gebhart/patrepeval huggingface dataset:
Detection of host and donor cells in sex‐mismatched rat nerve allografts using RT‐PCR for a Y chromosome (H‐Y) marker (2000)

The donor and host source of support cells, such as Schwann cells, in nerve allograft segments have been the subject of debate. The objective of the present study was to assess the utility of a molecular technique that probes for a Y chromosome expressed gene (H-Y) in distinguishing host from donor tissue in sex-mismatched nerve allograft segments. Forty-two Lewis rats received bilateral syngeneic Lewis or allogeneic ACI rat peroneal nerve grafts, with or without cyclosporin A (CsA) treatment. At different times thereafter animals were sacrificed and samples were harvested. We transplanted males and females reciprocally, to study both survival of donor cells (persisting H-Y mRNA in male grafts by transcription polymerase chain reaction (RT-PCR), and graft infiltration by host cells (detectable H-Y mRNA in female grafts). A kinetic analysis revealed a progressive loss of viable donor cells (loss of H-Y mRNA signal) from allografts, beginning 2-3 weeks, and culminating at 4 weeks, with little detectable H-Y in the absence of CsA treatment. CsA treatment led to prolonged survival of allograft cells, confirmed by detectable H-Y mRNA. By studying female grafts in male rats we could confirm that loss of viable donor tissue in allografts was accompanied by infiltration of host (H-Y mRNA positive) cells, whereas no H-Y mRNA signal was seen in males receiving autografts from females or in immunosuppressed allograft segments. These data suggest that reverse RT-PCR analysis for a Y chromosome gene product can be a valuable tool to assess the origin of viable cells in sex-mismatched nerve allotransplantation tissue.
Estimation of systemic vascular bed parameters for artificial heart control (1998)

An extended Kalman filter estimator for the identification of systemic circulation model parameters during cardiac ejection and cardiac filling is described. The estimator has been developed for use in the control of a cardiac ventricular assist device. A lumped element circuit with a time-varying capacitor was used to represent the systemic circulation and the left ventricle. Since the haemodynamic variables that are measurable in patients with impaired cardiac function vary dramatically as the patients move through different levels of care, the estimator was designed so that it can be used with different sets of blood pressure and flow measurements. Preliminary evaluation of the performance of the estimator using data from a computer simulation and from a patient during open-heart surgery is presented. The robustness of the estimator to variations in parameter initialization is also described.
Conclusion générale : Le macronisme et le « pacte girondin », encore à la recherche d’un nouveau monde (2020)

Spire est le dépôt institutionnel de la production scientifique de Sciences Po et contient le texte intégral des articles, ouvrages, chapitres d’ouvrages, working papers et communications dans des conférences de la communauté académique de Sciences Po.
Search for excited $\tau$-leptons and leptoquarks in the final state with $\tau$-leptons and jets in pp collisions at $\sqrt{s} = 13$ TeV with the ATLAS detector (2023)

A search is reported for excited $\tau$-leptons and leptoquarks in events with two hadronically decaying $\tau$-leptons and two or more jets. The search uses proton-proton (pp) collision data at $\sqrt{s} = 13$ TeV recorded by the ATLAS experiment during the Run 2 of the Large Hadron Collider in 2015-2018. The total integrated luminosity is 139 fb$^{-1}$. The excited $\tau$-lepton is assumed to be produced and to decay via a four-fermion contact interaction into an ordinary $\tau$-lepton and a quark-antiquark pair. The leptoquarks are assumed to be produced in pairs via the strong interaction, and each leptoquark is assumed to couple to a charm or lighter quark and a $\tau$-lepton. No excess over the background prediction is observed. Excited $\tau$-leptons with masses below 2.8 TeV are excluded at 95% CL in scenarios with the contact interaction scale $\Lambda$ set to 10 TeV. At the extreme limit of model validity where $\Lambda$ is set equal to the excited $\tau$-lepton mass, excited $\tau$-leptons with masses below 4.6 TeV are excluded. Leptoquarks with masses below 1.3 TeV are excluded at 95% CL if their branching ratio to a charm quark and a $\tau$-lepton equals 1. The analysis does not exploit flavour-tagging in the signal region.
Tensor-Network Simulations of the Surface Code under Realistic Noise (2017)

The surface code is a many-body quantum system, and simulating it in generic conditions is computationally hard. While the surface code is believed to have a high threshold, the numerical simulations used to establish this threshold are based on simplified noise models. We present a tensor-network algorithm for simulating error correction with the surface code under arbitrary local noise. We use this algorithm to study the threshold and the subthreshold behavior of the amplitude damping and systematic rotation channels. We also compare these results to those obtained by making standard approximations to the noise models.
Session 1 overview - plenary session (2005)

The Plenary Session commences with the formal opening of the Conference by the Executive- Committee Chair, Tim Tredwell. He is followed by the first of three Plenary Presentations. Next, the ISSCC, SSCS, JSSC, and IEEE awards are presented. After a short break, the second and third Plenary Presentations are given. All three Plenary Presentations are related to the Conference theme: "Entering the Nanoelectronic Integrated-Circuit Era", which was chosen to highlight this moment in time when the semiconductor industry no longer concentrates exclusively on dimensions of tenths of microns, but begins to design and process circuits with transistors having nanometer dimensions. The plenary talks are briefly summarized.
Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture (2023)

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.
Amyloid-associated increases in soluble tau relate to tau aggregation rates and cognitive decline in early Alzheimer’s disease (2022)

For optimal design of anti-amyloid-β (Aβ) and anti-tau clinical trials, we need to better understand the pathophysiological cascade of Aβ- and tau-related processes. Therefore, we set out to investigate how Aβ and soluble phosphorylated tau (p-tau) relate to the accumulation of tau aggregates assessed with PET and subsequent cognitive decline across the Alzheimer's disease (AD) continuum. Using human cross-sectional and longitudinal neuroimaging and cognitive assessment data, we show that in early stages of AD, increased concentration of soluble CSF p-tau is strongly associated with accumulation of insoluble tau aggregates across the brain, and CSF p-tau levels mediate the effect of Aβ on tau aggregation. Further, higher soluble p-tau concentrations are mainly related to faster accumulation of tau aggregates in the regions with strong functional connectivity to individual tau epicenters. In this early stage, higher soluble p-tau concentrations is associated with cognitive decline, which is mediated by faster increase of tau aggregates. In contrast, in AD dementia, when Aβ fibrils and soluble p-tau levels have plateaued, cognitive decline is related to the accumulation rate of insoluble tau aggregates. Our data suggest that therapeutic approaches reducing soluble p-tau levels might be most favorable in early AD, before widespread insoluble tau aggregates.
Test structures for delay variability (2002)

With continued technology scaling, yield loss due to timing variation is becoming a significant concern. In particular, random and systematic process variation in devices and interconnect results in variable delay and operating speed along different logic and signal paths; these variations can erode timing windows and ultimately contribute to circuit failure. In this work, a test structure methodology is developed to support the evaluation of process variation and its impact on circuit speed.A newly designed variation test chip enables relatively simple measurement and evaluation of timing variation resulting from process and layout-induced variation. First, the fundamental test structure is a nine-stage ring oscillator (RO); a frequency-divided readout of the RO frequency serves as a clearly defined measure of circuit speed. A large family of ring oscillator test structures has been designed, where each structure is made sensitive to a particular device or interconnect variation source. Front-end-of-line (FEOL) or device variation sensitive structures enable examination of channel length variation as a function of different layout practices, including gate length (finger width), spacing between multiple fingers, orientation (vertical or horizontal), and density of poly fill. Back-end-of-line (BEOL) or interconnect sensitive structures enable examination of variation in dielectric or metal thickness at different metal levels and impact on interconnect capacitance.The second key element of the test structure methodology is a scan-chain architecture enabling independent operation and readout of replicated ring oscillator test structures. In this second version test chip, designed and fabricated in $0.25 m technology, over 2000 ring oscillators per chip can be measured using simple digital control and readout circuitry interfaced to the packaged chip. The scan chain approach involves reading in a control word to each ring oscillator, which specifies if that oscillator is to operate and if the RO frequency is to be put onto an output bus into frequency division and output circuitry. Additional test chip design elements include separate ring oscillator and control logic power grids, so that the frequency dependence of the ring oscillators on power supply voltage can also be measured, enabling separation of channel length and threshold voltage variation contributions.A $0.25 µm version of the test chip has been fabricated, and measurement and statistical analysis of 35 chips have been successfully conducted. Results indicate that within-wafer variation continues to be larger than within-chip variation; however, systematic spatial patterns and layout-dependent variations within the chip are substantial and of particular concern in timing (which depends on matched signal delays across a chip or logic block). The test chip can be ported to other advanced technologies to provide information on layout-dependent and spatially-dependent process variation sources of timing variation, to aid in statistical timing analysis as well as help specify layout practices and design rules to minimize variation.
Synthesis of Nucleoside α-Thiotriphosphates via an Oxathiaphospholane Approach† (2005)

[reaction: see text]. Nucleoside 5'-O-(alpha-thiotriphosphates) were obtained in reactions of the appropriate nucleoside 5'-O-(2-thio-1,3,2-oxathiaphospholanes) with pyrophosphate in the presence of DBU. The presented method allows also for preparation of alpha-seleno congeners and corresponding alpha-modified diphosphates.
Practising Controlled Language through a Help system integrated into the Medical Speech Translation System (MedSLT) (2005)

In this paper, we present evidence that providing users of a speech to speech translation system for emergency diagnosis (MedSLT) with a tool that helps them to learn the coverage greatly improves their success in using the system. In MedSLT, the system uses a grammar-based recogniser that provides more predictable results to the translation component. The help module aims at addressing the lack of robustness inherent in this type of approach. It takes as input the result of a robust statistical recogniser that performs better for out-of-coverage data and produces a list of in-coverage example sentences. These examples are selected from a defined list using a heuristic that prioritises sentences maximising the number of N-grams shared with those extracted from the recognition result.
Tetrahydrofuran amino acids: β- and γ-azidotetrahydrofurancarboxylic acid monomers derived from D-glucoheptonolactone as building blocks for β- and γ-oligopeptides (2000)

The synthesis of both a β (L-allono) and a γ (D-allono) tetrahydrofuran azido acid from a single heptono sugar lactone as monomers for peptidomimetic oligomers is described.
Molecular subtyping of colorectal cancer for identification of patients with a mesenchymal tumor type who might benefit from TGF-beta inhibition. (2014)

3618 Background: Currently, most colorectal cancer (CRC) patients receive chemotherapy treatment, even though many patients do not benefit. Therefore, a better understanding of the biology is required to identify those patients who will benefit from chemotherapy and to find a more tailored therapy plan for all other patients. Methods: A molecular subtype classification (A-, B-, C-type) was developed using expression data of 188 stage I-IV CRC patients and validated in 543 stage II and III patients. Subtypes were correlated to clinical factors, prognosis and treatment benefit (stage III). To determine whether TGF-β signaling is elevated, 78 patient biopsies were analyzed for TGF-beta (receptor) and phospho-SMAD2/3 expression. To analyze the effect of TGF-β activation, we studied the effects of C-type-like cell lines under treatment with Cisplatin, Oxaliplatin or 5-FU. We analyzed the presence of subtypes in all stages (TCGA data, n=218), and investigate the stability of classification in multiple biopsies from the same tumor and in matching primary and liver metastases samples. Results: We developed a diagnostic test that allows the classification of colorectal cancer tumors into different intrinsic molecular subtypes. The heterogeneity of these subtypes is largely based on 3 biological hallmarks of the tumor. Especially C-type CRC is of clinical interest, as C-type patients have the worst outcome, a mesenchymal phenotype and show no benefit from chemotherapy treatment. The C-type subgroup has elevated TGF-β signaling (TGFB1, p=0.0012; TGFBR1, p=0.0005) and increased p-SMAD2/3 staining in the tumor cells (1.9-fold, p=0.0002). In cell line experiments, up-regulation of TGF-β signaling resulted in resistance against chemotherapy. We confirmed the presence of C-type tumors in stage IV CRC (16%) and currently investigate the stability of the subtype phenotype in 33 pairs of matching primary tumor and metastases. Conclusions: The molecular subtypes differ largely in prognosis and response to chemotherapy. A treatment strategy combining standard drugs with agents suppressing TGF-β signaling might benefit C-type patients.
Control-oriented analysis and quality assessment of gear shifting in motorcycles (2011)

This paper addresses the analysis of the gear shifting maneuver for motorcycles and it constitutes, to our best knowledge, the first contribute to study this aspect in two-wheeled vehicles. Specifically, a comparison between automatic and manual gear shifting is discussed, based on which some cost functions are proposed to quantitatively evaluate the maneuver quality from measured data. Based on such cost functions, we are able to automatically classify the performed maneuver and label it with a quality attribute matching that assigned by the rider.
Effect of Nanofiber-Coated Surfaces on the Proliferation and Differentiation of Osteoprogenitors In Vitro (2008)

The osteoconductive property of titanium (Ti) surfaces is important in orthopedic and dental implant devices. Surface modifications of Ti have been proposed to further improve osseointegration. In this study, three different materials, silicon (Si), silicon oxide (SiO(2)), and titanium oxide (TiO(2)), were used to construct nanofibers for surface coating of Ti alloy Ti-6Al-4 V (Ti alloy). MC3T3-E1 osteoprogenitor cells were seeded on nanofiber-coated discs and cultured for 42 days. DNA, alkaline phosphatase, osteocalcin, and mineralization nodules were measured using PicoGreen, enzyme-linked immunosorbent assay, and calcein blue staining to detect the attachment, proliferation, differentiation, and mineralization of MC3T3-E1 cells, respectively. The results demonstrated that the initial cell attachments on nanofiber-coated discs were significantly lower, although cell proliferation on Si and SiO(2) nanofiber-coated discs was better than on Ti alloy surfaces. TiO(2) nanofibers facilitated a higher cellular differentiation capacity than Ti alloy and tissue culture-treated polystyrene surfaces. Thus, surface modification using nanofibers of various materials can alter the attachment, proliferation, and differentiation of osteoprogenitor cells in vitro.
Improvement of melting and freezing curves for fixed-point calibration of a transfer reference thermometer by size-of-source-effect correction (2010)

The size-of-source effect (SSE) of a radiation thermometer is a critical uncertainty component in the fixed-point blackbody calibration of a transfer reference thermometer in the low-temperature range where the field of view is comparable to the size of the blackbody cavity opening. The SSE causes the signal difference between the melting and freezing plateaus to increase, and steepens the slopes of the plateaus. We propose a new method that can recover the signals of the melting and freezing curves that are deteriorated by the SSE, and thereby flatten the plateaus. The improvement has been successfully demonstrated using a tin-point blackbody. The signal difference between the melting and freezing plateaus was reduced from 81 mK to 18 mK, and the freezing-point signal was corrected by 1.30 K. In addition, the slopes on the plateaus have been dramatically flattened.
Insertion of poly (ethylene glycol)-lipid reduces the liposome-encapsulated hemoglobin-induced thrombocytopenic reaction (2007)

Interaction with platelets has been recognized as a concern in the development of liposome-encapsulated hemoglobin as an oxygen carrier. This reaction causes a significant drop in circulating platelets in a rapid and transient fashion. We studied the effect of lipid bilayer charge on the magnitude of drop in circulating platelets. We also investigated the effect of post-inserted PEG-lipid on this phenomenon. PEG-DSPE was inserted in the outer lipid layer of neutral and anionic LEHs. Autologous rabbit platelets were radiolabeled with In-111-oxime and allowed to circulate for 30 min before administering a small dose of LEH preparation. Circulating radioactivity as well as the number of platelets was monitored by sampling blood at various time points. Anionic LEH induced the largest decrease (64%) in circulating platelets. PEGylation of anionic LEH significantly inhibited thrombocytopenic reaction (45.3% decrease). PEGylated neutral LEH demonstrated the least thrombocytopenia (23.8% decrease). In all cases, the reaction was transient, and the platelet counts recovered to reach the baseline level. The recovery time, however, was dependent on the charge and surface PEGylation of LEH preparations. The results indicate that the platelet reaction is significantly influenced by the surface charge carried by the liposomal surface. Hiding the charge by surface PEGylation appears to be an effective means of reducing the thrombocytopenic reaction shown by the LEH.
Abstract PR01: Assessment of PARPi and cisplatin resistance in BRCA1 exon 11 mutant patient -derived xenografts (2020)

Abstract Introduction: The BRCA1 protein contributes to homologous recombination (HR) repair of DNA breaks. BRCA1 mutations often result in dysfunction or absence of BRCA1 proteins. Consequently, BRCA1 mutations induce PARP inhibitor (PARPi) and cisplatin sensitivity. BRCA1 exon 11 is the largest exon and harbors a plethora of germline mutations. BRCA1 exon 11 is subject to alternative splicing and can generate the BRCA1-Δ11q isoform. This isoform is a hypomorphic variant that removes germline exon 11 mutations allowing for translation through to the end of the protein. In this study we examined PARPi and cisplatin sensitivity and resistance in a panel of BRCA1 exon 11 mutant PDX tumors. Experimental Procedures: Wild-type BRCA1 PDX036, exon 13 truncating BRCA1 mutant PDX1126, and BRCA1 exon 11 mutants PDX017, PDX056, and PDX124 were utilized. Using these models, we developed several isogenic sets of cisplatin and PARPi sensitive/resistant PDX using serial passaging and treatments. Additionally, we developed a method for lentiviral manipulation of PDX models to study resistance mechanisms. We assessed tumors for cisplatin and PARPi sensitivity and examined BRCA1 and 53BP1 expression by Western blotting and immunohistochemistry. Results: We observed variable responses to cisplatin and PARPi treatments among PDX models despite the presence of BRCA1 mutations that abrogated expression of full-length BRCA1. PDX196 expressed an abundance of BRCA1-Δ11q and exhibited resistance to both PARPi and cisplatin treatments. Interestingly, exon 11 mutant PDX017, 056, and 124 initially responded to both cisplatin and PARPi treatments. Serial passaging and treatments ultimately elicited resistance in each of these models and in some tumors coincided with an increase in BRCA1-Δ11q expression. Additionally, PARPi and cisplatin-resistant PDX017 tumors exhibited a simultaneous reduction of 53BP1 and increased BRCA1-Δ11q expression. In contrast to the BRCA1 exon 11 mutant PDX models, exon 13 mutant PDX1126 failed to develop resistance after multiple rounds of serial passaging with either cisplatin or PARPi treatments. However, when PDX1126 cells were transduced with lentivirus containing BRCA1-Δ11q cDNA, a rapid acquisition of cisplatin resistance occurred. Conclusions: Our data indicate BRCA1-Δ11q expression is variable in BRCA1 exon 11 mutant tumors, but nevertheless, when abundantly expressed, supports resistance to cisplatin and PARPi. This abstract is also being presented as Poster A46. Citation Format: John J Krais, Emma Clausen, Vladimir Khazak, Igor Astsaturov, Clare L Scott, Neil Johnson. Assessment of PARPi and cisplatin resistance in BRCA1 exon 11 mutant patient -derived xenografts [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr PR01.