2)2, formic acid, and hydrazine. A constant growth rate of 0.47−0.50 Å/cycle was observed at growth temperatures between 100 and 170 °C. The resulting films are high purity and have low resistivities.
Quantitative telomerase enzyme activity determination using droplet digital PCR with single cell resolution (2014)

The telomere repeat amplification protocol (TRAP) for the human reverse transcriptase, telomerase, is a PCR-based assay developed two decades ago and is still used for routine determination of telomerase activity. The TRAP assay can only reproducibly detect ∼ 2-fold differences and is only quantitative when compared to internal standards and reference cell lines. The method generally involves laborious radioactive gel electrophoresis and is not conducive to high-throughput analyzes. Recently droplet digital PCR (ddPCR) technologies have become available that allow for absolute quantification of input deoxyribonucleic acid molecules following PCR. We describe the reproducibility and provide several examples of a droplet digital TRAP (ddTRAP) assay for telomerase activity, including quantitation of telomerase activity in single cells, telomerase activity across several common telomerase positive cancer cells lines and in human primary peripheral blood mononuclear cells following mitogen stimulation. Adaptation of the TRAP assay to digital format allows accurate and reproducible quantification of the number of telomerase-extended products (i.e. telomerase activity; 57.8 ± 7.5) in a single HeLa cell. The tools developed in this study allow changes in telomerase enzyme activity to be monitored on a single cell basis and may have utility in designing novel therapeutic approaches that target telomerase.