gebhart/patrepeval huggingface dataset:
Complete Mitochondrial Genome of the Medicinal Mushroom Ganoderma lucidum (2013)

Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the understanding of the functions and evolution of fungal mitochondrial DNA.
Supplementary Glioma Genes from A Hypermutation Phenotype and Somatic <i>MSH6</i> Mutations in Recurrent Human Malignant Gliomas after Alkylator Chemotherapy (2023)

Supplementary Glioma Genes from A Hypermutation Phenotype and Somatic &lt;i&gt;MSH6&lt;/i&gt; Mutations in Recurrent Human Malignant Gliomas after Alkylator Chemotherapy
Patellar instability. (2014)

Patellar instability is a complex pathoanatomical phenomenon that requires an intricate understanding in order to properly treat patients. Often, the etiology of this entity is multifactorial, combining a series of physiologic and anatomic variables. A thorough history and physical as well as correct radiographic examinations are critical in both establishing the diagnosis and instituting the correct treatment. Non-operative management of recurrent instability has a high failure rate. Current operative techniques have been shown to be instrumental in correcting anatomic abnormalities, reducing symptoms of instability, and giving patients an appropriate chance of returning to their previous level of activity.
DESIGN CRITERIA FOR THE SPATIAL ORIENTATION TRAINER. (1967)

Spatial disorientation continues to cause at least 4% of the aircraft accidents in the Air Force. At the USAF School of Aerospace Medicine, the Spatial Orientation Trainer has been designed to help eliminate such accidents. The more deadly of the vestibular illusions of flight (namely, the Coriolis illusion, the oculogravic illusion, and the graveyard spin) can be reproduced and used to stress the pilot while he is performing a simulated mission in the trainer. Such exposure gives him practice in overcoming the sensory conflicts that result in disorientation and practice in proper aircraft control in spite of disorientation. The methods by which the illusions of flight are to be produced and the criteria upon which effectiveness of the trainer is to be judged are discussed in detail. (Author)
Spectral induced polarization of shaly sands: Influence of the electrical double layer (2012)

I developed a new model named POLARIS describing the complex conductivity of (pyrite‐free) shaly poorly sorted sands. This model is based on the solution given by the effective medium theory for grains coated by an electrical double layer and immersed in a background electrolyte. The electrical double layer comprises the Stern layer and the diffuse layer. Both layers play very distinct roles in the in‐phase and quadrature conductivities. The polarization of the shaly sands is mainly controlled by the polarization of the Stern layer (except at very high salinities) with a very small mobility of the counterions contained in this layer. The in‐phase component of the conductivity is controlled by the conductivity of the pore water with a contribution associated with the diffuse layer (the contribution of the Stern layer seems negligible). The fraction of counterions in the Stern layer is computed from a simple sorption isotherm and is used to infer the quadrature conductivity. The quadrature conductivity is assumed to be frequency independent, which is a reasonable approximation in clayey sands and sandstones, in agreement with observations. The polarization model is also based on the assumption that the Stern layer is discontinuous between grains, an assumption that is consistent with recent models of ionic transport in clayey sands. POLARIS explains the dependence of the quadrature conductivity on the salinity, cation exchange capacity, specific surface area (or specific surface per unit pore volume), and temperature. It can be used to predict the saturation and the permeability (inside 1 order of magnitude).
Bone Marrow Edema and Its Relation to Progression of Knee Osteoarthritis (2003)

Bone marrow edema is a potent risk factor for structural deterioration in knee osteoarthritis, and its relation to progression is explained in part by its association with limb alignment.
Etude de nanostructures metalliques resonnant dans le domaine optique, application a l'optique de champ proche (1998)

La microscopie optique en champ proche pose le probleme de l'efficacite des sondes utilisees pour l'illumination d'un echantillon ou la collection de la lumiere. Deux parametres permettant de mesurer l'efficacite d'une sonde sont mis en avant : resolution (confinement de la lumiere) et efficacite de diffraction/transmission. Un etat de l'art des sondes fait ressortir l'interet de la notion de sonde resonante. Les antennes optiques resonantes (aor), sujet de ce travail, sont des nanostructures metalliques dont les proprietes de resonance et de confinement de la lumiere sont determinees par leur geometrie. Deux types d'aor sont decrits, a savoir les antennes composees d'une seule structure isolee, et les antennes de type dipole bien connues en technologie hyperfrequence. Des modeles physiques simples ont ete utilises pour decrire la physique des resonances apparaissant dans ces structures lorsqu'elles sont realisees dans des metaux nobles. Ainsi, dans des structures simples de petites dimensions, les resonances sont dues a l'excitation d'un plasmon localise. Dans des antennes allongees, elles proviennent d'oscillations de charges suivant l'axe de l'antenne, qui resonne alors comme une cavite pour un champ electrique longitudinal. Des simulations en elements finis ont permis de montrer ces proprietes pour des geometries realistes d'antennes realisees sur un substrat dielectrique. Par ailleurs, des antennes en or ont ete realisees et caracterisees, montrant des resonances moins fortes que celles attendues ; la raison en est expliquee. Un dispositif experimental mettant en oeuvre les aor avec une methode originale d'asservissement en hauteur a ete realise. Des resolutions en intensite de /4 ont ete montrees, ainsi que l'existence d'un signal magneto-optique en champ proche. Un modele semi-analytique a ete mis en place pour comprendre la formation des images en champ proche au moyen de ce dispositif.
A Flexible Ball-End Milling System Model for Cutting Force and Machining Error Prediction (1996)

This paper presents a flexible system model for the prediction of cutting forces and the resulting machining errors in the ball-end milling process. Unlike the previously developed rigid system model, the present model takes into account the instantaneous and regenerative feedback of cutting system deflections to establish the chip geometry in the cutting force calculation algorithm. The deflection-dependent chip geometry is identified by using an iterative procedure to balance the cutting forces and the associated cutting system deflections. A series of steady state 3D cross-feed ball-end milling cuts were performed to validate the capability of the present model in predicting the cutting forces and the resulting machining errors. It is shown that the flexible system model gives significantly better predictions of the cutting forces than the rigid system model. Good agreement between the predicted and measured machining errors is demonstrated for the simple surfaces generated by horizontal cuts.
Design and synthesis of 2-(arylamino)-4(3H)-quinazolinones as novel inhibitors of rat lens aldose reductase (1986)

A number of 2-(arylamino)-4(3H)-quinazolinones (2a-i) that possess several of the pharmacophore moieties necessary for binding to the inhibitor site of the enzyme aldose reductase were synthesized and tested for their ability to inhibit crude aldose reductase obtained from rat lens. Only those quinazolinones that possess an acidic moiety on the 2-(arylamino) substituent were found to display significant inhibitory activity. Of these, the most potent compound is the 4'-CO2H derivative (2i) with an IC50 of 34 microM, while the least potent is the 4'-OH derivative (2c) with an IC50 of 75 microM. All of the 2-(arylamino)-4(3H)-quinazolinones tested are less potent than other known inhibitors of aldose reductase, such as alrestatin and sorbinil, indicating that the pharmacophore moieties present in these compounds may not be positioned optimally relative to one another for maximal interaction with the enzyme.
Stress Predictors in Nursing Students during the COVID-19 Pandemic Confinement (2022)

Background: The COVID-19 pandemic has largely impacted nursing education. Owing to the element of confinement, emergency education fostered conflicts between problems and their solutions, leading to higher stress among students. Objective: The aim of the study was to identify the determinants of perceived stress in nursing students during confinement due to the COVID-19 pandemic. Methods: This multicentric, quantitative, and cross-sectional study employed the multiple linear regression model. The study was conducted at seven nursing graduate schools in the Iberian Peninsula, with 1,058 nursing graduate students in confinement. An online questionnaire was administered to nursing students between April 23 rd and May 02 nd , 2020. According to socio-demographic data, COVID-19 experience, satisfaction with learning strategies, and coping strategies ( Brief COPE scale ) of the nursing students, the model was developed with the Perceived Stress Scale as the explained variable. Results: Stress is predictable in the form of greater coping-avoidance (b = 2.415; p &lt; .001) when a family member is infected (b = -2.354; p = .005) and in younger students (b = -.104; p = .002). It tends to be lower with higher coping-reflective (b = -2.365; p &lt; .001) and when the students have a more favourable self-perceived life (b = -1.206; p &lt; .001). Furthermore, the stress has been found to be higher in Portuguese students (b = -1.532; p &lt; .001) and women (b = 2.276; p &lt; .001) than their Spain and male counterparts, respectively. Among variables related to academics, perceived stress is higher when the students are dissatisfied with the time spent on the computer (b = 1.938) and with the evaluation methods (b = 1.448). Conclusion: Personal factors and the ease of mobilisation of the proposed training strategies affect the students’ ability to deal with stress. Emergency education should consider stress predictors so that the students can adapt to training better.
From Defense to Degree: Accelerating Degree Opportunities for Military Veterans (2020)

Abstract From Defense to Degree: Accelerating Degree Opportunities for Military VeteransThis paper is a continuation of reported progress on program development to address curricularimprovements towards integrating post-9/11 veterans into the engineering workforce. Based onthe high demand and increased opportunities for veterans in the workforce, a program has beendeveloped to acclimate and accelerate veterans into an electrical and computer engineeringdegree. The projected shortage of trained technical personnel in renewable energy and energydistribution systems areas has been the targeted initial technical focus.This paper will focus on the impact and progress made by this program with developed tools andmaterials necessary to acclimate and accelerate military veterans onto a successful path towardsbachelor degrees in engineering. First, an initial and thorough evaluation of the veterans’training, experiences, and expertise are conducted as early as possible during the admissionprocess by a trained academic advisor or faculty. Academic credit for previous academic andmilitary courses can then be assessed and granted credit where appropriate. Required coursehours already identified for consideration of assigning experiential credit include the following:Introduction to Personal and Professional Development, social science/humanities elective andone technical elective.The tools developed for this program include on-line pre-assessments and linked subject-basedtutorials to accelerate the veteran’s entry or re-entry into the traditional math sequence beginningwith Calculus I or higher. The same concept of online pre-assessment and tutorials followed bya proctored final assessment is also being developed for entry level engineering courses. In thefield of electrical engineering the course to be used for evaluation is Circuit Theory I andtherefore it’s prerequisite Introduction to Electrical Engineering. These courses present basicconcepts in electrical theory, engineering applications and an introduction to the circuitslaboratory. As in mathematics, veterans would complete an on-line pre-test with linked subjectbased tutorials ahead of enrolling in the degree program. Then veteran would have the option ofcompleting a one-time proctored post-test for course credit (C or better). This approachleverages the veterans’ existing technical knowledge acquired through the nature of their serviceposts and accelerates their entry ahead to follow-on technical courses.Student success (C or better) in Calculus 1 (or higher) and follow-on entry level engineeringcourses will be the primary evaluation metric in both cases. Students and evaluation metrics willbe tracked as individuals enter the program and reported when a significant number of metricsare accumulated.
Molecular and genetic features of a labeled class of spinal substantia gelatinosa neurons in a transgenic mouse (2005)

Genetic incorporation in a mouse of a transgene containing the prion promoter and the green fluorescent protein (GFP) coding sequence labels a set of substantia gelatinosa (SG) neurons (SG-GFP) homogenous in morphology, electrophysiology, and gamma-amino-butyric acid expression. In the present analysis the SG-GFP neurons are established to have protein kinase C-betaII immunoreactivity and to lack evidence for the presence of calbindin D-28k, parvalbumin, and protein kinase C-gamma. These neurons were hyperpolarized by mediators of descending control, norepinephrine and serotonin. Sequential polymerase chain reactions established the insertion of the transgene to be in the receptor protein tyrosine phosphatase kappa (RPTP-kappa) and the laminin receptor 1 (ribosomal protein SA) pseudogene 1 locus. RPTP-kappa expression in both GFP-labeled dorsal root ganglia and SG neurons raises the possibility that homophilic interactions of RPTP-kappa contribute to establishment of connections between specific classes of primary afferent and SG neurons.
Data from Brain-Derived Neurotrophic Factor Promotes Tumorigenesis via Induction of Neovascularization: Implication in Hepatocellular Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Brain-derived neurotrophic factor (BDNF) has emerged as a novel angiogenic factor, and yet its impact on tumorigenesis is unclear. This study aimed at investigating the roles of BDNF in angiogenesis and tumor development.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; BDNF was overexpressed in a mouse endothelial cell (EC) line by stable transfection, and angiogenic properties of the transfectants were assessed. Microarray analysis was employed to explore the molecular pathways. The impact of modulating BDNF levels in two mouse EC lines on tumorigenic potential of a transformed mouse liver cell line was evaluated by an &lt;i&gt;in vivo&lt;/i&gt; cotransplantation model. BDNF and tropomyosin receptor kinase B (TrkB) protein levels were determined in 50 pairs of human hepatocellular carcinoma (HCC) tissues by Western blotting and immunohistochemistry. Survival analysis was carried out to determine their clinical significance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Overexpression of BDNF could promote EC proliferation, migration, invasion, and survival. Microarray and molecular studies showed that RhoA, caspase-9, caspase-3, growth arrest specific 6, and VEGF could mediate BDNF/TrkB-induced angiogenesis. The cotransplantation experiment showed that high BDNF-expressing ECs could facilitate tumor angiogenesis and growth, whereas knockdown of BDNF by short hairpin RNAs impaired such effects. Furthermore, examination on human HCC tissues revealed upregulation of BDNF and TrkB protein levels in 46.0% and 33.3% of the cases studied, respectively. Immunohistochemistry disclosed strong BDNF reactivity in both tumor and endothelial cells. High TrkB expression was associated with shorter overall survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; BDNF/TrkB system was crucial for tumor angiogenesis and growth, which may represent a potential target for antiangiogenic therapy in HCC. &lt;i&gt;Clin Cancer Res; 17(10); 3123–33. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Optimal Transport for Unsupervised Hallucination Detection in Neural Machine Translation (2023)

International audience
FPGA-based Optical Kerr Effect Emulator (2022)

We propose a digital emulator of the optical Kerr effect, suitable for FPGA implementation. In addition, we study a combined PMD and Kerr emulator implementation with respect to DSP hardware aspects such as fixed-point performance.
Transcatheter Arterial Embolization for Pelvic Fractures May Potentially Cause a Triad of Sequela: Gluteal Necrosis, Rectal Necrosis, and Lower Limb Paresis (2008)

Suzuki, Takashi MD; Kataoka, Yuichi MD; Minehara, Hiroaki MD; Nakamura, Kousin MD; Uchino, Masataka MD; Kawai, Kohsei MD; Soma, Kazui MD Author Information
Targeting of drugs 2 : optimization strategies (1990)

Biological Dispersion and the Design of Site-Specific Protein Therapeutic Systems.- Recombinant Ligand-Toxin Conjugates, Domain Engineering and the Search for Targeted Pharmaceuticals.- Extravascular Diffusion and Convection of Antibodies in Tumors.- Antitumor Effects of Six Ricin A-Chain Immunotoxins of Potential Use in the Treatment of Hodgkin's Disease.- Enhancement of Hormone Activity by Monoclonal Antibodies.- Modeling of Cell Membrane Targeting: Specific Recognition, Binding and Protein Domain Formation in Ligand- Containing Model Biomembranes.- Endocytosis of Cell Surface Molecules and Intracellular Delivery of Materials Encapsulated in Targeted Liposomes.- Tissue Specific Serum Opsonins and Phagocytosis of Liposomes.- Liposome Targeting to Tumor Cells In Vivo.- Stabilization of Lipid Microstructures: Fundamentals and Applications.- Non-Ionic Surfactant Vesicles as Carriers of Doxorubicin.- Targeted Therapy of Liver Carcinoma.- Drug Delivery Systems: The Industrial View.- Controlled Delivery to the Brain.- Polymeric Delivery Systems.- Participants Photograph.- Contributors.
Cell penetrating peptide decorated magnetic porous silicon nanorods for glioblastoma therapy and imaging (2022)

Glioblastoma multiforme (GBM) is the most malignant primary brain tumor of the central nervous system. Despite advances in therapy, it remains largely untreatable, in part due to the low permeability of chemotherapeutic drugs across the blood-brain barrier (BBB) which significantly compromises their effectiveness. To circumvent the lack of drug efficiency, we designed multifunctional nanoparticles based on porous silicon. Herein, we propose an innovative synthesis technique for porous silicon nanorods (pSiNRs) with three-dimensional (3D) shape-controlled nanostructure. In order to achieve an efficient administration and improved treatment against GBM cells, a porous silicon nanoplatform is designed with magnetic guidance, fluorescence tracking and a cell-penetrating peptide (CPP). A NeuroFilament Light (NFL) subunit derived 24 amino acid tubulin binding site peptide called NFL-TBS.40-63 peptide or NFL-peptide was reported to preferentially target human GBM cells compared to healthy cells. Motivated by this approach, we investigated the use of magnetic-pSiNRs covered with superparamagnetic iron oxide nanoparticles (SPIONs) for magnetic guidance, then decorated with the NFL-peptide to facilitate targeting and enhance internalization into human GBM cells. Unexpectedly, under confocal microscope imaging, the internalized multifunctional nanoparticles in GBM cells induce a remarkable exaltation of green fluorescence instead of the red native fluorescence from the dye due to a possible Förster resonance energy transfer (FRET). In addition, we showed that the uptake of NFL-peptide decorated magnetic-pSiNRs was preferential towards human GBM cells. This study presents the fabrication of magnetic-pSiNRs decorated with the NFL-peptide, which act as a remarkable candidate to treat brain tumors. This is supported by <i>in vitro</i> results and confocal imaging.
Electrochemistry in Nanovials Fabricated by Combining Screen Printing and Laser Micromachining (1999)

The coupling of screen-printing and laser micromachining technology has been used to create a nanovial with "built-in" working and reference electrodes. The volume of the nanovial was calculated to be 7.2 nL using dimensions determined by SEM. The electrochemical nanovial was characterized using the ferri/ferrocyanide redox couple. Cyclic voltammetry and chronoamperometry experiments were performed with electrochemical nanovials utilizing 5% (v/v) glycerin in the solutions and a humidified headspace to control evaporation of the small-volume samples. Chronoamperometry experiments gave results consistent with a diffusion-limited process and revealed a working electrode surface area of 2.6 x 10(4) micron 2. The ultrasmall-volume cells represent a simple, reliable, low-cost approach for the fabrication of complete electrochemical nanovials.