gebhart/patrepeval huggingface dataset:
Evaluation by histology, immunohistology and PCR of protocollized renal biopsies 1 week post-transplant in relation to subsequent rejection episodes (1995)

Renal biopsies were performed 1 week following renal transplantation at a time without clinical evidence of rejection in 43 patients (13 females, mean age 48 years range 18-60 and 30 males, mean age 43 years range 17-59 years). Thirty-six biopsies were available for histological or immunohistochemical analysis. Immunohistochemical analyses were performed with monoclonal antibodies against leukocytes (CD45), monocytes (WT14), complement factor 3 (C3), T-cells (Leu4), T-cell receptor alpha beta and gamma delta, tumour necrosis factor alpha (TNF alpha), IL-2 receptor (IL2-R, TAC), intercellular adhesion molecule-1 (ICAM1) and HLA-DR. The slides were scored semiquantitatively with the observers having no knowledge of clinical or patient data. TNF alpha and IL-2R were also measured by quantative PCR. None of the studied parameters correlated to delayed graft function or graft loss. Histological analysis showed that both focal interstitial infiltrate (18/35) and tubular basement membrane disruption (11/35) were followed by a higher incidence of subsequent rejection (P = 0.03 and 0.02 respectively). Also positivity for WT14 around tubuli (P = 0.02) was associated with subsequent occurrence of rejection. The intensity of staining of ICAM-1 on PTC as well as TAC on proximal tubular cells was associated with the number of subsequent rejection episodes. The association between the IL-2 receptor and subsequent rejection was also found applying PCR to the tissue specimens. We conclude that the presence of focal interstitial infiltrates and tubulitis in 1-week biopsies from well-functioning grafts carries an increased risk of subsequent rejection.(ABSTRACT TRUNCATED AT 250 WORDS)
Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica (2012)

The phenomenon of genomic imprinting is conserved in Therians, but the marked difference in the number and location of imprinted genes and DMRs between metatherians and eutherians indicates that imprinting is not fully conserved between the two Therian infra-classes. The identification of a novel DMR at a non-conserved location as well as the first demonstration of histone modifications at imprinted loci in the opossum suggest that genomic imprinting may have evolved in a common ancestor of these two Therian infra-classes with subsequent divergence of regulatory mechanisms in the two lineages.
Comparative Risk of Cardiovascular Events With Biologic and Synthetic Disease‐Modifying Antirheumatic Drugs in Patients With Rheumatoid Arthritis: A Systematic Review and Meta‐Analysis (2019)

Based on meta-analysis, as compared to TNFi, tocilizumab may be associated with a reduced risk of MACE, whereas csDMARDs may be associated with an increased risk of MACE and stroke.
A geometric approach to modeling microstructurally small fatigue crack formation: II. Physically based modeling of microstructure-dependent slip localization and actuation of the crack nucleation mechanism in AA 7075-T651 (2010)

The objective of this paper is to develop further a framework for computationally modeling microstructurally small fatigue crack growth in AA 7075-T651 (Bozek et al 2008 Modelling Simul. Mater. Sci. 16 065007). The focus is on the nucleation event, when a crack extends from within a second-phase particle into a surrounding grain, since this has been observed to be an initiating mechanism for fatigue crack growth in this alloy. It is hypothesized that nucleation can be predicted by computing a non-local nucleation metric near the crack front. The hypothesis is tested by employing a combination of experimentation and finite element modeling in which various slip-based and energy-based nucleation metrics are tested for validity, where each metric is derived from a continuum crystal plasticity formulation. To investigate each metric, a non-local procedure is developed for the calculation of nucleation metrics in the neighborhood of a crack front. Initially, an idealized baseline model consisting of a single grain containing a semi-ellipsoidal surface particle is studied to investigate the dependence of each nucleation metric on lattice orientation, number of load cycles and non-local regularization method. This is followed by a comparison of experimental observations and computational results for microstructural models constructed by replicating the observed microstructural geometry near second-phase particles in fatigue specimens. It is found that orientation strongly influences the direction of slip localization and, as a result, influences the nucleation mechanism. Also, the baseline models, replication models and past experimental observation consistently suggest that a set of particular grain orientations is most likely to nucleate fatigue cracks. It is found that a continuum crystal plasticity model and a non-local nucleation metric can be used to predict the nucleation event in AA 7075-T651. However, nucleation metric threshold values that correspond to various nucleation governing mechanisms must be calibrated.
Safety and Immunogenicity of a Second Dose of an Investigational Maternal Trivalent Group B Streptococcus Vaccine in Nonpregnant Women 4–6 Years After a First Dose: Results From a Phase 2 Trial (2019)

NCT02690181.
Sensory Over-responsivity and Aberrant Plasticity in Cerebellar Cortex in a Mouse Model of Syndromic Autism (2021)

Our findings suggest that this genetic abnormality causes a pathological inflation of CF signaling, possibly resulting from enhanced NRXN1 expression, with consequences for the representation of sensory stimuli by the CF input and for PF synaptic organization and plasticity.
The Amino Acid Sequence of the δ Subunit (Calmodulin) of Rabbit Skeletal Muscle Phosphorylase Kinase (1981)

The amino acid sequence of the phosphorylase kinase delta subunit has been determined using cyanogen bromide peptides. These peptides were ordered by isolation of the tryptic peptides containing carboxyl[14C]methylmethionine. The protein is identical to bovine uterus calmodulin and differs from bovine brain calmodulin only in amide assignments. The delta subunit contains 148 amino acids, including one residue of trimethyllysine, and has a molecular weight of 16680. The N terminus is blocked, probably with an acetyl group, and the protein has a net overall charge at pH 7 of -24. The asparagine residues 60 and 97 have been shown to be partially deamidated in the protein. The sequence of the N-terminal tripeptide and the amide assignments on residues 58 and 60 were not determined unequivocally.
Structures and Reactivity Patterns of Group 9 Metallocorroles (2009)

Group 9 metallocorroles 1-M(PPh(3)) and 1-M(py)(2) [M = Co(III), Rh(III), Ir(III); 1 denotes the trianion of 5,10,15-tris-pentafluorophenylcorrole] have been fully characterized by structural, spectroscopic, and electrochemical methods. Crystal structure analyses reveal that average metal-N(pyrrole) bond lengths of the bis-pyridine metal(III) complexes increase from Co (1.886 A) to Rh (1.957 A)/Ir (1.963 A); and the average metal-N(pyridine) bond lengths also increase from Co (1.995 A) to Rh (2.065 A)/Ir (2.059 A). Ligand affinities for 1-M(PPh(3)) axial coordination sites increase dramatically in the order 1-Co(PPh(3)) < 1-Rh(PPh(3)) < 1-Ir(PPh(3)). There is a surprising invariance in the M(+/0) reduction potentials within the five- and six-coordinate corrole series, and even between them; the average M(+/0) potential of 1-M(PPh(3)) is 0.78 V vs Ag/AgCl in CH(2)Cl(2) solution, whereas that of 1-M(py)(2) is 0.70 V under the same conditions. Electronic structures of one-electron-oxidized 1-M(py)(2) complexes have been assigned by analysis of electron paramagnetic resonance spectroscopic measurements: oxidation is corrole-centered for 1-Co(py)(2) (g = 2.008) and 1-Rh(py)(2) (g = 2.003), and metal-centered for 1-Ir(tma)(2) (g(zz) = 2.489, g(yy) = 2.010, g(xx) = 1.884, g(av) = 2.128) and 1-Ir(py)(2) (g(zz) = 2.401, g(yy) = 2.000, g(xx) = 1.937, g(av) = 2.113).
ASSOCIATION OF THE EXTENT OF DIABETIC MACULAR EDEMA AS ASSESSED BY OPTICAL COHERENCE TOMOGRAPHY WITH VISUAL ACUITY AND RETINAL OUTCOME VARIABLES (2009)

This optical coherence tomography based assessment of the extensiveness of diabetic macular edema did not explain additional variation in baseline visual acuity above that explained by other known important variables nor predict changes in macular thickness or visual acuity after laser photocoagulation.
Load balanced routing for low power and lossy networks (2013)

The RPL routing protocol published in RFC 6550 was designed for efficient and reliable data collection in low-power and lossy networks. Specifically, it constructs a Destination Oriented Directed Acyclic Graph (DODAG) for data forwarding. However, due to the uneven deployment of sensor nodes in large areas, and the heterogeneous traffic patterns in the network, some sensor nodes may have much heavier workload in terms of packets forwarded than others. Such unbalanced workload distribution will result in these sensor nodes quickly exhausting their energy, and therefore shorten the overall network lifetime. In this paper, we propose a load balanced routing protocol based on the RPL protocol, named LB-RPL, to achieve balanced workload distribution in the network. Targeted at the low-power and lossy network environments, LB-RPL detects workload imbalance in a distributed and non-intrusive fashion. In addition, it optimizes the data forwarding path by jointly considering both workload distribution and link-layer communication qualities. We demonstrate the performance superiority of our LB-RPL protocol over original RPL through extensive simulations.
Abstract 4928: Impact of E. hirae on the tumoricidal activity of cyclophosphamide (2017)

Abstract The tumor microenvironment is influenced by anticancer therapies, and even more so by those affecting the gut homeostasis. We previously reported that a deviated repertoire of the intestinal microbiome called « dysbiosis », caused by broad spectrum antibiotics compromised the efficacy of cyclophosphamide (CTX), an immunomodulatory alkylating agent exerting cytotoxic effects against cancer, highlighting the importance of the gut microbiota in this mechanism (Viaud, Science, 2013). CTX is responsible for disrupting the gut barrier integrity as well as intestinal homeostasis, allowing a NOD2-dependent translocation of several Gram-positive bacteria into secondary lymphoid organs. CTX breaks the intestinal tolerance towards the intestinal microbiota and leads to immunization of the host against some bacterial strains. Here, we identified a Gram positive bacteria, Enterococcus hirae, which markedly modulates the intestinal and systemic immunity through the elicitation of bacterial-specific Th1 and pathogenic Th17 cells. Moreover, we have shown that E. hirae is capable of enhancing tumor-specific CD4+ and CD8+ T cell responses against candidate tumor antigens. In parallel, we have demonstrated that intestinal epithelial cells NOD2 receptors represent ‘‘gut immune checkpoints’’ restricting the immunogenicity of E. hirae. Finally, E. hirae specific-memory Th1 immune responses selectively predicted longer progression-free survival in advanced lung or ovarian cancer patients treated with immunotherapy and chemotherapy (platinum salts- or CTX-based chemotherapy) (Daillère, Immunity, 2016). Altogether, E. hirae represents a valuable probiotic against cancer, an oncomicrobiotic ameliorating the efficacy of the most common alkylating immunomodulatory compound. Citation Format: Romain Daillere, Marie Vetizou, Laurence Zitvogel. Impact of E. hirae on the tumoricidal activity of cyclophosphamide [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4928. doi:10.1158/1538-7445.AM2017-4928
Management of synchronized network activity by highly active neurons (2008)

Increasing evidence supports the idea that spontaneous brain activity may have an important functional role. Cultured neuronal networks provide a suitable model system to search for the mechanisms by which neuronal spontaneous activity is maintained and regulated. This activity is marked by synchronized bursting events (SBEs)--short time windows (hundreds of milliseconds) of rapid neuronal firing separated by long quiescent periods (seconds). However, there exists a special subset of rapidly firing neurons whose activity also persists between SBEs. It has been proposed that these highly active (HA) neurons play an important role in the management (i.e. establishment, maintenance and regulation) of the synchronized network activity. Here, we studied the dynamical properties and the functional role of HA neurons in homogeneous and engineered networks, during early network development, upon recovery from chemical inhibition and in response to electrical stimulations. We found that their sequences of inter-spike intervals (ISI) exhibit long time correlations and a unimodal distribution. During the network's development and under intense inhibition, the observed activity follows a transition period during which mostly HA neurons are active. Studying networks with engineered geometry, we found that HA neurons are precursors (the first to fire) of the spontaneous SBEs and are more responsive to electrical stimulations.
Cutaneous necrosis caused by systemically administered heparin. (1981)

Two cases of cutaneous necrosis occurred that were caused by intravenous administration of porcine heparin for deep venous thrombophlebitis. The lesions grossly resembled those of warfarin sodium-induced skin necrosis. However, histologically, no fibrin thrombi were noted in capillaries and vessels, a characteristic finding in warfarin necrosis. There was no evidence of vasculitis in the lesions. Both patients subsequently received warfarin without complications.
Efficient Preparation of ((3‐Chloro‐2‐fluoro‐phenyl)‐[7‐methoxy‐8‐(3‐morpholin‐4‐yl‐propoxy)‐10,11‐dihydro‐5‐oxa‐2,4,11‐triaza‐dibenzo(a,d)cyclohepten‐1‐yl]‐amine) for In‐Vivo Study (2006)

Abstract An improved route for the preparation of highly functionalized 5,6‐dihydro‐pyrimido[4,5‐b][1,4]oxazepine 1a in multigram quantities was developed. This new methodology was highlighted by the proper methoxy disposition via a regioselective methylation of 2,4,5‐trihydroxy‐benzaldehyde followed by a magnesium sulfate–promoted cyclization.
Étude de propriétés électroniques de nanostructures par microscopie à force atomique sous ultra-vide (2009)

We study the electronic properties of nanostructures using atomic force microscopy in ultra-high vacuum environment. The first part of this work consists in the characterization of silicon and germanium nanowires grown by metal-catalyzed chemical vapour deposition on silicon substrates, using conducting atomic force microscopy. The electrical transport at room and low-temperature through individual nanowires has been measured as a function of the position along tilted nanowires. It is shown that the conduction properties of as-grown intrinsic silicon nanowires are dominated by the presence of gold catalyst residues along their surface, which can be either partially suppressed (e.g. by a de-oxidation step), or enhanced upon heat treatment. The second part of this work consists in studying the charge transfer and ionization properties of hydrogen-passivated phosphorus-doped and boron-doped silicon nanocrystals grown by plasma enhanced chemical vapor deposition on silicon substrates, using ultra high vacuum amplitude modulation Kelvin force microscopy. It is demonstrated that the charge transfer from silicon nanocrystals follows an energy compensation mechanism, which is enhanced by quantum confinement. The results provide a measurement of the nanocrystal conduction band-gap opening due to quantum confinement in the 2-50nm range, in agreement with parametrized tight-binding calculations. They also put forward the possibility to use doped nanocrystals as electron sources to achieve a controlled remote doping of nanostructures and devices with typical two-dimensional charge densities in the range of 2×10 11-10 14 cm-2, or linear charge densities in the range of 8×10 5-2×10 7 cm-1.
A cubic regularization algorithm for unconstrained optimization using line search and nonmonotone techniques (2016)

In recent years, cubic regularization algorithms for unconstrained optimization have been defined as alternatives to trust-region and line search schemes. These regularization techniques are based on the strategy of computing an (approximate) global minimizer of a cubic overestimator of the objective function. In this work we focus on the adaptive regularization algorithm using cubics (ARC) proposed in Cartis et al. [Adaptive cubic regularisation methods for unconstrained optimization. Part I: motivation, convergence and numerical results, Mathematical Programming A 127 (2011), pp. 245–295]. Our purpose is to design a modified version of ARC in order to improve the computational efficiency preserving global convergence properties. The basic idea is to suitably combine a Goldstein-type line search and a nonmonotone accepting criterion with the aim of advantageously exploiting the possible good descent properties of the trial step computed as (approximate) minimizer of the cubic model. Global convergence properties of the proposed nonmonotone ARC algorithm are proved. Numerical experiments are performed and the obtained results clearly show satisfactory performance of the new algorithm when compared to the basic ARC algorithm.
Organic-on-organic semiconductor heterojunctions: building block for the next generation of optoelectronic devices (1989)

A novel class of optoelectronic devices utilizing thin films of stable crystalline organic semiconductors layered onto inorganic semiconductor substrates is described. The electrical properties of these devices are determined by the energy barrier at the heterojunction contact between the organic and inorganic materials, and in many ways are similar to those of ideal diffused-junction inorganic semiconductor devices. The organic materials can be layered onto semiconductor substrates without inducing large strains in either material, hence allowing a wide range of material combinations with a similarly broad range of optoelectronic functions to be realized. As examples, high-bandwidth photodetectors and field-effect transistors made using organic/inorganic semiconductor heterojunctions are discussed. Modification of the optical and electronic properties of the organic films by irradiation with energetic electron and ion beams is considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Table 1 from TLR3 as a Biomarker for the Therapeutic Efficacy of Double-stranded RNA in Breast Cancer (2023)

Supplementary Table 1 from TLR3 as a Biomarker for the Therapeutic Efficacy of Double-stranded RNA in Breast Cancer
EGRI and FOSB gene expressions in cancer stroma are independent prognostic indicators for epithelial ovarian cancer receiving standard therapy (2011)

Stromal components interact with cancer cells to promote growth and metastasis. The purpose of this study was to identify genes expressed in stroma, which could provide prognostic information in epithelial ovarian cancer (EOC). Seventy-four patients were included. We performed gene expression profiling and confirmed array data using RT-PCR and immunohistochemistry. By microarray analysis, 52 candidate genes associated with progression free survival (PFS) were identified (P < 0.005). Expression of the early growth response 1 (EGR1) and FBJ murine osteosarcoma viral oncogene homolog B (FOSB) genes was further analyzed. Array data were confirmed by RT-PCR and multivariate analysis demonstrated that both EGR1 and FOSB expression in cancer stroma, and EGR1 expression in cancer are independent prognostic factors in EOC. Immunohistochemically, EGR1 protein is localized in cancer cells and α-smooth muscle actin positive stromal fibroblasts. The EGR1 and FOSB expression in stromal cells and EGR1 expression in cancer cells are prognostic indicators in EOC.
Experimental characterization and numerical simulations of dispersion-managed breathing-mode semiconductor mode-locked ring laser (2004)

Strong self-phase modulation (SPM) in semiconductor gain media induces nonlinear chirp impressed on propagating pulses, which can be difficult to compensate. Our approach is to employ an intracavity dispersion management scheme to decrease the detrimental effect of SPM by utilizing the concept of chirped pulse amplification inside a laser cavity. Stretching the pulse before the cavity gain element minimizes SPM and extracts energy more efficiently. The subsequently compressed pulse bleaches the semiconductor saturable absorber (SA) more easily. The breathing-mode semiconductor mode-locked ring laser regime describes how the pulse alternately experiences stretching and compression while propagating within the ring cavity.
Molecular Manipulations and Intestinal Stem Cell-Derived Organoids in Inflammatory Bowel Disease (2022)

The pathogenesis of inflammatory bowel diseases (IBD) involves genetic predisposition, environmental factors, and a broadly dysregulated intestinal immune response to the commensal intestinal microflora. The interface between genetic predisposition and environmental factors is reflected in the epigenetic regulation at the transcriptional level. Treatment targets now involve mucosal and histological healing, but the future might additionally include normalization of intestinal cellular functions also at the molecular level, for example comprising complete restoration of phenotypic, genotypic, and epigenetic states. Recent developments in patient-derived epithelial intestinal stem cell (ISC) organoid technologies have opened exciting new therapeutic opportunities to potentially attain molecular healing by combining stem cell therapy with molecular manipulations using (epi)drugs and/or CRISPR/Cas9 genome editing. Here, we are the first to discuss the possibility for phenotypic, genotypic, and epigenetic restoration via molecular manipulations and stem cell therapy in IBD from a clinical perspective.
Super-Resolution in Phase Space (2015)

This work considers the problem of super-resolution. The goal is to resolve a Dirac distribution from knowledge of its discrete, low-pass, Fourier measurements. Classically, such problems have been dealt with parameter estimation methods. Recently, it has been shown that convex-optimization based formulations facilitate a continuous time solution to the super-resolution problem. Here we treat super-resolution from low-pass measurements in Phase Space. The Phase Space transformation parametrically generalizes a number of well known unitary mappings such as the Fractional Fourier, Fresnel, Laplace and Fourier transforms. Consequently, our work provides a general super- resolution strategy which is backward compatible with the usual Fourier domain result. We consider low-pass measurements of Dirac distributions in Phase Space and show that the super-resolution problem can be cast as Total Variation minimization. Remarkably, even though are setting is quite general, the bounds on the minimum separation distance of Dirac distributions is comparable to existing methods.