gebhart/patrepeval huggingface dataset:
Combination of human tau and islet amyloid polypeptide exacerbates metabolic dysfunction in transgenic mice (2021)

Amyloid plaques and neurofibrillary tangles composed of hyperphosphorylated tau are important contributors to Alzheimer's disease (AD). Tau also impacts pancreatic beta cell function and glucose homeostasis. Amyloid deposits composed of islet amyloid polypeptide (IAPP) are a pathological feature of type 2 diabetes (T2D). The current study investigates the role of human tau (hTau) in combination with human IAPP (hIAPP) as a potential mechanism connecting AD and T2D. Transgenic mice expressing hTau and hIAPP in the absence of murine tau were generated to determine the impact of these pathological factors on glucose metabolism. Co-expression of hIAPP and hTau resulted in mice with increased hyperglycaemia, insulin resistance, and glucose intolerance. The hTau-hIAPP mice also exhibited reduced beta cell area, increased amyloid deposition, impaired insulin processing, and reduced insulin content in islets. Tau phosphorylation also increased after stimulation with high glucose. In addition, brain insulin content and signalling were reduced, and tau phosphorylation was increased in these animals. These data support a link between tau and IAPP amyloid, which seems to act co-ordinately to impair beta cell function and glucose homeostasis, and suggest that the combined pathological actions of these proteins may be a potential mechanism connecting AD and T2D. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Potential SARS-CoV-2 Immune Correlates of Protection in Infection and Vaccine Immunization (2021)

Both SARS-CoV-2 infections and vaccines induce robust immune responses. Current data suggested that high neutralizing antibody titers with sustained Th1 responses might correlate with protection against viral transmission and disease development and severity. In addition, genetic and innate immune factors, including higher levels of type I interferons, as well as the induction of trained immunity and local mucosal immunity also contribute to lower risk of infection and amelioration of disease severity. The identification of immune correlates of protection will facilitate the development of effective vaccines and therapeutics strategies.
Effect of low molecular weight heparin and different heparin molecular weight fractions on the activity of the matrix‐degrading enzyme aggrecanase: Structure–function relationship (2005)

The matrix-degrading enzyme aggrecanase has been identified in cartilage and is largely responsible for cartilage breakdown. The present study determined the efficacy of different heparin molecular weight fractions (HMWFs) and low molecular weight heparins (LMWHs) on aggrecanase activity. Aggrecanase activity was determined using biotinylated peptide substrate, which was immobilized onto streptavidin-coated 96-well plates; aggrecanase enzyme was then added. Proteolysis of the substrate at the specific amide bond was detected using specific antibody for the neoepitope generated. HMWFs ranging from 1,700 to 12,000 Da demonstrated a concentration-dependent inhibitory efficacy of aggrecanase activity, with a Ki ranging from 5,000 nM down to 1 nM as a function of the molecular weight. The higher the molecular weight distribution, the greater the inhibitory efficacy of the heparin fragments toward aggrecanase activity. The absence or presence of antithrombin did not alter the affinity of heparin in inhibiting aggrecanase. Additionally, tissue factor pathway inhibitor at various levels did not alter the activity of aggrecanase. LMWHs demonstrated different levels of potency in inhibiting aggrecanase activity as a function of their average molecular weight distribution. Tinzaparin (average molecular weight = 6,500 Da) and enoxaparin (average molecular weight = 4,500 Da) demonstrated a Ki of 20 and 80 nM, respectively. The aggrecanase inhibitory effect of LMWH might contribute to blocking inflammation and tumor invasion by inhibiting aggrecanase activity and maintaining an intact extracellular matrix barrier.
Efficient selection of focusing optics in non linear microscopy design trough THG analysis (2004)

International audience
Procedure for Organizing a Post-FDA-approval Evaluation of Antidepressants (2022)

We present a procedure for constructing a cohort using claims data. A surrogate measure for self-reported symptom remission based on the patterns of use of antidepressants has been proposed to address the absence of outcomes in claims. Future studies can use the procedures described here to organize studies of the comparative effectiveness of antidepressants.
A Direct Linear Reconstruction Method for Spectrally Resolved 3D Bioluminescence Tomography (2006)

Spectrally-resolved BioLuminescence optical Tomography (sBLT) is used to recover images of Luciferase activity within a 3D mouse model using multi-wavelength emission data from multiple internal bioluminescence sources. The images show that the location of sources can be reconstructed accurately using a fast, direct and linear reconstruction algorithm.
Catalogue des Ascomycètes récoltés dans la Loire. 1er addendum (2010)

This note is the first addendum to the check-list of Ascomycetes collected in the French department of Loire, previously published in the Bulletin mensuel de la Société linnéenne de Lyon, with the late Antoine Ayel. It has been written due to new collections made during mycological sessions organized in this department in 2008 and 2010
Molecular dynamics simulations of sliding friction of Langmuir–Blodgett monolayers (1996)

Molecular dynamics simulations have been used to study friction in Langmuir–Blodgett monolayers of perfluorocarboxylic acid and hydrocarboxylic acid on SiO2. The frictional force of perfluorocarboxylic acid is found to be about three times as large as that of hydrocarboxylic acid. The qualitative aspects of this simulation results are consistent with known experimental results. In order to interpret the difference in the frictional force, a series of simulations have been carried out by changing molecular potential parameters. The simulation results suggest that the 1–4 van der Waals interaction is the main cause of the larger frictional force for perfluorocarboxylic acid than that for hydrocarboxylic acid. The results also show that frictional force is roughly proportional to the excess root mean square fluctuation of the potential energy under shear from the equilibrium. The relation between the frictional force and the energy needed for molecular deformation under shear condition is also discussed.
Binocular Photometric Stereo (2011)

This paper considers the problem of computing scene depth from a stereo pair of cameras under a sequence of illumination directions. By integrating parallax and shading cues, we obtain both metric depth and fine surface details. Casting this problem into the filter flow framework [16], enables a convex formulation of the problem, and thus a globally optimal solution. We demonstrate high quality, continuous depth maps on a range of examples.
Variable plant spacing (1988)

The goal of this project was to develop a system for varying the spacings between soybean plants as they grow to maximize the number of plants grown in a given volume. The project was studied to aid in the development of NASA's Controlled Ecological Life Support System (CELSS). The resulting design consists of plant trays which are three dimensional trapezoids arranged into circles in a compact geometrical configuration. These circles are stacked together in back to back pairs to form a long cylinder. In each growth tray, plants will be housed in individual containers containing a nutrient delivery system and a plant support mechanism. Between the containers, a half trellis has been designed to space the plants for maximum space efficiency. The design allows for localized seeding and harvesting mechanisms due to the chambers' geometrical configuration. In addition, the components have been designed for ease of cleaning and minimal maintenance. Next semester, the individual components will be constructed and tested to determine the success of the design.
Characterization of a cystathionine β-synthase allele with three mutations in cis in a patient with B6 nonresponsive homocystinuria (1994)

We used SSCP to survey reverse transcribed-PCR amplified cystathionine synthase cDNAs from patients with homocystinuria. In a single CBS allele, we identified one synonymous and two missense mutations in a portion of the cDNA encoded by a single 135 bp exon which also encodes K119, the putative site of cofactor, pyridoxal 5'-phosphate, binding. The patient, a B6-nonresponsive homocystinuric of Irish descent, is homozygous for a G-->A transition at cDNA position 374, a G-->A transversion at position 393, and a G-->A transition at position 453 resulting in R125Q, E131D and P145P, respectively. Family studies confirmed that all three mutations are present in cis and none were present in 54 Irish and 58 North American controls. R125 is conserved in rat CBS while E131D is conserved in rat CBS, and a related enzyme, O-acetylserine(thiol)-lyase, from a variety of plant and bacterial species. Expression studies showed that both R125Q and E131D, either individually or together, inactivate CBS. The apparently simultaneous appearance of more than one mutation in a single exon suggests they may have arisen by a gene conversion event or by nonhomologous recombination.
Aberrant B1 cell migration into the thymus results in activation of CD4 T cells through its potent antigen‐presenting activity in the development of murine lupus (2004)

B1 cells have different origin and function from conventional B (B2) cells and are considered to be involved in autoantibody production in the development of autoimmune disease. We found that B1 cells preferentially accumulated in the target organs including thymus in aged BWF1 mice, a murine model for systemic lupus erythematosus, and that B lymphocyte chemoattractant (BLC/CXCL13) expression was increased in the thymus before the onset of lupus nephritis, while stromal cell-derived factor-1 (SDF-1/CXCL12) and secondary lymphoid tissue chemokine (SLC/CCL21) expression remained unchanged. Adhesion molecules such as peripheral node addressin (PNAd), ICAM-1, and VCAM-1 were also expressed on endothelial cells in the enlarged thymic perivascular space (PVS) in aged BWF1 mice. BLC protein and PNAd were co-localized on these high-endothelial-venules-like vessels in enlarged PVS. B1 cells expressed higher level of costimulatory molecules and showed a potent antigen-presenting activity in allogeneic mixed lymphocyte reaction comparable to splenic dendritic cells. Interestingly, B1 cells stimulated proliferation of autologous thymic CD4 T cells in the presence of IL-2. These results indicate that aberrant B1 cell trafficking into the thymus due to ectopic high expression of BLC may result in an activation of self-reactive T cells in the development of murine lupus.
Phase-change Optical Disk with Nitride Interface Layers (1998)

Our DVD-RAM/2.6GB was just commercialized in this year. Today, our R/D activities are aimed toward the next generation of DVD-RAM media and even the generation beyond that. We are striving to achieve higher recording density, a higher data transfer rate and higher reliability (cyclability). Through our study, we have found that a nitride interface layer was very effective for increasing the performance of phase-change optical disks. In this paper, we will present a new disk structure having Ge-N layers at the interface between the Ge-Sb-Te active layer and the ZnS-SiO 2 protective layers. The effects of the nitride layer and the disk performance will also be described.
8x8 Programmable Many-Mode Interferometer Operating with Visible-Wavelength Piezo-Cantilever Modulators (2021)

We report a visible-wavelength, programmable 8x8 many-mode interferometer based on silicon nitride waveguides and piezo-cantilever optical phase-shifters with sub 1-μs response times to address applications in photonics and quantum technologies.
Molecular Detection of Targeted Major Histocompatibility Complex I-Bound Peptides Using a Probabilistic Measure and Nanospray MS3 on a Hybrid Quadrupole-Linear Ion Trap (2010)

A nanospray MS(3) method deployed on a quadrupole linear ion trap hybrid can detect targeted peptides with high dynamic range and high sensitivity from complex mixtures without separations. The method uses a recognition algorithm that is a modification of the relative (Kullback-Leibler, KL) entropy characterization of probabilistic distance to detect if reference MS(3) fragmentation patterns are components of acquired MS(3) spectra. The recognition reflects the probabilistic structure of physical MS measurements unlike the Euclidean or inner product metrics widely used for comparing spectra. It capably handles spectra with a significant chemical ion background in contrast to the Euclidean metric or the direct relative entropy. The full nanospray MS(3) method allows both the detection and quantitation of targets without the need to obtain isotopically labeled standards. By avoiding chromatographic separations and its associated surface losses, the detection can be applied to complex samples on a very limited material scale. The methodology is illustrated by applications to the medically important problem of detecting targeted major histocompatibility complex (MHC) I associated peptides extracted from limited cell numbers.
In vivo persistence of expanded clones specific for bacterial antigens within the human T cell receptor alpha/beta CD4-8- subset. (1993)

We analyzed the T cell receptor (TCR) rearrangements of 100 TCR-alpha/beta CD4-CD8- (double negative [DN]) T cell clones from normal individuals. We found that in four out of six donors this subset contains expanded clones that often account for 0.5% and, in one individual, even 7% of all peripheral blood lymphocytes. By combining limiting dilution analysis and N region oligotyping of polymerase chain reaction amplified TCR cDNA, we could measure the clonal size and show that two of these expanded clones remain stable in size for up to 4 yr in peripheral blood. The expanded clones analyzed ex vivo are not cycling and CD45 RAhi ROlo, but express high levels of alpha 4/beta 1 integrins, suggesting that they may have reverted to resting cells after activation. One of these expanded DN clones proliferates in vitro in response to Escherichia coli presented by monocytes cultured in GM-CSF plus IL-4 and kills CD1a+ Molt-4 cells. In contrast to what was found in the alpha/beta DN subset, alpha/beta CD4+ T cell clones specific for a tetanus toxin epitope showed a very small clonal size (< 1 in 10(7)) and could not be reisolated after 2 yr. Taken together, these results indicate that large clonal size and persistence are distinctive features of alpha/beta DN cells specific for bacterial antigens. These cells may use antigen-presenting cells, restriction molecules, and selection routes different from those used by antigen-specific CD4+ T cells.
Exploring the mechanism of BK polyomavirus-associated nephropathy through consensus gene network approach (2023)

BK polyomavirus-associated nephropathy occurs in kidney transplant recipients under immunosuppressive treatment. BK polyomavirus is implicated in cancer development and invasion, and case reports of renal cell carcinoma and urothelial carcinoma possibly associated with BK polyomavirus has been reported. Further, it has been suggested that the immune responses of KT-related diseases could play a role in the pathogenesis and progression of renal cell carcinoma. Thus, we thought to examine the relationship between BK polyomavirus-associated nephropathy and renal cell carcinoma in terms of gene expression. To identify the common and specific immune responses involved in kidney transplantation-related diseases with a specific focus on BK polyomavirus-associated nephropathy, we performed consensus weighted gene co-expression network analysis on gene profile datasets of renal biopsy samples from different institutions. After the identification of gene modules and validation of the obtained network by immunohistochemistry of the marker across kidney transplantation-related diseases, the relationship between prognosis of renal cell carcinoma and modules was assessed. We included the data from 248 patients and identified the 14 gene clusters across the datasets. We revealed that one cluster related to the translation regulating process and DNA damage response was specifically upregulated in BK polyomavirus-associated nephropathy. There was a significant association between the expression value of hub genes of the identified cluster including those related to cGAS-STING pathway and DNA damage response, and the prognosis of renal cell carcinoma. The study suggested the potential link between kidney transplantation-related diseases, especially specific transcriptomic signature of BK polyomavirus associated nephropathy and renal cell carcinoma.
l-Arabinose suppresses gluconeogenesis through modulating AMP-activated protein kinase in metabolic disorder mice (2020)

l-Arabinose is a kind of plant-specific five-carbon aldose with benefits in type 2 diabetes mellitus. It has been shown to have good properties in improving glucose homeostasis, but the underlying molecular mechanisms are still not clear. Hepatic gluconeogenesis is critical for regulating glucose homeostasis. Here, this study aimed to investigate whether l-arabinose could improve glucose metabolism via suppressing hepatic gluconeogenesis. High-fat-high-sucrose diet (HFHSD) or high-sucrose diet (HSD)-fed mice were supplemented with or without l-arabinose for 12 weeks. Fasting blood glucose levels were measured and glucose tolerance test and the histological analysis were performed after l-arabinose administration. AMP-activated protein kinase (AMPK), acetyl-CoA carboxylase (ACC), peroxisome proliferator activated receptor-γ coactivator-1α (PGC1α), Forkhead box O1 (FoxO1), phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) expression levels were determined by RT-PCR and western blotting. As expected, l-arabinose apparently decreased body weight and attenuated hyperglycemia and glucose intolerance caused by HFHSD or HSD. l-Arabinose also had beneficial effects on glycogen synthesis by inactivating GSK3β. The expression levels of gluconeogenic genes were all decreased by l-arabinose administration in vivo and in vitro. In addition, our work revealed that AMPK is required for the inhibitory effects of l-arabinose on hepatic gluconeogenesis. l-Arabinose significantly up-regulated the phosphorylated levels of AMPK and its downstream protein ACC. Furthermore, blocking AMPK signaling through an inhibitor (compound C) or siAMPK significantly attenuated the inhibition of hepatic gluconeogenesis and the promotion of glycogen synthesis with l-arabinose, indicating that the inhibitory effect of l-arabinose on hepatic gluconeogenesis was AMPK dependent. Our work revealed that l-arabinose is a promising natural product for the regulation of hyperglycemia through inhibition of hepatic gluconeogenesis by activating AMPK.
Fatigue Fractures of Thompson Prostheses A Clinical and Biomechanical Study of Revision Procedures (1982)

In four patients with fatigue fractures of Thompson prostheses, all had been in place for more than five years. All the patients were very active following the original operative procedure. Radiographs showed a varus position of the implant in three of the four patients, and the proximal fragment appeared loose; this was confirmed at revision operation. The distal fragment was rigidly held, and was only removed after the femoral shaft had been fenestrated. If a window had been cut in the shaft of the femur, the bone was considerably weakened. This clinical impression was confirmed by cadaver studies, which revealed that a lateral window weakens the femur more than an anterior window. For revision operations, replacement with a long-stemmed prosthesis is desirable. This protects the weakened segment of the femur, and provides sufficient strength for immediate weight-bearing.
Moving Frailty Toward Clinical Practice: NIA Intramural Frailty Science Symposium Summary (2019)

Frailty has long been an important concept in the practice of geriatric medicine and in gerontological research, but integration and implementation of frailty concepts into clinical practice in the United States has been slow. The National Institute on Aging (NIA) Intramural Research Program and the Johns Hopkins Older Americans Independence Center sponsored a symposium to identify potential barriers that impede the movement of frailty into clinical practice and to highlight opportunities to facilitate the further integration of frailty into clinical practice. Primary and subspecialty care providers, and investigators working to integrate and translate new biological aging knowledge into more specific preventive and treatment strategies for frailty provided the meeting content. Recommendations included a call for more specific language that clarifies conceptual differences between frailty definitions and measurement tools; the development of randomized controlled trials to test whether specific intervention strategies for a variety of conditions differently affect frail and non-frail individuals; development of implementation studies and therapeutic trials aimed at tailoring care as a function of pragmatic frailty markers; the use of deep learning and dynamic systems approaches to improve the translatability of findings from epidemiological studies; and the incorporation of advances in aging biology, especially focused on mitochondria, stem cells, and senescent cells, toward the further development of biologically targeted intervention and prevention strategies that can be used to treat or prevent frailty. J Am Geriatr Soc 67:1559-1564, 2019.
A study on error reduction of joint torque estimation using wearable sensor system (2020)

This study aims to error reduction in estimation of joint torque using wearable sensor system. The wearable sensor system consists of wearable motion sensor installing the inertial and magnetic field sensors and wearable force plate installing several compact force sensors and inertial and magnetic field sensors. The wearable motion sensor outputs the angular velocity, the acceleration, and magnetic field, and the wearable force plate outputs the 6-axis force components and the motion sensor output. We conducted the measurement experiment of gait analysis using the wearable sensor system and the optimal motion capture system. We established the compensation method of error reduction in the effect by attaching on skin and clothes. This method was assumed the effect of error elements by using the spring and damping elements. We compared the posture information of knee joint in the results of without compensation and with compensation. The analytical results of the Roll angle indicated the effectiveness of this method.