gebhart/patrepeval huggingface dataset:
Biomarker time out (2014)

The advancement of knowledge relies on scientific investigations. The timing between asking a question and data collection defines if a study is prospective or retrospective. Prospective studies look forward from a point in time, are less prone to bias and are considered superior to retrospective studies. This conceptual framework conflicts with the nature of biomarker research. New candidate biomarkers are discovered in a retrospective manner. There are neither resources nor time for prospective testing in all cases. Relevant sources for bias are not covered. Ethical questions arise through the time penalty of an overly dogmatic concept. The timing of sample collection can be separated from testing biomarkers. Therefore the moment of formulating a hypothesis may be after sample collection was completed. A conceptual framework permissive to asking research questions without the obligation to bow to the human concept of calendar time would simplify biomarker research, but will require new safeguards against bias.
Dual-task standing and walking in people with lower limb amputation (2018)

Understanding how people with lower limb amputation use increased attention in balance and gait to compensate for limb loss can inform prosthetic interventions and training. Dual-task research suggests that people with amputation use increased cognitive control for standing compared to controls and microprocessor-controlled knees improve dual-task walking in people with limited mobility.
Atomistic Origins of Temperature-Dependent Shear Strength in 2D Materials (2018)

We present a model that predicts the macroscale temperature-dependent interfacial shear strength of 2D materials like MoS2 based on atomistic mechanisms and energetic barriers to sliding. Atomistic simulations were used to systematically determine the lamellar size-dependent rotation and translation energy barriers, that were used to accurately predict a broad range of experimental data. This framework provides insight about the origins of characteristic shear strengths of 2D materials.
Tag Augmenté Récupérateur d’Énergie pour Alimentation Autonome d'un Capteur de Température (2016)

National audience
Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by routing through transporter nodes (2023)

A massively parallel computer system contains an inter-nodal communications network of node-to-node links. An automated routing strategy routes packets through one or more intermediate nodes of the network to reach a destination. Some packets are constrained to be routed through respective designated transporter nodes, the automated routing strategy determining a path from a respective source node to a respective transporter node, and from a respective transporter node to a respective destination node. Preferably, the source node chooses a routing policy from among multiple possible choices, and that policy is followed by all intermediate nodes. The use of transporter nodes allows greater flexibility in routing.
Experimental study for selection of electrode material for ZnO‐based memristors (2014)

The fabrication and characterisation of 400 nm‐thick zinc oxide (ZnO)‐based memristor devices with platinum (Pt), chromium (Cr) and gold (Au) metal electrodes are presented. The effect of these electrode materials on the performance of ZnO‐based memristors has been experimentally studied. Metal/ZnO contact limits the memristor switching mechanism, dominating during the resistive switching. It is observed that the ZnO‐based memristor with the Pt electrode shows a better hysteresis compared to Cr and Au metal electrodes. In the case of the Pt electrode, a current ratio of six times in magnitude is observed between the high resistive state and low resistive state at 1 V, where a maximum current density value of 1.25 A/cm 2 is measured. The capacitance of these devices strongly depends on the charge distributed on the surface. Therefore, the capacitance–voltage ( C–V ) behaviour can be used to understand the charge distribution, under various bias conditions. The C–V behaviour of the Pt memristor, so as to understand the contact interface, where the maximum capacitance of 2.3 × 10 −7 F/cm 2 is obtained at 0 V, is also explained.
DAP12 Signaling Regulates Plasmacytoid Dendritic Cell Homeostasis and Down-Modulates Their Function during Viral Infection (2006)

DAP12 is an ITAM-containing adaptor molecule conveying activating properties to surface receptors on many cell types. We show here that DAP12 paradoxically down-modulates plasmacytoid dendritic cell (pDC) cytokine production in vivo during murine CMV (MCMV) infection. Higher levels of IFN-alphabeta and IL-12 were detected upon MCMV infection or CpG treatment in DAP12-deficient (DAP12(o)) mice as compared with wild-type (WT) mice. This resulted from altered homeostasis and enhanced responsiveness of pDCs in DAP12(o) animals. Increased numbers of pDCs were observed in the periphery of both naive and MCMV-infected DAP12(o) mice. A higher proportion of pDCs was activated in infected DAP12(o) mice, as demonstrated by intracellular staining using an optimized protocol for simultaneous detection of IFN-alpha and IFN-beta. The homeostasis of WT and DAP12(o) pDCs did not differ in mixed bone marrow chimeric mice. In addition, a similar efficiency of pDC differentiation was observed in vitro in Fms-like tyrosine kinase receptor 3 ligand cultures of WT and DAP12(o) bone marrow cells. This suggests that DAP12 signaling effects on pDC homeostasis are indirect. In contrast, in response to CpG, DAP12-mediated effects on both IL-12 and IFN-alphabeta production were intrinsic to the pDCs. However, in response to MCMV, only IL-12 but not IFN-alphabeta production was affected by pDC-intrinsic DAP12 signaling. Thus, DAP12 signaling in pDCs can mediate different regulatory effects on their functions, depending on the mechanisms of pDC activation. The potential implications of the regulation of pDC functions by DAP12 for promoting health over disease are discussed.
Advanced photomask repair technology for 65nm lithography (3) (2005)

The 65nm photomasks have to meet tight specifications and improve the production yield due to high production cost. The 65nm optical lithography was thought to have two candidates, 157nm and 193nm. However, at the advent of immersion lithography, it is certain that 193nm lithography will be adopted. Therefore, we decided to develop the FIB machine, SIR7000FIB, proior to the EB machine. We optimized repair conditions of FIB system, SIR7000FIB, and evaluated this system. First, we demonstrated minute defect repair using about 15nm defect mask. Then, we confirmed that the repeatability of repair accuracy was below 7nm on a MoSi HT mask patterned 360nm and 260nm L&S patterns with opaque and clear defects by AFM. Consequently, we have achieved the target specifications of this system.
Sub-Profiling by Linguistic Dimensions to Solve the Authorship Attribution Task (2012)

In this paper, we describe a modified version of the profile-based ap- proach for the Authorship Attribution (AA) task of the PAN 2012 challenge. Our PAN system for AA utilizes the concept of linguistic modalities 1 on profile-based (PB) approaches. We concatenate all the training documents from the same author and build author-specific sub-profiles, one per linguistic modality. Then instead of using all the different types of features to compute the similarity of a test doc- ument against an author's profile in a single step, we compute several similarity scores using one set of features (modality) at a time. Each modality will assign the test document to the author whose sub-profile has the highest cosine similarity in that modality. Final classification decisions are based on the combination of deci- sions from each modality using majority voting. We achieved competitive results on PAN 2012, with encouraging results on the closed-class authorship attribution.
Abstract 1445: Tumor-specific T cell engineering for enhanced effector function via microfluidic delivery of bioactive molecules (2019)

Background: Tumor-specific T cells possess unique potential for cancer therapy but are limited by T cell exhaustion and anergy induced in the tumor microenvironment. Ex vivo manipulation of these T cells to maintain their full function is critical to their success clinically. Yet, limitations of existing ex vivo delivery approaches dramatically restrict their function and thus limit their therapeutic use.Methods: Genome-wide profiling was used to identify the impact of optimized electroporation treatment and the SQZ cell therapy platform on gene expression in human T cells. The profiling was paired with a 42 key T cell cytokine-multiplex analysis comprised of to assess perturbation of cytokine secretion. We then compared the in vivo functionality of immune checkpoint deleted antigen-specific T cells, modified by either electroporation or SQZ delivery of CRISPR/Cas9, and adoptively transferred into tumor bearing mice. Finally, genomic editing of tumor infiltrating leukocyte (TIL) derived T cells was compared using either electroporation or SQZ and subsequent effector response upon re-exposure to tumor cells.Results: Impactful disruptions in transcript expression after treatment with electroporation (17% of genes mis-regulated, FDR q <0.1) we identified, whereas cells treated with SQZ had similar expression profiles to untreated control cells (0% of genes mis-regulated, FDR q <0.1). These genetic disruptions result in concomitant perturbation of cytokine secretion and effector response. Ultimately, the effects at the transcript and protein level resulted in functional deficiencies in vitro and in vivo with electroporated antigen-specific and TIL derived T cells failing to demonstrate sustained antigen-specific effector responses and tumor control with or without immune checkpoint editing.Conclusions: This work demonstrates that functional modifications to tumor-specific T cells ex vivo can restore and improve their function upon re-exposure to tumor cells but that the delivery mechanism used is critical to the desired phenotype. The significant differences in outcomes from the two techniques tested here underscores the importance of understanding the impact of intracellular delivery methods on cell function for research and clinical applications. For both research and therapeutic applications with primary T cells, the functional consequences of the selected intracellular delivery technique and its impact on cell phenotype should be carefully evaluated.Citation Format: Luke Cassereau, Julie M. Cole, Roslyn Yi, Jacquelyn L. Hanson, Josh Bugge, Tia DiTommaso, Howard Bernstein, Armon Sharei. Tumor-specific T cell engineering for enhanced effector function via microfluidic delivery of bioactive molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1445.
A thermally erasable silicon oxide layer for molecular beam epitaxy (2022)

Abstract We present a systematic study of the oxidation and deoxidation behaviours of several kinds of ultrathin silicon oxide layers frequently used in silicon (Si) technology, which in this work serve as surface protecting layers for molecular beam epitaxy (MBE). With various characterization techniques, we demonstrate that a chemically grown silicon oxide layer is the most promising candidate for subsequent removal in an ultra-high vacuum chamber at a temperature of 1000 ∘ C, without making use of a reducing agent. As a demonstration, a tensile-strained Ge(100) layer is epitaxially grown on the deoxidised wafer with an atomically flat surface and a low threading dislocation density of 3.33 × 10 8 cm −2 . Our findings reveal that the ultra-thin oxide layer grown using a chemical approach is able to protect Si surfaces for subsequent MBE growth of Ge. This approach is promising for the growth of III/V-on-Si (using Ge as a buffer) and all group-IV related epitaxy for integration on the Si photonics platforms.
Diagnosis and management of tropomyosin receptor kinase (TRK) fusion sarcomas: expert recommendations from the World Sarcoma Network (2020)

Sarcomas are a heterogeneous group of malignancies with mesenchymal lineage differentiation. The discovery of neurotrophic tyrosine receptor kinase (NTRK) gene fusions as tissue-agnostic oncogenic drivers has led to new personalized therapies for a subset of patients with sarcoma in the form of tropomyosin receptor kinase (TRK) inhibitors. NTRK gene rearrangements and fusion transcripts can be detected with different molecular pathology techniques, while TRK protein expression can be demonstrated with immunohistochemistry. The rarity and diagnostic complexity of NTRK gene fusions raise a number of questions and challenges for clinicians. To address these challenges, the World Sarcoma Network convened two meetings of expert adult oncologists and pathologists and subsequently developed this article to provide practical guidance on the management of patients with sarcoma harboring NTRK gene fusions. We propose a diagnostic strategy that considers disease stage and histologic and molecular subtypes to facilitate routine testing for TRK expression and subsequent testing for NTRK gene fusions.
Force-induced focal adhesion translocation: effects of force amplitude and frequency (2004)

Vascular endothelial cells rapidly transduce local mechanical forces into biological signals through numerous processes including the activation of focal adhesion sites. To examine the mechanosensing capabilities of these adhesion sites, focal adhesion translocation was monitored over the course of 5 min with GFP-paxillin while applying nN-level magnetic trap shear forces to the cell apex via integrin-linked magnetic beads. A nongraded steady-load threshold for mechanotransduction was established between 0.90 and 1.45 nN. Activation was greatest near the point of forcing (<7.5 microm), indicating that shear forces imposed on the apical cell membrane transmit nonuniformly to the basal cell surface and that focal adhesion sites may function as individual mechanosensors responding to local levels of force. Results from a continuum, viscoelastic finite element model of magnetocytometry that represented experimental focal adhesion attachments provided support for a nonuniform force transmission to basal surface focal adhesion sites. To further understand the role of force transmission on focal adhesion activation and dynamics, sinusoidally varying forces were applied at 0.1, 1.0, 10, and 50 Hz with a 1.45 nN offset and a 2.25 nN maximum. At 10 and 50 Hz, focal adhesion activation did not vary with spatial location, as observed for steady loading, whereas the response was minimized at 1.0 Hz. Furthermore, applying the tyrosine kinase inhibitors genistein and PP2, a specific Src family kinase inhibitor, showed tyrosine kinase signaling has a role in force-induced translocation. These results highlight the mutual importance of force transmission and biochemical signaling in focal adhesion mechanotransduction.
Norwegian e-Infrastructure for Life Sciences (NeLS) (2018)

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs). NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK. In this article, we outline the architecture of NeLS and discuss possible directions for further development.
A Flexible, Convergent Approach to Polycyclic Indole Structures: Formal Synthesis of (±)-Mersicarpine (2009)

The formal synthesis of (+/-)-mersicarpine was achieved using an intermolecular radical addition-radical cyclization cascade. This key reaction represents a flexible, convergent route to numerous polycyclic indole derivatives.
Magnetic Material Modeling (2017)

This chapter introduces some shape preserving interpolation (including extrapolation) schemes. It shows that the derivative of the linear interpolant discontinues at each sampling point, which may cause the Newton-Raphson iteration in finite element analysis (FEA) not to converge to a smaller error. The quadratic spline interpolation is also based on the pre-selected discrete derivative set. Anisotropic behavior is often encountered not only in the grain oriented but also in the laminated grain non-oriented magnetic cores in electromagnetic devices. The chapter presents case study of a 400 W 4-pole synchronous reluctance motor with axially laminated anisotropic rotors. Permanent magnet (PM) machines are usually designed with reasonable demagnetization in normal working conditions. In some occasional cases, a PM motor may operate at an overloaded torque. The chapter presents an algorithm to construct demagnetization curves for magnetization.
Studies of immunologic tolerance to host minor histocompatibility antigens following allogeneic bone marrow transplantation in mice. (1990)

We showed previously that transplantation of 10(7) unmanipulated C57BL/6 marrow cells to irradiated LP mice yields healthy (B6-LP) chimeras showing no signs of rejection or graft-versus-host disease (GVHD). The aim of this work was to gain more insight into the mechanism(s) responsible for tolerance to host minor histocompatibility antigens following allogeneic bone marrow transplantation (BMT). (B6-LP) chimeras showed very good immune reconstitution when studied in vitro for proliferative response to mitogens and alloantigens and generation of T cell cytotoxic activity. In co-culture experiments their spleen cells showed no natural suppressor activity. When used as cell donors, their capacity to initiate GVHD in four strains of mice presenting H-2 differences was normal when compared to C57BL/6 donors. However, they provoked no GVHD in the three strains of H-2 compatible mice studied. Re-irradiated (B6-LP) chimeras rapidly died of GVHD following injection of C57BL/6 marrow + spleen cells. (B6-LP.R111) chimera cells appeared tolerant to LP minor antigens presented in the context of H-2r or H-2b. No anamnestic anti-idiotypic suppressor response was noted when stable (B6-LP) chimeras were stimulated with naive C57BL/6 cells. These findings suggest that in BMT chimeras transplanted across minor histocompatibility barriers: (1) both host and donor-derived antigen-presenting cells can present host antigens to donor T cells whose numbers in the marrow inoculum will determine if GVHD or tolerance will ensue, (2) GVHD can be triggered by only a limited number of 'dominant' minor antigens, and (3) we found no evidence for the presence of natural suppressors, veto cells or anti-idiotypic suppressor T cells.
A Dynamic Multiscale Magnifying Tool for Exploring Large Sparse Graphs (2008)

We present an information visualization tool, known as GreenMax, to visually explore large small-world graphs with up to a million graph nodes on a desktop computer. A major motivation for scanning a small-world graph in such a dynamic fashion is the demanding goal of identifying not just the well-known features but also the unknown–known and unknown–unknown features of the graph. GreenMax uses a highly effective multilevel graph drawing approach to pre-process a large graph by generating a hierarchy of increasingly coarse layouts that later support the dynamic zooming of the graph. This paper describes the graph visualization challenges, elaborates our solution, and evaluates the contributions of GreenMax in the larger context of visual analytics on large small-world graphs. We report the results of two case studies using GreenMax and the results support our claim that we can use GreenMax to locate unexpected features or structures behind a graph.
Clinical Outcome After Primary Triple Arthrodesis*† (2000)

Triple arthrodesis for the treatment of various deformities and etiologies is effective in relieving pain and improving functional deficits. Although a high prevalence of subsequent arthritis of the ankle was noted clinically and radiographically, we could detect no association between satisfaction of the patient and arthritis.
Long-Term Health of Dopaminergic Neuron Transplants in Parkinson's Disease Patients (2014)

To determine the long-term health and function of transplanted dopamine neurons in Parkinson's disease (PD) patients, the expression of dopamine transporters (DATs) and mitochondrial morphology were examined in human fetal midbrain cellular transplants. DAT was robustly expressed in transplanted dopamine neuron terminals in the reinnervated host putamen and caudate for at least 14 years after transplantation. The transplanted dopamine neurons showed a healthy and nonatrophied morphology at all time points. Labeling of the mitochondrial outer membrane protein Tom20 and α-synuclein showed a typical cellular pathology in the patients' own substantia nigra, which was not observed in transplanted dopamine neurons. These results show that the vast majority of transplanted neurons remain healthy for the long term in PD patients, consistent with clinical findings that fetal dopamine neuron transplants maintain function for up to 15-18 years in patients. These findings are critically important for the rational development of stem-cell-based dopamine neuronal replacement therapies for PD.
Automatic labeling of liver veins in CT by probabilistic backward tracing (2014)

The mapping and labeling of the major intra-hepatic blood vessels may facilitate planning liver interventions and surgery. However, the automatic labeling of liver veins is challenging due to imperfect segmentations caused by partial volume effects and image resolution that result in undesirable false connections between hepatic and portal veins. In this paper, we propose a novel method to model the continuity of consecutive venous branches in a probabilistic manner. Then the model is automatically labeled via inference. The method incorporates low-level metrics for neighboring nodes and mid-level metrics for neighboring branches. Making use of these metrics, the automatic labeling becomes a probabilistic tracing procedure starting from each end nodes of the vessel skeleton. The method has only one free parameter whose value is not critical to labeling results. Experiments using data from healthy and pathological patients were performed and the results illustrate an accuracy of 0.97±0.08.