gebhart/patrepeval huggingface dataset:
Quantitation of T-Cell Receptor Frequencies by Competitive Polymerase Chain Reaction: Dynamics of T-Cell Clonotype Frequencies in an Expanding Tumor-Infiltrating Lymphocyte Culture (2000)

The use of T-cell receptor (TCR) genes as markers for antigen-reactive T cells is dependent on the ability of the TCR genes to rapidly identify antigen-reactive T-cell clonotypes in patient samples. We recently reported a competitive reverse-transcriptase polymerase chain reaction (cRT-PCR) method that can measure the frequency of individual TCRBV subfamilies and clonotypes in mixed lymphocyte populations more accurately than other semiquantitative PCR assays. However, it is impractical to measure changes in the absolute frequency of each TCRBV subfamily to identify those T cells with increasing frequency after antigen stimulation in vivo or in vitro. Therefore, we have modified our cRT-PCR method to more rapidly identify expanding T-cell populations by combining all of the TCRBV subfamily-specific competitors into a single sample to determine the relative abundance of each TCRBV subfamily. Using an expanding TIL 620 culture, we identified four TCRBV (BV2, BV12, BV17, and BV23) subfamilies that expanded over a 23-day period. These subfamilies accounted for 23% of the T cells in the day 35 culture and increased to 57%, 92%, and 80% of the days 44, 51, and 58 cultures respectively. Analysis of DNA sequences demonstrated that the observed expansion was caused primarily by a single clonotype within each subfamily. T cells expressing BV17 and BV23 recognized gp100 and MART-1 respectively. Therefore, this cRT-PCR method can detect expanding T-cell populations based solely on their TCRBV subfamily expression. Furthermore, T-cell expansion in a mixed TIL population was a good predictor of antigen reactivity.
Concurrency control using locking with deferred blocking (2002)

The concurrency control method employed can be critical to the performance of transaction processing systems. The conventional locking scheme tends to suffer from the blocking phenomenon. The proposed scheme reduces the blocking probability by deferring the blocking behavior of transactions to the later stages of their execution. The transaction execution can then be divided into a nonblocking phase, in which transactions wait for locks but do not block other transactions, and a blocking phase, as in conventional locking. Data accessed during the nonblocking phase can lead to transaction abort. By properly balancing the blocking and abort effects, the proposed scheme can lead to better performance at all data and resource contention levels than either conventional locking or the optimistic concurrency control schemes. Both simulation and analytical models are used for estimating the performance of this scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ionic conductance pathways in the mouse medullary thick ascending limb of Henle. The paracellular pathway and electrogenic Cl- absorption. (1986)

Net Cl- absorption in the mouse medullary thick ascending limb of Henle (mTALH) involves a furosemide-sensitive Na+:K+:2 Cl- apical membrane symport mechanism for salt entry into cells, which occurs in parallel with a Ba++-sensitive apical K+ conductance. The present studies, using the in vitro microperfused mouse mTALH, assessed the concentration dependence of blockade of this apical membrane K+-conductive pathway by Ba++ to provide estimates of the magnitudes of the transcellular (Gc) and paracellular (Gs) electrical conductances (millisiemens per square centimeter). These studies also evaluated the effects of luminal hypertonicity produced by urea on the paracellular electrical conductance, the electrical Na+/Cl- permselectivity ratio, and the morphology of in vitro mTALH segments exposed to peritubular antidiuretic hormone (ADH). Increasing luminal Ba++ concentrations, in the absence of luminal K+, produced a progressive reduction in the transcellular conductance that was maximal at 20 mM Ba++. The Ba++-sensitive transcellular conductance in the presence of ADH was 61.8 +/- 1.7 mS/cm2, or approximately 65% of the total transepithelial conductance. In phenomenological terms, the luminal Ba++-dependent blockade of the transcellular conductance exhibited negative cooperativity. The transepithelial osmotic gradient produced by luminal urea produced blebs on apical surfaces, a striking increase in shunt conductance, and a decrease in the shunt Na+/Cl- permselectivity (PNa/PCl), which approached that of free solution. The transepithelial conductance obtained with luminal 800 mM urea, 20 mM Ba++, and 0 K+ was 950 +/- 150 mS/cm2 and provided an estimate of the maximal diffusion resistance of intercellular spaces, exclusive of junctional complexes. The calculated range for junctional dilution voltages owing to interspace salt accumulation during ADH-dependent net NaCl absorption was 0.7-1.1 mV. Since the Ve accompanying ADH-dependent net NaCl absorption is 10 mV, lumen positive, virtually all of the spontaneous transepithelial voltage in the mouse mTALH is due to transcellular transport processes. Finally, we developed a series of expressions in which the ratio of net Cl- absorption to paracellular Na+ absorption could be expressed in terms of a series of electrical variables. Specifically, an analysis of paired measurement of PNa/PCl and Gs was in agreement with an electroneutral Na+:K+:2 Cl- apical entry step. Thus, for net NaCl absorption, approximately 50% of Na+ was absorbed via a paracellular route.
Serum microRNA profile enables preoperative diagnosis of uterine leiomyosarcoma (2019)

Uterine leiomyosarcoma (ULMS) is the major subtype of uterine sarcoma (US) and contributes to uterine cancer deaths. Although preoperative diagnosis of US remains challenging, frequent application of laparoscopic surgery for benign uterine leiomyomas (ULM) requires precise exclusion of US. MicroRNAs are stably present in the bloodstream, and the application of circulating miRNAs as disease biomarkers has been recognized. In the present study, we aimed to identify diagnostic biomarkers for distinguishing US from ULM by focusing on circulating miRNAs. All serum samples were collected preoperatively between 2009 and 2017, and all cases were histopathologically diagnosed. Whole miRNA profiles were obtained using a miRNA microarray. By analyzing expression levels of the miRNAs, candidate miRNAs were selected based on diagnostic performance in discriminating US from ULM, and a diagnostic model was then constructed. A total of 90 serum samples were analyzed, and clustering analyses revealed that the profiles of ULMS were distinct from those of controls. Based on leave-one-out cross-validation, seven miRNAs were selected as biomarker candidates. Based on model construction, the optimal model consisted of two miRNAs (miR-1246 and miR-191-5p), with an area under the receiver operating characteristic curve (AUC) for identifying ULMS of 0.97 (95% confidence interval [CI], 0.91-1.00). In contrast, serum lactate dehydrogenase had an AUC of only 0.64 (95% CI, 0.34-0.94). Seven serum miRNAs with high diagnostic performance for preoperative US screening were detected, and a promising diagnostic model for ULMS was generated.
Blind Estimation and Compensation of Frequency-Flat I/Q Imbalance Using Cyclostationarity (2008)

I/Q imbalance is one of the major concerns in the design of direct-conversion front-end receivers in high data rate wireless networks. To address the challenge, various I/Q imbalance estimation and compensation algorithms have been proposed in the literature. In this paper, we propose a blind cyclostationary based estimation and compensation of frequency-flat I/Q imbalance. The proposed blind estimation algorithm uses second-order statistics to compensate I/Q imbalance without estimating the mismatch parameters and is an unbiased estimator when a DC offset exists at the receiver. The performance of our approach is evaluated and compared to other existing blind I/Q imbalance estimation algorithms.
Data from A2AR Antagonism with CPI-444 Induces Antitumor Responses and Augments Efficacy to Anti–PD-(L)1 and Anti–CTLA-4 in Preclinical Models (2023)

&lt;div&gt;Abstract&lt;p&gt;Adenosine signaling through A2A receptors (A2AR) expressed on immune cells suppresses antitumor immunity. CPI-444 is a potent, selective, oral A2AR antagonist. Blockade of A2AR with CPI-444 restored T-cell signaling, IL2, and IFNγ production that were suppressed by adenosine analogues &lt;i&gt;in vitro&lt;/i&gt;. CPI-444 treatment led to dose-dependent inhibition of tumor growth in multiple syngeneic mouse tumor models. Concentrations of extracellular adenosine in the tumor microenvironment, measured using microdialysis, were approximately 100–150 nmol/L and were higher than corresponding subcutaneous tissue. Combining CPI-444 with anti–PD-L1 or anti–CTLA-4 treatment eliminated tumors in up to 90% of treated mice, including restoration of immune responses in models that incompletely responded to anti–PD-L1 or anti–CTLA-4 monotherapy. Tumor growth was fully inhibited when mice with cleared tumors were later rechallenged, indicating that CPI-444 induced systemic antitumor immune memory. CD8&lt;sup&gt;+&lt;/sup&gt; T-cell depletion abrogated the efficacy of CPI-444 with and without anti–PD-L1 treatment, demonstrating a role for CD8&lt;sup&gt;+&lt;/sup&gt; T cells in mediating primary and secondary immune responses. The antitumor efficacy of CPI-444 with and without anti–PD-L1 was associated with increased T-cell activation, a compensatory increase in CD73 expression, and induction of a Th1 gene expression signature consistent with immune activation. These results suggest a broad role for adenosine-mediated immunosuppression in tumors and justify the further evaluation of CPI-444 as a therapeutic agent in patients with solid tumors. &lt;i&gt;Cancer Immunol Res; 6(10); 1136–49. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Euclidean reconstruction and reprojection up to subgroups (1999)

The necessary and sufficient conditions for being able to estimate scene structure, motion and camera calibration from a sequence of images are very rarely satisfied in practice. What exactly can be estimated in sequences of practical importance, when such conditions are not satisfied? In this paper we give a complete answer to this question. For every camera motion that fails to meet the conditions, we give explicit formulas for the ambiguities in the reconstructed scene, motion and calibration. Such a characterization is crucial both for designing robust estimation algorithms (that do not try to recover parameters that cannot be recovered), and for generating novel views of the scene by controlling the vantage point. To this end, we characterize explicitly all the vantage points that give rise to a valid Euclidean reprojection regardless of the ambiguity in the reconstruction. We also characterize vantage points that generate views that are altogether invariant to the ambiguity. All the results are presented using simple notation that involves no tensors nor complex projective geometry, and should be accessible with basic background in linear algebra.
Fast Differentiation of HepaRG Cells Allowing Hepatitis B and Delta Virus Infections (2020)

HepaRG cells are liver bipotent progenitors acquiring hepatocytes features when differentiated in the presence of dimethylsulfoxide (DMSO). Differentiated HepaRG (dHepaRG) are considered the best surrogate model to primary human hepatocytes (PHH) and are susceptible to several hepatotropic viruses, including Hepatitis B Virus (HBV) and Hepatitis Delta Virus (HDV) infection. Despite these advantages, HepaRG cells are not widely used for the study of these two viruses because of their long differentiation process and their rather low and variable infection rates. Here, we tested the use of a cocktail of five chemicals (5C) combined or not with DMSO to accelerate the cells' differentiation process. We found that NTCP-mediated HDV entry and replication are similar in HepaRG cells cultivated for only 1 week with 5C and DMSO or differentiated with the regular 4-week protocol. However, even though the NTCP-mediated HBV entry process seemed similar, cccDNA and subsequent HBV replication markers were lower in HepaRG cells cultivated for 1 week with 5C and DMSO compared to the regular differentiation protocol. In conclusion, we set up a new procedure allowing fast differentiation and efficient HDV-infection of HepaRG cells and identified differential culture conditions that may allow to decipher the mechanism behind the establishment of the HBV minichromosome.
Mutations in the NPxxY motif stabilize pharmacologically distinct conformational states of the α 1B - and β 2 -adrenoceptors (2019)

G protein-coupled receptors (GPCRs) convert extracellular stimuli to intracellular responses that regulate numerous physiological processes. Crystallographic and biophysical advances in GPCR structural analysis have aided investigations of structure-function relationships that clarify our understanding of these dynamic receptors, but the molecular mechanisms associated with activation and signaling for individual GPCRs may be more complex than was previously appreciated. Here, we investigated the proposed water-mediated, hydrogen-bonded activation switch between the conserved NPxxY motif on transmembrane helix 7 (TMH7) and a conserved tyrosine in TMH5, which contributes to α<sub>1B</sub>-adrenoceptor (α<sub>1B</sub>-AR) and β<sub>2</sub>-AR activation. Disrupting this bond by mutagenesis stabilized the α<sub>1B</sub>-AR and the β<sub>2</sub>-AR in inactive-state conformations, which displayed decreased agonist potency for stimulating downstream IP<sub>1</sub> and cAMP signaling, respectively. Compared to that for wild-type receptors, agonist-mediated β-arrestin recruitment was substantially reduced or abolished for all α<sub>1B</sub>-AR and β<sub>2</sub>-AR inactive-state mutants. However, the inactive-state β<sub>2</sub>-ARs exhibited decreased agonist affinity, whereas the inactive-state α<sub>1B</sub>-ARs had enhanced agonist affinity. Conversely, antagonist affinity was unchanged for inactive-state conformations of both α<sub>1B</sub>-AR and β<sub>2</sub>-AR. Removing the influence of agonist affinity on agonist potency gave a measure of signaling efficacy, which was markedly decreased for the α<sub>1B</sub>-AR mutants but little altered for the β<sub>2</sub>-AR mutants. These findings highlight the pharmacological heterogeneity of inactive-state GPCR conformations, which may facilitate the rational design of drugs that target distinct conformational states of GPCRs.
Rationale for Regenerative Treatment in Neonatology (2012)

In this issue of the "Klinische Pädiatrie" Gortner et al. [8] report on regenerative treatment modalities in neonatology to overcome long term sequelae of prematurity and asphyxia, since both are associated with a high risk of adverse outcome leading to lifelong severe disability. According to the review by Gortner et al. [8] severe bronchopulmonary dysplasia (BPD) and hypoxic-ischaemic encephalopathia (HIE) might be preferable fields for regenerative treatment in neonatology using cord blood stem cells (CBSC), endothelial progenitor cells (EPC), mesenchymal stem cells (MSC) or MSC derived exosomes.
All4student. Ultimate portal for students. (2010)

Keywords: Travail et entreprise ; Strategie d'entreprise ; Sections STI, SC, IN Reference EPFL-STUDENT-168356 Record created on 2011-08-29, modified on 2017-05-12
Cryo-CMOS for Quantum System On-Chip Integration: Quantum Computing as the Development Driver (2021)

Quantum computing (QC) is a new paradigm that exploits fundamental principles of quantum mechanics, such as superposition and entanglement, to tackle problems in mathematics, chemistry, and material science that are well beyond the reach of supercomputers [1]. Its power is derived from a quantum bit (qubit) that can simultaneously exist in a superposition of both zero and one states and become entangled with other qubits. It has been shown that quantum computers can speed up algorithms and, potentially, model any physical process [2]. QC is now the main driver behind the phenomenal development of cryogenic CMOS, or cryo-CMOS [3]. The starting point was the sudden emergence of rudimentary quantum computers from obscure physics labs [4]. In the past, there was simply no sufficient motivation to go through the pain of designing IC circuits at deep cryogenic temperatures, where the silicon substrate is known to freeze out electrically and where no Spice models exist. Hence, we cannot find any remarkable literature related to cryo-CMOS from back then. Now that cryo-CMOS work has seriously begun, the designed circuits are being deployed for other applications, such as astronomy and physics experiments [5]-[12].
Intravenous infusion of human bone marrow mesenchymal stromal cells promotes functional recovery and neuroplasticity after ischemic stroke in mice (2017)

Transplantation of human bone marrow mesenchymal stromal cells (hBM-MSC) promotes functional recovery after stroke in animal models, but the mechanisms underlying these effects remain incompletely understood. We tested the efficacy of Good Manufacturing Practices (GMP) compliant hBM-MSC, injected intravenously 3.5 hours after injury in mice subjected to transient middle cerebral artery occlusion (tMCAo). We addressed whether hBM-MSC are efficacious and if this efficacy is associated with cortical circuit reorganization using neuroanatomical analysis of GABAergic neurons (parvalbumin; PV-positive cells) and perineuronal nets (PNN), a specialized extracellular matrix structure which acts as an inhibitor of neural plasticity. tMCAo mice receiving hBM-MSC, showed early and lasting improvement of sensorimotor and cognitive functions compared to control tMCAo mice. Furthermore, 5 weeks post-tMCAo, hBM-MSC induced a significant rescue of ipsilateral cortical neurons; an increased proportion of PV-positive neurons in the perilesional cortex, suggesting GABAergic interneurons preservation; and a lower percentage of PV-positive cells surrounded by PNN, indicating an enhanced plastic potential of the perilesional cortex. These results show that hBM-MSC improve functional recovery and stimulate neuroprotection after stroke. Moreover, the downregulation of "plasticity brakes" such as PNN suggests that hBM-MSC treatment stimulates plasticity and formation of new connections in the perilesional cortex.
Selective Excitation of Concomitant Electrochemiluminophores: Tuning Emission Color by Electrode Potential (2012)

ECL in 3D: Die simultane selektive Elektrochemilumineszenz (ECL) von Ruthenium- und Iridiumkomplexen in Lösung lässt sich über das Elektrodenpotential beeinflussen (siehe Bild; λem=Emissionswellenlänge). Die lumineszierenden Redoxsysteme bieten neue Ansätze für den Nachweis mehrerer Analyte mit ECL, die Bewertung gekoppelter elektrochemischer und spektroskopischer Eigenschaften und die Einstellung der Farbe von Leuchtelementen.
A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling (2017)

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
A Questionnaire-Based Assessment of Symptoms Associated with Tear Film Dysfunction and Lid Margin Disease in an Asian Population (2009)

STFD are present in 6.5% of Singapore Malay adults and is associated with cigarette smoking, presence of thyroid disease and a reduced visual function-related quality of life.
“Alveolar Recruitment Strategy” Improves Arterial Oxygenation During General Anaesthesia (2000)

TUSMAN, G.; BÖHM, S. H.; ANDA, G. F. VAZQUEZ DE; CAMPO, J. L. DO; LACHMANN, B. Author Information
Inflammatory Cardiomyopathic Syndromes (2017)

Inflammatory activation occurs in nearly all forms of myocardial injury. In contrast, inflammatory cardiomyopathies refer to a diverse group of disorders in which inflammation of the heart (or myocarditis) is the proximate cause of myocardial dysfunction, causing injury that can range from a fully recoverable syndrome to one that leads to chronic remodeling and dilated cardiomyopathy. The most common cause of inflammatory cardiomyopathies in developed countries is lymphocytic myocarditis most commonly caused by a viral pathogenesis. In Latin America, cardiomyopathy caused by Chagas disease is endemic. The true incidence of myocarditis is unknown to the limited utilization and the poor sensitivity of endomyocardial biopsies (especially for patchy diseases such as lymphocytic myocarditis and sarcoidosis) using the gold-standard Dallas criteria. Emerging immunohistochemistry criteria and molecular diagnostic techniques are being developed that will improve diagnostic yield, provide additional clues into the pathophysiology, and offer an application of precision medicine to these important syndromes. Immunosuppression is recommended for patients with cardiac sarcoidosis, giant cell myocarditis, and myocarditis associated with connective tissue disorders and may be beneficial in chronic viral myocarditis once virus is cleared. Further trials of immunosuppression, antiviral, and immunomodulating therapies are needed. Together, with new molecular-based diagnostics and therapies tailored to specific pathogeneses, the outcome of patients with these disorders may improve.
Compact TiO2/Anatase TiO2 Single-Crystalline Nanoparticle Electron-Transport Bilayer for Efficient Planar Perovskite Solar Cells (2018)

Electron-transport layer (ETL)/perovskite interface modification plays a key task for producing efficient planar perovskite solar cells (PSCs). In this study, interfacial modification of compact TiO2 using novel, one-step hydrothermally synthesized single-crystalline anatase (AT) titania nanoparticles (TiO2 NPs) (average diameter = 6–10 nm) was applied as an ETL bilayer to enhance the efficient charge generation and extraction and eliminate the electron–hole recombination ratio. We report here an easy approach for enhancing the performance of planar PSCs by introducing a compact TiO2/AT TiO2 NPs bilayer through spray pyrolysis (SP) deposition and spin-coating (SC) techniques, respectively. The enhanced performance of the devices with an SP-TiO2/SC-AT TiO2 NPs bilayer facilitated more efficient electron transport, charge extraction, and low interfacial recombination. Ultimately, the best device had a 17.05% power conversion efficiency resulting from the significant decrease in J–V hysteresis, presenting almost a 12% performance improvement compared to the TiO2 only layer-based counterpart. Thus, the present study provides an important advance to the design of photovoltaic devices with respect to charge transport and electron–hole recombination.