gebhart/patrepeval huggingface dataset:
Blood T-cell receptor   chain transcriptome in multiple sclerosis. Characterization of the T cells with altered CDR3 length distribution (2004)

Multiple sclerosis is an inflammatory demyelinating disease of the CNS associated with T cells autoreactive for myelin components. In this study, we analysed the T-cell receptor (TCR) usage of the variable beta (Vbeta) chain transcriptome in the blood of multiple sclerosis patients at various stages of the disease using a global and quantitative comparison of the complementarity-determining region 3 length distribution (CDR3-LD) of transcripts of the 26 Vbeta genes. We investigated 35 patients: 12 with a high risk of multiple sclerosis, 10 with clinically definite multiple sclerosis, 13 with a relapsing-remitting worsening and active multiple sclerosis and 13 healthy individuals. Cells bearing the TCR transcripts with altered CDR3-LD were sorted and studied for CD4 or CD8 phenotype, cytokine transcript accumulation and response to human myelin basic protein (MBP). We show that patients from all the groups have a significantly skewed blood T-cell repertoire. Vbeta transcriptome patterns were more altered in patients from the clinically definite multiple sclerosis group and the worsening and active multiple sclerosis group than in the high risk group. The T cells sorted from Vbeta families with altered CDR3-LD concerned both CD4 and CD8 T cells, with a more pronounced skewing in the CD8 compartment. These cells displayed a significantly increased level of interferon-gamma, interleukin-2 and tumour necrosis factor-alpha transcripts compared with their counterparts from the healthy individual group. Furthermore, using interferon-gamma enzyme-linked immunospot (ELISPOT) assays, T cells from four out of seven altered Vbeta families tested from multiple sclerosis patients responded to human MBP, whereas no response was observed with human albumin or with altered Vbeta families from healthy individuals. Our data support the concept of an early autoimmune component in the disease and emphasize the possible involvement of CD8-positive T cells in multiple sclerosis.
Nonlinear load sharing in low voltage microgrid using negative virtual harmonic impedance (2015)

Harmonic power sharing is important in islanded microgrid due to the presence of excessive nonlinear loads in distribution network. The lack of effective harmonic power sharing techniques may lead to overloading of certain distributed generation (DG) units. The concept of variable negative virtual harmonic impedance to share non-linear load in an islanded microgrid has been proposed recently. This paper presents a negative virtual harmonic impedance technique to share nonlinear load in a low voltage microgrid with complex line impedance. A harmonic droop control based on harmonic output power and the virtual output impedance of the DG is implemented to achieve non-linear load sharing. MATLAB/Simulink based simulation studies are presented to validate the non-linear load sharing capability of the proposed strategy.
Pathway Tools Management of Pathway/Genome Data for Microbial Communities (2022)

The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.
Brightness-equalized quantum dots (2015)

As molecular labels for cells and tissues, fluorescent probes have shaped our understanding of biological structures and processes. However, their capacity for quantitative analysis is limited because photon emission rates from multicolour fluorophores are dissimilar, unstable and often unpredictable, which obscures correlations between measured fluorescence and molecular concentration. Here we introduce a new class of light-emitting quantum dots with tunable and equalized fluorescence brightness across a broad range of colours. The key feature is independent tunability of emission wavelength, extinction coefficient and quantum yield through distinct structural domains in the nanocrystal. Precise tuning eliminates a 100-fold red-to-green brightness mismatch of size-tuned quantum dots at the ensemble and single-particle levels, which substantially improves quantitative imaging accuracy in biological tissue. We anticipate that these materials engineering principles will vastly expand the optical engineering landscape of fluorescent probes, facilitate quantitative multicolour imaging in living tissue and improve colour tuning in light-emitting devices.
Gene set analysis of transcriptomics data identifies new biological processes associated with early markers of atherosclerosis but not with those of osteoporosis: Atherosclerosis-osteoporosis co/multimorbidity study in the Young Finns Study (2022)

This study identified novel biological processes associated with high CIMT but not with reduced BMD.
Study of the specific interaction between fluorescent PDMAEMA and Platelets compared to Erythrocytes (2013)

Nowadays synthetic polymers provide more and more functionalities in the biomedical world, in particular as part of medical devices and drug delivery systems. Looking for new applications in the cardiovascular field, our attention has been focused on the well-known poly(2-(dimethylamino)ethyl methacrylate polymer (PDMAEMA). This synthetic polycation has particularly been studied as a potential DNA carrier to promote cell transfection. However and surprisingly enough relative few studies have been published in order to better understand its hemoreactivity under a free form (thus not based on “PolyElectrolyte Complex”), but also its biodistribution and clearance kinetics. In order to facilitate the in vitro and in vivo monitoring of this polycation and especially to follow its reactivity with whole blood we have labeled it with fluorescein adopting a new chemical route of synthesis. After its thorough purification and full-characterization (NMR, SEC, fluorescent spectroscopy), we followed its interaction with erythrocytes and platelets using flow cytometry. Dose-response curves were established in whole blood and within incubation times ranging between 5 min to 3 h. Considering the largest area and more negative Zeta potential developed by red blood cells compared to platelets, we initially hypothesized that RBC should interact more quickly and efficiently with the polycation. Unexpectedly, platelets presented a higher affinity for the polycation with a saturation binding curve whilst a linear profile was observed for the erythrocyte adsorption curve. Aggregometry analyses also revealed this phenomenon, although displaying a weaker effect in whole blood compared to washed platelets. Ongoing research seeks to understand the molecular mechanism of interaction of this polymer with platelets.
Formation of Q-state CdS colloids using ultrasound (1994)

R. A. Hobson, P. Mulvaney and F. Grieser, J. Chem. Soc., Chem. Commun., 1994, 823 DOI: 10.1039/C39940000823
XNA ligation using T4 DNA ligase in crowding conditions (2018)

T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
Self-trapping of optical beams in photorefractive media (1993)

We study the possibility of self-trapping of an optical beam in a photorefractive medium under the combined influence of diffraction and self-scattering (two-wave mixing) of its spatial frequency components. We investigate the spectrum of solutions for the resulting photorefractive spatial solitons and discuss their unique properties. Design considerations and material requirements for experimental realization of these solitons, together with specific examples, are given.
Measurement of the Forward-Backward Charge Asymmetry and Extraction of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mrow><mml:mo>sin</mml:mo><mml:mo></mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup><mml:msubsup><mml:mi>θ</mml:mi><mml:mi>W</mml:mi><mml:mi>eff</mml:mi></mml:msubsup></mml:math>in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>p</mml:mi><mml:mover accent="true"><mml:mi>p</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo>→</mml:mo><mml:mi>Z</mml:mi><mml:mo>/</mml:mo><mml:msup><mml:mi>γ</mml:mi><mml:mo>*</mml:mo></mml:msup><mml:mo>+</mml:mo><mml:mi>X</mml:mi><mml:mo>→</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msup><mml:mi>e</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:mo>+</mml:mo><mml:mi>X</mml:mi></mml:math>Events Produced at<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>1.96</mml:mn><mml:mtext> </mml:mtext><mml:mtext> </mml:mtext><mml:mi>TeV</mml:mi></mml:math> (2008)

We present a measurement of the forward-backward charge asymmetry (A FB) in pp-->Z/gamma* + X-->e+e(-) + X events at a center-of-mass energy of 1.96 TeV using 1.1 fb(-1) of data collected with the D0 detector at the Fermilab Tevatron collider. A FB is measured as a function of the invariant mass of the electron-positron pair, and found to be consistent with the standard model prediction. We use the A FB measurement to extract the effective weak mixing angle sin2thetaWeff = 0.2326+/-0.0018(stat)+/-0.0006(syst).
Music therapy for posttraumatic stress in adults: A theoretical review. (2017)

Music therapy has been employed as a therapeutic intervention to facilitate healing across a variety of clinical populations. There is theoretical and empirical evidence to suggest that individuals with trauma exposure and Posttraumatic Stress Disorder (PTSD), a condition characterized by enduring symptoms of distressing memory intrusions, avoidance, emotional disturbance, and hyperarousal, may derive benefits from music therapy. The current narrative review describes the practice of music therapy and presents a theoretically-informed assessment and model of music therapy as a tool for addressing symptoms of PTSD. The review also presents key empirical studies that support the theoretical assessment. Social, cognitive, and neurobiological mechanisms (e.g., community building, emotion regulation, increased pleasure, anxiety reduction) that promote music therapy's efficacy as an adjunctive treatment for individuals with posttraumatic stress are discussed. It is concluded that music therapy may be a useful therapeutic tool to reduce symptoms and improve functioning among individuals with trauma exposure and PTSD, though more rigorous empirical study is required. In addition, music therapy may help foster resilience and engage individuals who struggle with stigma associated with seeking professional help. Practical recommendations for incorporating music therapy into clinical practice are offered along with several suggestions for future research.
Amplification of broadband light source for OPCPA (2006)

Basic experiments of OPCPA with a Type I BBO crystal were conducted using the supercontinuum generated in a PCF. Tunable amplification bandwidth of 100nm was demonstrated.
Asynchronous Network Formation in Unknown Unbounded Environments (2019)

In this paper, we study the Online Network Formation Problem (ONFP) for a mobile multi-robot system. Consider a group of robots with a bounded communication range operating in a large open area. One of the robots has a piece of information which has to be propagated to all other robots. What strategy should the robots pursue to disseminate the information to the rest of the robots as quickly as possible? The initial locations of the robots are unknown to each other, therefore the problem must be solved in an online fashion. For this problem, we present an algorithm whose competitive ratio is $O(H \cdot\max\{M,\ \sqrt{MH}\})$ for arbitrary robot deployments, where M is the largest edge length in the Euclidean minimum spanning tree on the initial robot configuration and H is the height of the tree. We also study the case when the robot initial positions are chosen uniformly at random and improve the ratio to $O(M)$. Finally, we present simulation results to validate the performance in larger scales and demonstrate our algorithm using three robots in a field experiment.
mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud (2016)

Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at.
The use of computerized peak deconvolution for determination of energy barrier to enantiomerization in dynamic gas chromatography (2000)

Computer-assisted peak deconvolution on chromatograms obtained by GC separation of enantiomers of 1-chloro-2,2-dimethylaziridine on modified α-, β-, and γ-cyclodextrin was used to determine the peak areas of enantiomers, prior to (AA, 0, BB, 0) and after the separation (AA, AB). Both Gaussian as well as exponentially modified Gaussian functions were used to approximate the peak shapes in the deconvolution procedures. Determined peak areas were used in the calculation of the rate constants and energy barriers to enantiomerization. A comparison of energy barriers determined using the deconvolution of chromatograms with data published in the literature by classical kinetics shows differences within ±5%. © 2001 John Wiley & Sons, Inc. J Micro Sep 12: 630–636, 2000
The Importance of Skills Assessment and Recording Personal Outcomes in the Future of Training (2011)

Careful documentation of performance is a crucial part of assessing progress in endoscopy training, and is increasingly recognized as important also in practice. In turn, results in practice can drive improvements in training.
Absorption of NO<sub>2</sub>/N<sub>2</sub>O<sub>4</sub> in nitric acid (1990)

Abstract Laboratory‐scale measurements were performed on the absorption of NO 2 gas into diluted nitric acid. The concentration of NO 2 gas, which represents an NO 2 /N 2 O 4 equilibrium, varied from 1000 to 20000 ppm, the carrier gas being nitrogen. The concentration of nitric acid ranged from 15 to 60 mass‐%. The absorption experiments were carried out in a double stirred cell, with a defined gas/liquid interface as the mass transfer area. The liquid phase was conducted periodically and the gas phase continuously. Mass flow rates were determined. The well‐known film model of absorption was used for analyzing the experimental results. Only the N 2 O 4 species was considered to pass the gas/liquid interface. The measured data yielded values of H ( k D 1 ) 1/2 as well as their variation with temperature and nitric acid concentration.
ChemInform Abstract: Considered Synthetic Methods and Reactions. Part 195. Convenient and Safe Electrochemical Synthesis of (Trifluoromethyl)trimethylsilane. (1995)

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.
Oncolytic Herpes Simplex Viruses as a Paradigm for the Treatment of Cancer (2017)

Oncolytic viruses are native or modified viruses that directly kill tumor cells but spare normal tissue and promote host antitumor immunity. Recently, an oncolytic herpes simplex virus (oHSV) type 1–encoding human granulocyte-macrophage colony-stimulating factor (GM-CSF) demonstrated significant clinical benefit in a randomized phase III clinical trial for patients with advanced melanoma, leading to regulatory approval in 2015. In this review, we provide a general characterization of herpes simplex viruses and discuss methods for vector modification, which can help limit viral pathogenicity and immunogenicity while promoting antitumor immunogenicity. We also provide insight into general strategies for using oHSV agents in tumor immunotherapy regimens for the treatment of cancer and briefly review some of the currently emerging preclinical and clinical data that support an important role for such agents in the treatment of cancer.
Simultaneous two-dimensional measurement of fuel–air ratio and temperature in a direct-injection spark-ignition engine using a new tracer-pair laser-induced fluorescence technique (2015)

A planar tracer laser–induced fluorescence technique using a new tracer pair is introduced and has been utilized for the simultaneous detection of the fuel–air ratio and the temperature to characterize mixture formation inside a direct-injection spark-ignition engine. The new tracer pair consists of triethylamine and 3-pentanone, which are simultaneously added to the surrogate fuel isooctane. Triethylamine was used for the determination of the fuel–air ratio. The temperature distribution was evaluated with the two-line excitation laser-induced fluorescence technique using 3-pentanone. Prior to the internal combustion engine measurements, the tracer mixture was first investigated in a flow cell to demonstrate the spectral separability of the fluorescence signals and for the extension of the calibration data basis. As a first application, the tracer pair was applied inside a direct-injection spark-ignition engine operated with a split-injection scheme. For the late second injection, the fuel and temperature stratification was studied during the compression stroke. The measured temperature drop due to evaporative cooling effects was found to be about 100 K in the averaged data and up to 125 K in the single-shot measurements. The relation between fuel-rich areas and strong temperature drop can clearly be seen in the results. Furthermore, the suitability of the tracer pair to resolve cyclic variations is visualized.
Turbocharging boosted transactions or (2009)

Boosted transactions offer an attractive method that enables programmers to create larger transactions that scale well and offer deadlock-free guarantees. However, as boosted transactions get larger, they become more susceptible to conflicts and aborts. We describe a linear-time algorithm to detect transactions that cannot make progress, which transactions need to be aborted, and when. The algorithm guarantees zero false positives with minimal aborts. Our proposals, as implemented in DSTM2, increase the transactional throughput of the system, often by more than 30%.
Organic Solar Cells: Three‐Dimensional Nanostructured Indium‐Tin‐Oxide Electrodes for Enhanced Performance of Bulk Heterojunction Organic Solar Cells (Adv. Energy Mater. 7/2014) (2014)

A three-dimensional indium tin oxide (ITO) nanohelix array is used as a multifunctional photoelectrode for bulk heterojunction organic solar cells. In article number 1301566, Jong-Lam Lee, Jong Kyu Kim, and co-workers demonstrate that the unique structural and optical properties of the ITO nanohelix array enable simultaneous improvements in light harvesting and charge transport efficiencies, resulting in enhanced power conversion efficiency.
3He gas scintillation spectrometer for fusion neutron measurements (1985)

A high-efficiency, good resolution neutron spectrometer can obtain time-resolved fusion rates and mean ion energies from yield and Doppler width measurements of the 2.5 -MeV neutron peak. Gas scintillation spectrometers are capable of operating at high data rates. In order to obtain adequate energy resolution large light yields and uniform light collection over the active detector volume are required. We have measured the absolute light yield from He–Xe gas mixtures. With a high light collection efficiency the detected photon yield from the 3He(n, p)t reaction due to D–D neutrons will give adequate statistics for resolutions of a few percent. Calculations have been performed to model the detector optics in an effort to optimize the light yield and the uniformity of response. Measurements of detector resolution and time response have been made.
Towards a Synthesis of Vigabatrin Using Glycal Chemistry (2005)

Application of the Ferrier rearrangement led to a novel carbohydrate based synthetic route to 4-aminohexenoic acid viz. (R) and (S)-vigabatrin. The potential of D- glucose or D-galactose as the chiral starting materials for the synthesis of (R) and (S)- vigabatrin has been explored.
Improving harmonic rejection for spectrum sensing using crosscorrelation (2012)

Harmonic downmixing may cause a spectrum sensing device to erroneously flag parts of the spectrum as occupied. Receivers employing harmonic rejection (HR) rarely obtain more than 60 dB of HR, which may not be enough for spectrum sensing for dynamic spectrum access. We improve HR by employing two RF-receivers, integrated in a single 65nm CMOS IC, and using a small offset in their LO-frequencies. The offset is corrected in the digital baseband, after which the final receiver outputs are crosscorrelated. Our measurements show that the HR can be significantly improved without calibration or time penalty, even for high initial HR, but that the improvement is limited by crosstalk between the receivers.
Supplementary Figure 7 from T-Cell Exhaustion Signatures Vary with Tumor Type and Are Severe in Glioblastoma (2023)

&lt;p&gt;T cell counts per gram of tumor across tumor models&lt;/p&gt;