gebhart/patrepeval huggingface dataset:
Label-Free and Enzyme-Free Homogeneous Electrochemical Biosensing Strategy Based on Hybridization Chain Reaction: A Facile, Sensitive, and Highly Specific MicroRNA Assay (2015)

Homogenous electrochemical biosensing strategies have attracted substantial attention, because of their advantages of being immobilization-free and having rapid response and improved recognition efficiency, compared to heterogeneous biosensors; however, the high cost of labeling and the strict reaction conditions of tool enzymes associated with current homogeneous electrochemical methods limit their potential applications. To address these issues, herein we reported, for the first time, a simple label-free and enzyme-free homogeneous electrochemical strategy based on hybridization chain reaction (HCR) for sensitive and highly specific detection of microRNA (miRNA). The target miRNA triggers the HCR of two species of metastable DNA hairpin probes, resulting in the formation of multiple G-quadruplex-incorporated long duplex DNA chains. Thus, with the electrochemical indicator Methylene Blue (MB) selectively intercalated into the duplex DNA chain and the multiple G-quadruplexes, a significant electrochemical signal drop is observed, which is dependent on the concentration of the target miRNA. Thus, using this "signal-off" mode, a simple, label-free and enzyme-free homogeneous electrochemical strategy for sensitive miRNA assay is readily realized. This strategy also exhibits excellent selectivity to distinguish even single-base mismatched miRNA. Furthermore, this method also exhibits additional advantages of simplicity and low cost, since both expensive labeling and sophisticated probe immobilization processes are avoided. Therefore, the as-proposed label-free and enzyme-free homogeneous electrochemical strategy may become an alternative method for simple, sensitive, and selective miRNA detection, and it has great potential to be applied in miRNA-related clinical diagnostics and biochemical research.
Supplementary Table 1 from Enumeration and Molecular Characterization of Tumor Cells in Lung Cancer Patients Using a Novel <i>In Vivo</i> Device for Capturing Circulating Tumor Cells (2023)

&lt;p&gt;Supplementary Table 1. Additional table showing summarized patient data correlated to the appearance of CTCs.&lt;/p&gt;
Evaluation of Planar-Type Thin Film ZnO Varistors Fabricated Using Pulsed Laser Ablation (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Control of hepatitis B in China: prevention and treatment (2010)

A high rate of chronic HBV infection in China is mainly the result of perinatal or early childhood transmission. Therefore, universal vaccination against HBV in infants has been very successful in the control of chronic HBV infection, with the prevalence of hepatitis B surface antigen decreasing from nearly 10% to approximately 7% in the general population. Adoption of Good Clinical Practice and proper conduction of well-designed clinical trials on conventional and pegylated interferons and nucleos(t)ide analogs have generated important clinical data. The publication and promotion of the evidence-based national guidelines have greatly improved the standard of clinical practice on the prevention and treatment of chronic hepatitis B. The ongoing national key scientific projects on the optimization of vaccination strategy and current anti-HBV therapy will yield important clinical evidence. Inclusion of conventional and pegylated interferons and nucleos(t)ides into the new national reimbursement list will increase the availability and affordability of anti-HBV therapies, thereby further decreasing the morbidity and mortality associated with chronic HBV infection.
INJURIES OF THE URINARY TRACT DUE TO EXTERNAL TRAUMA (1960)

Early examination and accurate diagnosis in urinary tract injuries are essential to obtain best results from treatment. Extravasation of urine must be prevented or treated immediately. Roentgenographic studies are usually necessary. Of 13 patients with straddle injuries in a five-year period, 11 were treated without surgery, while perineal repair was necessary in only one. Urethrography was needed for diagnosis in but one case. Insertion of an indwelling catheter sufficed for 14 patients with injuries of the pendulous urethra. Thirteen of 15 patients with ruptured or transected injuries of posterior urethra required surgery. All but one of 54 patients with bladder injuries required surgery. Five ureteral injuries caused by gunshot wounds were repaired and splinted with good results. Of 126 patients with renal injuries, 62 were treated with conservative measures. The others required surgery.
Methods and tools for performance evaluation and validation of vehicle-roadside communications proposed for standardization (2002)

Analytical methods as well as the simulative tools developed for the performance evaluation and validation of the dedicated vehicle roadside short-range communication (DSRC) protocols proposed for standardization in Europe (CEN/TC278/WG9) and in North America are presented. First, the basic concept of the medium access control protocol for vehicles entering the communication zone of a roadside beacon is described. Then, the analytical methods and tools (MARCO) for medium access using new multilevel Markov chain models are presented, in which the dynamic arrival of up to n vehicles and the completion of the full transaction (AFC, automatic fee collection) is taken into account. Furthermore, the characteristics of the two simulative tools SIMCO-F/DSRC and SIMCO3++/DSRC are described. These tools are validated by comparison of the analytical results of the MARCO tool with the results of the simulative tools. Finally, the disadvantages, advantages and recommended usage of these methods and tools for the validation of the dedicated vehicle-roadside short-range communications as well as for the DSRC system calibration are discussed.
Volumetric faults in field-sized reservoir simulation models: A first case study (2016)

Conduit fault zones and fault zones that can accommodate long-distance along-fault flow are well-documented phenomena. In reservoir simulation models, flow within these features is more correctly captured using volumetric representations of fault zones instead of employing standard two-dimensional fault planes. The present study demonstrates a method for generating fault envelope grids on full-field reservoir models, within which fault cores (i.e., regions where most of fault zone displacement is accommodated) are modeled. The modeled fault core elements are lenses and slip zones. They are defined as facies units and populated in the fault envelope grids using combined object-based simulation and deterministic techniques. Using the facies property, four reservoir simulation models are generated by modulating fault core thickness and slip zone type and permeability. Membrane slip zones (slip zones that act as partial barriers to fluid flow) cause the fault cores to form baffle–conduit systems. Along-strike positioned injector–producer pairs focus flow into the fault cores, decreasing sweep efficiency. In contrast, injected fluids of injector–producer pairs positioned to drain perpendicular to the fault cores are partitioned and distributed by the fault cores and therefore increase overall sweep efficiency. In reservoir models with conduit slip zones (slip zones that enhance flow along them and act as partial barriers to flow across them), the fault cores act as thief zones. Fluids preferentially move through the fault cores toward the nearby producers instead of through sedimentary layers with high permeability. Sweep efficiency in the reservoir models with conduit fault cores has less dependency on injector–producer configuration. Our study suggests that the improved realism added by incorporating volumetrically expressed fault cores substantially influences forecasts of field behavior and consequently should be considered during oil and gas production planning.
Mechanisms of progression of chronic kidney disease (2007)

Chronic kidney disease (CKD) occurs in all age groups, including children. Regardless of the underlying cause, CKD is characterized by progressive scarring that ultimately affects all structures of the kidney. The relentless progression of CKD is postulated to result from a self-perpetuating vicious cycle of fibrosis activated after initial injury. We will review possible mechanisms of progressive renal damage, including systemic and glomerular hypertension, various cytokines and growth factors, with special emphasis on the renin-angiotensin-aldosterone system (RAAS), podocyte loss, dyslipidemia and proteinuria. We will also discuss possible specific mechanisms of tubulointerstitial fibrosis that are not dependent on glomerulosclerosis, and possible underlying predispositions for CKD, such as genetic factors and low nephron number.
Hepatocyte injury in tyrosinemia type 1 is induced by fumarylacetoacetate and is inhibited by caspase inhibitors (1998)

Tyrosinemia type 1, caused by mutations in the fumarylacetoacetate hydrolase gene (Fah), is characterized by severe liver injury. We earlier developed a tyrosinemic mouse model with two genetic defects, Fah and 4-hydroxyphenylpyruvate dioxygenase (Hpd) deficiencies. Apoptosis of hepatocytes was induced and an acute onset of liver failure occurred after administration of homogentisic acid (HGA), the intermediate metabolite between the enzymes HPD and FAH. Cytochrome c was released from mitochondria prior to liver failure in the Fah-/- Hpd-/- double-mutant mice after the administration of HGA. In a cell-free system, the addition of fumarylacetoacetate induced the release of cytochrome c from the mitochondria. We also found that caspase inhibitors were highly effective in preventing the liver failure induced by HGA in the double-mutant mice. Therefore, fumarylacetoacetate apparently induces the release of cytochrome c, which in turn triggers activation of the caspase cascade in hepatocytes of subjects with hereditary tyrosinemia type 1.
Design and Processing of Novel Ceramic Composite Structures for Use in Medical Surgery (2017)

International audience
Malicious UAV Detection Using Integrated Audio and Visual Features for Public Safety Applications (2020)

Unmanned aerial vehicles (UAVs) have become popular in surveillance, security, and remote monitoring. However, they also pose serious security threats to public privacy. The timely detection of a malicious drone is currently an open research issue for security provisioning companies. Recently, the problem has been addressed by a plethora of schemes. However, each plan has a limitation, such as extreme weather conditions and huge dataset requirements. In this paper, we propose a novel framework consisting of the hybrid handcrafted and deep feature to detect and localize malicious drones from their sound and image information. The respective datasets include sounds and occluded images of birds, airplanes, and thunderstorms, with variations in resolution and illumination. Various kernels of the support vector machine (SVM) are applied to classify the features. Experimental results validate the improved performance of the proposed scheme compared to other related methods.
Transport and confinement in toroidal devices : 2nd Workshop on Magnetic Confinement Fusion, Santander, Spain, 2-6 July 1990 (1992)

Neoclassical transport in torroidal systems, H. Wobig recent results on confinement in JET, D.J. Campbell basic concepts of fully developed turbulence, P.W. Terry and P.H. Diamond microinstabilities and anomalous transport, J.W. Connor resistive MHD turbulence, B.A. Carreras edge turbulence, A.J. Wootton measurement of fluctuations in the plasma edge - particularly on ATF, C. Hidalgo measurements of fluctuations by reflectometry, J. Sanchez transport and fluctuations in reversed field pinches, S.C. Prager stellarator review, C. Alejaldre transport in the boundary layer of tokamaks, G.M. McCracken recent developments in the theory and simulation of trapped ion convective cell turbulence, D.E. Newman et al effect of the radial electric field on turbulence, B.A. Carreras and V.E. Lynch transport studies needed for next step devices, F. Engelmann.
Secreted ORF8 is a pathogenic cause of severe COVID-19 and is potentially targetable with select NLRP3 inhibitors (2021)

ABSTRACT COVID-19 is a significant cause of morbidity and mortality in blood cancer patients, especially those on immunosuppressive therapy. Despite extensive research, the specific factor associated with SARS-CoV-2 infection that mediates the life-threatening inflammatory cytokine response in patients with severe COVID-19 remains unidentified. Herein we demonstrate that the virus-encoded Open Reading Frame 8 (ORF8) protein is abundantly secreted as a glycoprotein in vitro and in symptomatic patients with COVID-19. ORF8 specifically binds to the NOD-like receptor family pyrin domain-containing 3 (NLRP3) in CD14 + monocytes to induce a non-canonical inflammasomal response, and a canonical response when the second activation signal is present. Levels of ORF8 protein in the blood correlate with severity and disease-specific mortality in patients with acute SARS-CoV-2 infection. Furthermore, the ORF8-induced inflammasome response was readily inhibited by the NLRP3 inhibitor MCC950 in vitro . Our study identifies a dominant cause of pathogenesis, its underlying mechanism, and a potential new treatment for severe COVID-19. Key points Secreted glycoprotein ORF8 induces monocytic pro-inflammatory cytokines involving the activation of the NLPR3 inflammasome pathway. ORF8 is prognostically present in the blood of symptomatic patients with covid-19 and is targetable with NLRP3 inhibitor MCC-950.
Clonal Abnormalities in MSC Derived from AML Bone Marrows (2008)

Abstract Bone marrow-derived mesenchymal stem cells (BM-MSC) have the capacity to differentiate into various cell types in specific conditions, to support normal and malignant hematopoiesis and protect leukemic cells from chemotherapy. However, little is known about the molecular genetics and cytogenetics of these cells. In this study, we established and expanded BM-MSC from bone marrow of patients with acute myeloid leukemias (AML). A total of 10 cases including from patients with normal (n=7) and abnormal karyotypes (n=3) were analyzed by conventional cytogenetic methods, array-CGH and FISH. Ten metaphases were analyzed in each case. Genomic DNA from the MSC was extracted and array comparative genomic hybridization (a CGH) was performed using the PerkinElmer Constitutional Chip 4.0 that contains 5,200 BAC clones printed in triplicate that detects and maps changes in copy number of DNA sequences. In a CGH, DNA from MSC and a reference genome (genomic DNA from a normal individual) are differentially labeled with fluorescent dyes and hybridized to a representation of the human genome, in this assay a DNA microarray containing BAC clones with human DNA inserts. Hybridization of repetitive sequences is blocked by the addition of Cot-1 DNA. The fluorescence ratio of the test and reference hybridization signals is determined at different positions along the genome and provides information on the relative copy number of sequences in the test genome compared with a normal diploid genome. The final plots were generated by SpectralWare software using appropriate normalization. For confirmation, individual BAC DNAs were labeled using the Invitrogen DNA labeling kit for FISH. Results demonstrate that G-banding analysis did not show chromosome rearrangement in 9 cases. There was 47,XX, +5 in one case that had 46, XX, der(16)t(1;16)(q21;q12.1) in the primary AML sample. This finding was confirmed by FISH and aCGH. At variance to BM-MSC derived from normal donors, all 10 cases of AML-derived MSC showed abnormalities (gain or loss) in different regions of chromosomes. The most frequently involved chromosomes were No. 3, 4, 6, 7, 8, 10, 15, 16, 19, and 22. The abnormalities were confirmed by FISH. Case CG of primary samples CG in MSC aCGH-results 1 46,XY 46, XY Gain-16q11.2q12.1) Gain-3p26.3 Gain-14q31.3 2 46XX,del(5)(q13q33) 46, XX Loss-7p21.3 Gain-3p26.3b Gain-16p12 3 46XX, der(16)t(1;16) (q21;q12.1) 46, XX(9), 47,XX,+5(1) Gain-5 4 46, XY 46, XY Gain-10q11.22 Gain-7q11.23 Loss-17q12 5 46,XX 46, XX Loss-15p13 Loss-3q12.3 6 46,XY, 46XY,del(5)(p13q13)(2) 46, XY Gain-10qter Gain-2q37.3 Loss-3p26.3 Gain-15q11.2 7 46, XY 46, XY Gain-5q14 8 46, XY 46, XY Gain-4q35.2 Gain-6q16 Loss-15q11.2 loss-16p11.2 Loss-22q12 9 46, XY 46, XY loss-8q21.3q22 Loss-7p21.3 10 46, XY 46, XY loss-19p13.2 Loss-8q21.2b Loss-14q12 These results indicate that BM-MSC derived from AML have genomic abnormalities which may be important for their support of leukemia cell growth and resistance to chemotherapeutic agents.
ERRATUM: Direct Fuel Injector Power Drive System Optimization (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;As published, Figures 4, 6, 22, and 26 contained errors and are corrected in the erratum.&lt;/div&gt;&lt;/div&gt;
Retinal Imaging Techniques for Diabetic Retinopathy Screening (2016)

Due to the increasing prevalence of diabetes mellitus, demand for diabetic retinopathy (DR) screening platforms is steeply increasing. Early detection and treatment of DR are key public health interventions that can greatly reduce the likelihood of vision loss. Current DR screening programs typically employ retinal fundus photography, which relies on skilled readers for manual DR assessment. However, this is labor-intensive and suffers from inconsistency across sites. Hence, there has been a recent proliferation of automated retinal image analysis software that may potentially alleviate this burden cost-effectively. Furthermore, current screening programs based on 2-dimensional fundus photography do not effectively screen for diabetic macular edema (DME). Optical coherence tomography is becoming increasingly recognized as the reference standard for DME assessment and can potentially provide a cost-effective solution for improving DME detection in large-scale DR screening programs. Current screening techniques are also unable to image the peripheral retina and require pharmacological pupil dilation; ultra-widefield imaging and confocal scanning laser ophthalmoscopy, which address these drawbacks, possess great potential. In this review, we summarize the current DR screening methods using various retinal imaging techniques, and also outline future possibilities. Advances in retinal imaging techniques can potentially transform the management of patients with diabetes, providing savings in health care costs and resources.
SU‐GG‐J‐113: Interfraction Dose Variations for Head and Neck Cancer Assessed Using Daily KVCT (2008)

Purpose: The interfraction variations during head and neck cancer radiotherapy can be significant due to the setup errors, neck rotation and organ shrinkage. We investigated the dosimetric consequence of these interfraction variations, so that the proper correction strategies can be considered. Method and Materials: Daily kVCT images for 20 head and neck cancer patients treated with CT‐guided repositioning using a linac and CT‐on‐Rails combo (CTVision, Siemens) were analyzed. Complete structure sets including multiple targets and critical structures were generated by deformable registration (MIMvista, OH) on each daily CT of the entire treatment course. Original plans were applied on each daily CT with and without the repositioning shifts recorded during the daily IGRT process. The daily doses were analyzed and compared to the planned doses. Results: The rotation of neck is difficult to reproduce everyday for head and neck cancer treatments. Generally, the daily repositioning based on the rigid body registration can correct for most of the interfraction dosimetric deviations from the planned doses. For example, on average, D95 (dose covers 95% of the target volume) was 3% lower than that planned after repositioning. It was observed that, for certain treatment fractions, the targets were significantly underdosed (&gt;%), and/or the cord doses were increased by more than 5%. A margin of 0.5 cm for cord could ensure the cord dose does not exceed the dose limit. Conclusion: Although large interfraction variations in neck rotation, organ shrinkage, and setup errors during head and neck RT, the overall dosimetric impact can be corrected in majority of treatment fractions with the current standard of rigid‐body repositioning during IGRT. More complex correction strategies are needed for a small portion of fractions.
Vasoactive intestinal peptide for granulomatous diseases – a case series. (2022)

Sarcoidosis is a granulomatous disease of unknown origin that mostly affects the lungs and lymphnodes. A lymphocytic alveolitis is an often finding and exaggerated TNF release contributes to its pathophysiology. However, chronic beryllium disease and immune checkpoint inhibitor therapy may also lead to granulomatous lung disease with comparable underlying pathophysiologies. Vasoactive intestinal peptide (VIP) dampens proinflammatory pathways and can be delivered to the alveolar compartment by inhalation. Therefore, we used the inhalation of 3x 67&nbsp;µg VIP as an individual treatment approach in patients with different granulomatous diseases in a named patient program. Clinical data were analyzed retrospectively from 13 consecutive patients (mean age 56 years, two female) with sufficient follow-up data within the next six months. 4 patients had sarcoidosis, 6 berylliosis and 3 ICI pneumonitis. Initially 9 patients were treated with corticosteroids, the mean prednisolone dose was 7,1mg/d, which was decreased to 2,5mg/d after six months. FVC and FeV1 increased under treatment with VIP (71,5 to 79,9 % predicted, p=0.03 and 61 % to 71 %, p=0.09), where TLCO remaind stable. Alveolar&nbsp;differential cytology did not alter during therapy, however spontaneous release of TNF and CCL18 by alveolar macrophages decreased significantly (4538 pg/ml to 2142 pg/ml, p= 0,04 and 35191 pg/ml to 8735 pg/ml, p=0,028). When available, King’s Sarcoidosis Questionnaire indicated an increase of quality of life under treatment with VIP.&nbsp;Taken together, inhalation of vasoactive intestinal peptide seems to be a potential therapeutic option in granulomatous diseases characterized by a high TNF release within the alveolar compartment.