gebhart/patrepeval huggingface dataset:
Review of: "The symptomatic expression of infection with the Omicron variant in Chinese patients; findings from the Clificol COVID-19 clinical case registry" (2022)

Review of: "The symptomatic expression of infection with the Omicron variant in Chinese patients; findings from the Clificol COVID-19 clinical case registry" Arash Ahmadivand Potential competing interests: The author(s) declared that no potential competing interests exist.This study provides a comprehensive understanding of the clinical presentation of COVID-19 variants, which has been acknowledged as an important platform for the selection of test-triggering symptoms.They investigations of the clinical presentation in response to different variants has shifted significantly and the findings confirmed this fact.This was indeed obtained through a comparison with first wave data from China, and it is shown that there is a fair amount of geographical stability in terms of the types of clinical symptoms reported, but that at the same time there is some between country variability in the prevalence of these symptoms.From the technical viewpoint, the conducted systematic and statistical study provides a deeper understanding of the expansion and behavior of COVID19 at different stages and multiple areas.The work has an immense potential to be published, however, there is a point that the authors must consider.1) Although the bibliography of the work contains important background of the topic, it must also consider the state of the art approaches that have been developed for the detection and diagnostic of this virus and its proteins.For example:
Near-Field Optical Simulation of Super-Resolution Near-Field Structure Disks (2001)

We describe the optical properties of readout signals from light-scatting-center super-resolution near-field structure disks by a numerical simulation using a three-dimensional finite-difference time-domain method (FDTD). Since the generation process of the near-field readout signals has a relationship between the direction of the mark train and the polarization direction of incident light, the optical properties of readout near-field signals strongly depended on the incident light polarization. It was found that the land &amp; groove structure, and the scattering center size also influenced the readout signals.
OMNeT++ BENZETİM ARACI KULLANILARAK MOBİL IPV6 KATMAN-2 HÜCRE GEÇİŞİ BAŞARIMININ ANALİZİ (2015)

One of the important factors for Mobile IP version 6 (MIPv6) is to ensure a seamless handover while a Mobile Node (MN) maintain active communication. A seamless handover can be realized by reducing or finishing the latency times during movement detection, a new address configuration and binding update procedures which have been defined in MIPv6 protocol clearly. However, MIPv6 handover process is a very complex due to Layer 2 (L2) and Layer 3 (L3) operations, and this drawback can cause significant performance degradation in macro mobility or real-time communications mainly. L3 handover is the most important factor to MIPv6 handover process because a major proportion of the total handover latency occurs in this stage. On the other hand, L2 handover results in the less latency than L3 handover. However, the researches on L2 handover also has an important place in literature because the events during L2 handover can trigger L3 handover in advance. By this way, seamless handover techniques have been realized. L2 approach is faster than L3 based solutions. Nevertheless, these methods are also limited to L2 handover latency. In this paper, we analyzed the L2 latency in MIPv6 handover using OMNeT++ simulator. These analyses will show the each components of the L2 handover latency separately.
Editorial comment (2005)

No AccessJournal of UrologyAdult urology1 Jan 2006Editorial comment Judd W. Moul Judd W. MoulJudd W. Moul More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)00267-3AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial comment." The Journal of Urology, 175(1), p. 129 Division of Urologic Surgery, Duke University Medical Center, Durham, North Carolina© 2006 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 1January 2006Page: 129 Advertisement Copyright & Permissions© 2006 by American Urological AssociationMetricsAuthor Information Judd W. Moul More articles by this author Expand All Advertisement PDF downloadLoading ...
Interplay between Epstein-Barr virus infection and environmental xenobiotic exposure in cancer (2021)

Epstein-Barr virus (EBV) is a herpesvirus associated with lymphoid and epithelial malignancies. Both B cells and epithelial cells are susceptible and permissive to EBV infection. However, considering that 90% of the human population is persistently EBV-infected, with a minority of them developing cancer, additional factors are necessary for tumor development. Xenobiotics such as tobacco smoke (TS) components, pollutants, pesticides, and food chemicals have been suggested as cofactors involved in EBV-associated cancers. In this review, the suggested mechanisms by which xenobiotics cooperate with EBV for carcinogenesis are discussed. Additionally, a model is proposed in which xenobiotics, which promote oxidative stress (OS) and DNA damage, regulate EBV replication, promoting either the maintenance of viral genomes or lytic activation, ultimately leading to cancer. Interactions between EBV and xenobiotics represent an opportunity to identify mechanisms by which this virus is involved in carcinogenesis and may, in turn, suggest both prevention and control strategies for EBV-associated cancers.
Quantification of bacterial populations in complex ecosystems using fluorescent in situ hybridization, confocal laser scanning microscopy and image analysis (2001)

A procedure for quantification of distinct bacterial populations in aggre-gated ecosystems was developed. It is based on fluorescent in situ hybridization coupled with confocal-laser-scanning microscopy and surface measurement of hybridized bacteria by image analysis. The proportion of a targeted bacterial species was ob-tained by comparison between the surface hybridized by a specific probe and the surface hybridized with a general bacterial reference probe. The accuracy of the re-sults obtained was evaluated by direct visual counting on the same sets of images. The analytical uncertainty of the image analysis procedure was determined and de-pended on the threshold values selected by the operator for cutting between signal and background fluorescence. The number of fields to be analyzed for reliable quantification was also determined. This procedure allows a quantification of the proportions of bacterial species in aggregated bacterial ecosystems which gives more accurate re-sults than visual counting because of the large number of bacteria counted. Moreover, since floc structures are preserved, it also gives information about the distribution of bacterial populations in the floc material which might reveal bacterial interactions within the community.
Computer-Aided Diagnosis in Multiparametric MRI of the Prostate: An Open-Access Online Tool for Lesion Classification with High Accuracy (2020)

Computer-aided diagnosis (CADx) approaches could help to objectify reporting on prostate mpMRI, but their use in many cases is hampered due to common-built algorithms that are not publicly available. The aim of this study was to develop an open-access CADx algorithm with high accuracy for classification of suspicious lesions in mpMRI of the prostate. This retrospective study was approved by the local ethics commission, with waiver of informed consent. A total of 124 patients with 195 reported lesions were included. All patients received mpMRI of the prostate between 2014 and 2017, and transrectal ultrasound (TRUS)-guided and targeted biopsy within a time period of 30 days. Histopathology of the biopsy cores served as a standard of reference. Acquired imaging parameters included the size of the lesion, signal intensity (T2w images), diffusion restriction, prostate volume, and several dynamic parameters along with the clinical parameters patient age and serum PSA level. Inter-reader agreement of the imaging parameters was assessed by calculating intraclass correlation coefficients. The dataset was stratified into a train set and test set (156 and 39 lesions in 100 and 24 patients, respectively). Using the above parameters, a CADx based on an Extreme Gradient Boosting algorithm was developed on the train set, and tested on the test set. Performance optimization was focused on maximizing the area under the Receiver Operating Characteristic curve (ROC<sub>AUC</sub>). The algorithm was made publicly available on the internet. The CADx reached an ROC<sub>AUC</sub> of 0.908 during training, and 0.913 during testing (<i>p</i> = 0.93). Additionally, established rule-in and rule-out criteria allowed classifying 35.8% of the malignant and 49.4% of the benign lesions with error rates of <2%. All imaging parameters featured excellent inter-reader agreement. This study presents an open-access CADx for classification of suspicious lesions in mpMRI of the prostate with high accuracy. Applying the provided rule-in and rule-out criteria might facilitate to further stratify the management of patients at risk.
Upregulation of mineralocorticoid receptor (MR) and sgk1 mRNA expression is associated with increased inflammatory markers [macrophage chemoattractant protein 1 (MCP1), transforming growth factor beta1 (TGF-beta1), interleukin-6 (IL-6)] in renal biopsies of patients with severe proteinuria (2005)

Aldosterone (A) has been emerged as a deleterious mediator of the RAAS in the heart, and MR blockade by spironolactone reduces morbidity in patients with severe heart failure. There is evidence that A contributes also to the development of renal fibrosis in several rat models. Investigations of the role of A in clinical renal disease are very rare and nothing is known about renal MR expression and MR effector mechanisms.
Supplementary Figure Legend from Carbonic Anhydrase Activity Monitored &lt;i&gt;In Vivo&lt;/i&gt; by Hyperpolarized &lt;sup&gt;13&lt;/sup&gt;C-Magnetic Resonance Spectroscopy Demonstrates Its Importance for pH Regulation in Tumors (2023)

&lt;p&gt;Supplementary Figure Legend. Legend for Supplementary Figure S1.&lt;/p&gt;
Abstract P40: Declining Morbidity From Subarachnoid Hemorrhage in the Last 4 Decades: A Pooled Analysis of 13,343 Patients (2021)

Introduction: Subarachnoid hemorrhage (SAH) mortality is decreasing, but data on functional outcomes over time is lacking. Methods: We created trends of good (Glasgow Outcomes Scale [GOS] of 4 or 5) and optimal (GOS of 5) functional outcomes and mortality (GOS of 1) using linear regression in 15 SAH trials and registries from 1982 to 2014. Models adjusted for age, sex, history of hypertension, World Federation of Neurological Surgeons grade, Fisher grade, aneurysm size, location, and repair modality, and whether data was from a clinical trial or registry. Analyses were repeated separately for the clinical trials and registries. Missing data were handled with multiple imputation. Results: Overall, 13,343 SAH patients were included. 9,524 (71%) patients had good functional outcome, while 1,608 (12%) died. There was a 0.6% adjusted improvement (95% confidence interval [CI]: 0.5% to 0.7%; p&lt;0.001) per year in good functional outcome and a 0.1% adjusted reduction (95% CI: -0.2% to -0.08%; p&lt;0.001) per year in mortality. For patients enrolled in clinical trials, there was no change good functional outcomes (0%; 95% CI: -0.2% to 0.1%; p=0.923) or mortality (0.0% change per year; 95% CI: -0.09% to 0.1%; p=0.676). Clinical registry patients experienced a 1.2% improvement (95% CI: 1.0% to 1.4%; p&lt;0.001) in good functional outcome and a 0.3% reduction (95% CI: -0.4% to -0.1%; p&lt;0.001) in mortality. Conclusions: SAH morbidity and mortality decreased from the 1980s to 2010s. This data can be helpful for researchers planning trials, clinicians discussing expected outcomes with patients and family members, and healthcare administrators planning resource utilization.
Scalable Deadlock-Free Deterministic Minimal-Path Routing Engine for InfiniBand-Based Dragonfly Networks (2017)

Dragonfly topologies are gathering great interest nowadays as one of the most promising interconnect options for High-Performance Computing (HPC) systems. However, Dragonflies contain physical cycles that may lead to traffic deadlocks unless the routing algorithm prevents them properly. In general, existing deadlock-free routing algorithms, either deterministic or adaptive, proposed for Dragonflies, use Virtual Channels (VCs) to prevent cyclic dependencies. However, these topology-aware algorithms are difficult to implement, or even unfeasible, in systems based on the InfiniBand (IB) architecture, which is nowadays the most widely used network technology in HPC systems. This is due to some limitations in the IB specification, specifically regarding the way Virtual Lanes (VLs), which are considered as similar to VCs, can be assigned to traffic flows. Indeed, none of the routing engines currently available in the official releases of the IB control software has been specifically proposed for Dragonflies. In this paper, we present a new deterministic, minimal-path routing for Dragonfly that prevents deadlocks using VLs according to the IB specification, so that it can be straightforwardly implemented in IB-based networks. We have called this proposal D3R (Deterministic Deadlock-free Dragonfly Routing). Specifically, D3R maps each route to a single, specific VL depending on the destination group, and according to a specific order, so that cyclic dependencies (so deadlocks) are prevented. D3R is scalable as it requires only 2 VLs to prevent deadlocks regardless of network size, i.e., fewer VLs than the required by the deadlock-free routing engines available in IB that are suitable for Dragonflies. Alternatively, D3R achieves higher throughput if an additional VL is used to reduce internal contention in the Dragonfly groups. We have implemented D3R as a new routing engine in OpenSM, the control software including the subnet manager in IB. We have evaluated D3R by means of simulation and by experiments performed in a real IB-based cluster, the results showing that, in general, D3R outperforms other routing engines.
Figures S1-S6, model files from Antibody Co-Administration Can Improve Systemic and Local Distribution of Antibody–Drug Conjugates to Increase &lt;i&gt;In Vivo&lt;/i&gt; Efficacy (2023)

&lt;p&gt;Supplementary figures and data&lt;/p&gt;
Similarity Rules for the Shot Peening Process Based on Finite Element Simulations (2005)

Multiple shot impacts are analyzed using a three-dimensional Finite Element model with a user defined temperature- and strain-rate-dependent material formulation. Based on this analysis, a method was developed for the prediction of changes in the material state in areas close to the surface by applying similarity mechanics. This approach provides a tool for the quick estimation of interesting work piece properties after peening especially when a vast field of process parameter variations has to be analyzed. The predictions of the applied similarity mechanics were compared with an explicit Finite Element analysis.
Iron‐Catalyzed Cyclotrimerization of Terminal Alkynes by Dual Catalyst Activation in the Absence of Reductants (2017)

Catalyzing C-C bond-forming reactions with earth-abundant metals under mild conditions is at the heart of sustainable synthesis. The cyclotrimerization of alkynes is a valuable atom-efficient reaction in organic synthesis that is enabled by several metal catalysts, including iron. This study reports an effective iron-catalyzed cyclotrimerization for the regioselective synthesis of 1,2,4-substituted arenes (1 mol % catalyst, toluene, 20 °C, 5 min). A dual activation mechanism (substrate deprotonation, reductive elimination) renders the simple Fe<sup>II</sup> precatalyst highly active in the absence of any reductant.
Sequential Pattern Mining of Longitudinal Adverse Events After Left Ventricular Assist Device Implant (2019)

Left ventricular assist devices (LVADs) are an increasingly common therapy for patients with advanced heart failure. However, implantation of the LVAD increases the risk of stroke, infection, bleeding, and other serious adverse events (AEs). Most post-LVAD AEs studies have focused on individual AEs in isolation, neglecting the possible interrelation, or causality between AEs. This study is the first to conduct an exploratory analysis to discover common sequential chains of AEs following LVAD implantation that are correlated with important clinical outcomes. This analysis was derived from 58,575 recorded AEs for 13,192 patients in International Registry for Mechanical Circulatory Support (INTERMACS) who received a continuous-flow LVAD between 2006 and 2015. The pattern mining procedure involved three main steps: (1) creating a bank of AE sequences by converting the AEs for each patient into a single, chronologically sequenced record, (2) grouping patients with similar AE sequences using hierarchical clustering, and (3) extracting temporal chains of AEs for each group of patients using Markov modeling. The mined results indicate the existence of seven groups of sequential chains of AEs, characterized by common types of AEs that occurred in a unique order. The groups were identified as: GRP1: Recurrent bleeding, GRP2: Trajectory of device malfunction & explant, GRP3: Infection, GRP4: Trajectories to transplant, GRP5: Cardiac arrhythmia, GRP6: Trajectory of neurological dysfunction & death, and GRP7: Trajectory of respiratory failure, renal dysfunction & death. These patterns of sequential post-LVAD AEs disclose potential interdependence between AEs and may aid prediction, and prevention, of subsequent AEs in future studies.
P1‐044: Validation of the rat pharmacodynamic model for amyloid‐beta peptide lowering agents (2011)

A critical requirement in the development of Alzheimer's disease (AD) therapeutics is a pre-clinical model allowing pharmacokinetic/pharmacodynamic (PK/PD) profiling of amyloid-beta (Abeta) peptide lowering compounds. One of the most frequently used models in AD research are transgenic mice over-expressing mutant forms of human amyloid precursor protein (APP) that are associated with early-onset familial AD. These mice exhibit an age-dependent accumulation of Abeta peptides as senile plaques in the brain and have extensively been used to study Abeta deposition. More recently, a non-transgenic rat model exhibiting endogenous Abeta production has been utilised. The advantages of this model include the ability to use a single animal species for efficacy and toxicology studies and the feasibility of cerebrospinal fluid (CSF) sampling. Here we describe the establishment of the rat pharmacodynamic model and its validation with a potent BACE1 inhibitor. Sensitive immunoassays were established to measure endogenous levels of Abeta (40) peptides in CSF and brain extracts of Sprague Dawley rats. To validate the rat model we utilised a BACE1 inhibitor that potently inhibits beta-cleavage of APP and Abeta production in cells. Time course and dose response studies were conducted to determine the degree of Abeta lowering that could be achieved in this model following a single oral dose of a BACE1 inhibitor. A sensitive immunoassay for sAPPbeta was also established to confirm the mechanism of action of the BACE1 inhibitor. The BACE1 inhibitor caused a significant dose-dependent decrease in Abeta (40) levels in the CSF and brain. A significant decrease in the level of sAPPbeta was also observed in the brain, consistent with the in vitro profile and mechanism of action of this compound. The rat PD model has been validated using a potent BACE1 inhibitor. The data obtained support the utility of the rat as an alternative pre-clinical model for profiling Abeta lowering agents. Besides from supporting PK/PD studies in a relevant safety species this model has the additional advantage of permitting a simultaneous assessment of compound effects in different CNS compartments.
Seeing Glass: Joint Point Cloud and Depth Completion for Transparent\n Objects (2021)

The basis of many object manipulation algorithms is RGB-D input. Yet,\ncommodity RGB-D sensors can only provide distorted depth maps for a wide range\nof transparent objects due light refraction and absorption. To tackle the\nperception challenges posed by transparent objects, we propose TranspareNet, a\njoint point cloud and depth completion method, with the ability to complete the\ndepth of transparent objects in cluttered and complex scenes, even with\npartially filled fluid contents within the vessels. To address the shortcomings\nof existing transparent object data collection schemes in literature, we also\npropose an automated dataset creation workflow that consists of\nrobot-controlled image collection and vision-based automatic annotation.\nThrough this automated workflow, we created Toronto Transparent Objects Depth\nDataset (TODD), which consists of nearly 15000 RGB-D images. Our experimental\nevaluation demonstrates that TranspareNet outperforms existing state-of-the-art\ndepth completion methods on multiple datasets, including ClearGrasp, and that\nit also handles cluttered scenes when trained on TODD. Code and dataset will be\nreleased at https://www.pair.toronto.edu/TranspareNet/\n
Quantitative proteomic analysis reveals AK2 as potential biomarker for late normal tissue radiotoxicity (2019)

These findings identify AK2 as a potential radiosensitivity candidate biomarker. Overall, our proteomic approach highlights the important role of oxidative stress in late radiation-induced toxicity, and paves the way for additional studies on NOXs and superoxide ion metabolism.
Serum Neurofilament Light is Elevated in COVID-19 Positive Adults in the ICU and is Associated with Co-Morbid Cardiovascular Disease, Neurological Complications, and Acuity of Illness (2021)

Abstract In critically ill COVID-19 patients, the risk of long-term neurological consequences is just beginning to be appreciated. While recent studies have identified that there is an increase in structural injury to the nervous system in critically ill COVID-19 patients, there is little known about the relationship of COVID-19 neurological damage to the systemic inflammatory diseases also observed in COVID-19 patients. The purpose of this pilot observational study was to examine the relationships between serum neurofilament light protein (NfL, a measure of neuronal injury) and co-morbid cardiovascular disease (CVD) and neurological complications in COVID-19 positive patients admitted to the intensive care unit (ICU). In this observational study of one-hundred patients who were admitted to the ICU in Tucson, Arizona between April and August 2020, 89 were positive for COVID-19 (COVID-pos) and 11 were COVID-negative (COVID-neg). A healthy control group (n=8) was examined for comparison. The primary outcomes and measures were subject demographics, serum NfL, presence and extent of CVD, diabetes, sequential organ failure assessment score (SOFA), presence of neurological complications, and blood chemistry panel data. COVID-pos patients in the ICU had significantly higher mean levels of Nfl (229.6±163 pg/ml) compared to COVID-neg ICU patients (19.3±5.6 pg/ml), Welch’s t-test, p =.01 and healthy controls (12.3±3.1 pg/ml), Welch’s t-test p =.005. Levels of Nfl in COVID-pos ICU patients were significantly higher in patients with concomitant CVD and diabetes (n=35, log Nfl 1.6±.09), and correlated with higher SOFA scores (r=.5, p =.001). These findings suggest that in severe COVID-19 disease, the central neuronal and axonal damage in these patients may be driven, in part, by the level of systemic cardiovascular disease and peripheral inflammation. Understanding the contributions of systemic inflammatory disease to central neurological degeneration in these COVID-19 survivors will be important to the design of interventional therapies to prevent long-term neurological and cognitive dysfunction.