gebhart/patrepeval huggingface dataset:
Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue (2018)

Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14<sup>+</sup> CD16<sup>+</sup> monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA-containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD.
Effects of Gravitational Mechanical Unloading in Endothelial Cells: Association between Caveolins, Inflammation and Adhesion Molecules (2013)

Mechanical forces including gravity affect endothelial cell (ECs) function, and have been implicated in vascular disease as well as physiologic changes associated with low gravity environments. The goal of this study was to investigate the impact of gravitational mechanical unloading on ECs phenotype as determined by patterns of gene expression. Human umbilical vascular endothelial cells were exposed to 1-gravity environment or mechanical unloading (MU) for 24 hours, with or without periods of mechanical loading (ML). MU led to a significant decrease in gene expression of several adhesion molecules and pro-inflammatory cytokines. On the contrary, eNOS, Caveolin-1 and -2 expression were significantly increased with MU. There was a decrease in the length and width of the cells with MU. Addition of ML during the MU period was sufficient to reverse the changes triggered by MU. Our results suggest that gravitational loading could dramatically affect vascular endothelial cell function.
CycleMix: A Holistic Strategy for Medical Image Segmentation from Scribble Supervision (2022)

Curating a large set of fully annotated training data can be costly, especially for the tasks of medical image segmentation. Scribble, a weaker form of annotation, is more obtainable in practice, but training segmentation models from limited supervision of scribbles is still challenging. To address the difficulties, we propose a new framework for scribble learning-based medical image segmentation, which is composed of mix augmentation and cycle consistency and thus is referred to as CycleMix. For augmentation of supervision, CycleMix adopts the mixup strategy with a dedicated design of random occlusion, to perform increments and decrements of scribbles. For regularization of supervision, CycleMix intensifies the training objective with consistency losses to penalize inconsistent segmentation, which results in significant improvement of segmentation performance. Results on two open datasets, i.e., ACDC and MSCMRseg, showed that the proposed method achieved exhilarating performance, demonstrating comparable or even better accuracy than the fully-supervised methods. The code and expert-made scribble annotationsfor MSCMRseg are publicly available at https://github.com/BWGZK/CycleMix.
Evaluation of the Zucker Diabetic Fatty (ZDF) Rat as a Model for Human Disease Based on Urinary Peptidomic Profiles (2012)

Representative animal models for diabetes-associated vascular complications are extremely relevant in assessing potential therapeutic drugs. While several rodent models for type 2 diabetes (T2D) are available, their relevance in recapitulating renal and cardiovascular features of diabetes in man is not entirely clear. Here we evaluate at the molecular level the similarity between Zucker diabetic fatty (ZDF) rats, as a model of T2D-associated vascular complications, and human disease by urinary proteome analysis. Urine analysis of ZDF rats at early and late stages of disease compared to age- matched LEAN rats identified 180 peptides as potentially associated with diabetes complications. Overlaps with human chronic kidney disease (CKD) and cardiovascular disease (CVD) biomarkers were observed, corresponding to proteins marking kidney damage (eg albumin, alpha-1 antitrypsin) or related to disease development (collagen). Concordance in regulation of these peptides in rats versus humans was more pronounced in the CVD compared to the CKD panels. In addition, disease-associated predicted protease activities in ZDF rats showed higher similarities to the predicted activities in human CVD. Based on urinary peptidomic analysis, the ZDF rat model displays similarity to human CVD but might not be the most appropriate model to display human CKD on a molecular level.
ISOC symposium on network and distributed systems security (1994)

article Free Access Share on ISOC symposium on network and distributed systems security Author: Dan Nessett View Profile Authors Info & Claims ACM SIGCOMM Computer Communication ReviewVolume 24Issue 2April 1994 pp 95–102https://doi.org/10.1145/185595.185657Published:01 April 1994Publication History 0citation289DownloadsMetricsTotal Citations0Total Downloads289Last 12 Months30Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
L-Histidinol Phosphate Tetrahydrate: Redetermination at 110 and 240K (1998)

In the crystal of l-histidinol phosphate tetrahydrate, C6H12N3O4P.4H2O, at 110 and 240 K, the l-histidinol phosphate residue exists as zwitterion in which the phosphate group is doubly ionized with the amino and imidazole moieties each accepting a proton from the acid group.
A rare case of primary carcinoma of gallbladder as a cause of Krukenberg tumors in both ovaries (2022)

Gallbladder cancer is frequently transmitted to the liver and other gastrointestinal organs through direct extension. Ovarian metastases of biliary origin are quite uncommon. We report a rare case having Krukenberg tumours in both ovaries, an uncommon metastatic location of biliary cancer. A thorough analysis of the proposed tactics was carried out after a thorough critical review. The final diagnosis was made using a combination of radiology, histology, and serum markers. In the case of gallbladder cancer, the presence of a Krukenberg tumour should be examined.
Enhancing the magnetization, dielectric loss and photocatalytic activity of Co–Cu ferrite nanoparticles via the substitution of rare earth ions (2021)

This study reports the impact of lanthanum (La) substituted Co–Cu ferrite nanoparticles on the rhodamine (RhB) dye disposal. Moreover, a complete investigation for the structural, magnetic and optical properties for Co0.5Cu0.5LaxFe2-xO4 (CCL) nanoferrites was executed. These nanocrystals were synthesized via a combustion approach with a peculiar lattice parameter behavior; which discussed through three hypotheses. The scanning transmission electron microscope - energy dispersive X-ray analysis (STEM-EDX) micrographs of some selective samples confirm the nanocrystalline nature with presence of all constituents’ chemical elements CCL nanoferrites. The saturation magnetization of CCL nanoferrites was tuned with La3+ ions substitution. Contrary to the expected results, anisotropy constant introduced a decrement behavior with La/Fe substitution process. The microwave frequency (ωM) values for all CCL nanoparticles are in the range 11.87–9.46 GHz. The band gap has a peculiar behavior; a red shift and followed by a blue one. Through photodegradation testing, we explicate the RhB degradation mechanisms over our CCL nanoferrites. The nanoferrite Co0.5Cu0.5La0.15Fe1.85O4 has a moderate saturation magnetization, highest coercivity, and lowest loss, which is a suitable candidate for data recording applications, furthermore can be utilized as a photocatalyst for RhB effluents removal with degradation efficiency 94.50% at 180 min solar radiation.
Research and clinical aspects of the late effects of poliomyelitis (1986)

This book contains 32 selections. Some of the titles are: Late effects of Polio: Historical Perspectives; Sleep-Disordered Breathing as a Late Effect of Poliomyelitis; Clinical Subtypes, DNA Repair Efficiency, and Therapeutic Trials in the Post-Polio Syndromes; and Post-Polio Muscle Function.
Effects of Molybdate Concentration on the Characteristics of Ni–Mo–P Diffusion Barriers Grown by Nonisothermal Electroless Deposition (2008)

Ternary Ni-based amorphous films can serve as a barrier layer for Cu interconnects in ultralarge-scale integration (ULSI) applications. In this paper, films deposited on silicon wafers without a complicated pretreatment such as Pd activation were prepared using a nonisothermal deposition (NITD) method. The deposition solutions and operating conditions for preparing the alloys are presented, and the effect of the concentration of added in electrolytes on the deposition rate is investigated. The surface morphology, microstructures, compositions, and electrical resistivity of the deposits are also thoroughly examined. Based on the experimental results, the Ni-based ternary alloys produced by the NITD method contain high levels of both Mo and P, and the properties of films are dependent on the concentration of molybdate in electrolytes. It is concluded that the thin films produced by the proposed approach in this study are promising for the technologies in ULSI.
The Future of Electricity Generation in New Zealand (2008)

Increasing demand for electricity in New Zealand requires approximately 150 megawatts of new capacity to be installed annually. Rapidly increasing global prices for fossil fuels; the New Zealand Energy Strategy with its focus on renewable technologies; climate change policies; and a gradual shift from an energy constrained electricity system to one with capacity constraints are all factors underlying a change in the type of generation plant being installed and the location of that plant. This paper examines the likely future of the generation sector over the next 20-30 years. It is based on the work undertaken by the Electricity Commission in preparing its Statement of Opportunities, which contains scenarios describing how electricity may be generated in the future. These scenarios are produced using the Commission’s generation expansion model.
Power-smart system-on-chip architecture for embedded cryptosystems (2005)

In embedded cryptosystems, sensitive information can leak via timing, power, and electromagnetic channels. We introduce a novel power-smart system-on-chip architecture that provides support for masking these channels by controlling, in real-time, the power and the current consumption of a system to predefined programmable values. The main components of the architecture are a processor core, a current sensor module, a dynamically controlled power supply module, a clock frequency control module, and a current injection module. Real-time current measurements and power-aware voltage control are used in closed loop architecture to regulate and minimize the total power consumption of the system. Simulation results show that the current consumption of the system can be regulated to a reference level with reduced power-to-security trade off (power overhead less than 12% of the total power).
PML isoform II plays a critical role in nuclear lipid droplet formation (2016)

Lipid droplets (LDs) in the nucleus of hepatocyte-derived cell lines were found to be associated with premyelocytic leukemia (PML) nuclear bodies (NBs) and type I nucleoplasmic reticulum (NR) or the extension of the inner nuclear membrane. Knockdown of PML isoform II (PML-II) caused a significant decrease in both nuclear LDs and type I NR, whereas overexpression of PML-II increased both. Notably, these effects were evident only in limited types of cells, in which a moderate number of nuclear LDs exist intrinsically, and PML-II was targeted not only at PML NBs, but also at the nuclear envelope, excluding lamins and SUN proteins. Knockdown of SUN proteins induced a significant increase in the type I NR and nuclear LDs, but these effects were cancelled by simultaneous knockdown of PML-II. Nuclear LDs harbored diacylglycerol O-acyltransferase 2 and CTP:phosphocholine cytidylyltransferase α and incorporated newly synthesized lipid esters. These results corroborated that PML-II plays a critical role in generating nuclear LDs in specific cell types.
Traumatic Cerebral Vascular Injury: The Effects of Concussive Brain Injury on the Cerebral Vasculature (2003)

In terms of human suffering, medical expenses, and lost productivity, head injury is one of the major health care problems in the United States, and inadequate cerebral blood flow is an important contributor to mortality and morbidity after traumatic brain injury. Despite the importance of cerebral vascular dysfunction in the pathophysiology of traumatic brain injury, the effects of trauma on the cerebral circulation have been less well studied than the effects of trauma on the brain. Recent research has led to a better understanding of the physiologic, cellular, and molecular components and causes of traumatic cerebral vascular injury. A more thorough understanding of the direct and indirect effects of trauma on the cerebral vasculature will lead to improvements in current treatments of brain trauma as well as to the development of novel and, hopefully, more effective therapeutic strategies.
Higher-Affinity Agonists of 5-HT1AR Discovered through Tuning the Binding-Site Flexibility (2015)

Discovery of high-affinity and high-selectivity agonists of 5-HT1AR has become very attractive due to their potential therapeutic effects on multiple 5-HT1AR-related psychological and neurological problems. On the basis of our previously designed lead compound FW01 (Ki = 51.9 nM, denoted as 9a in the present study), we performed large-scale molecular dynamics simulations and molecular docking operations on 5-HT1AR-9a binding. We found the flip-packing events for the headgroup of 9a, and we also found that its tail group could bind flexibly at the agonist-binding site of 5-HT1AR. By finely tuning the flip-packing phenomenon of the 9a headgroup and tuning the binding flexibility of 9a tail group, we virtually designed a series of new 9a derivatives through molecular docking operations and first-principles calculations and predicted that these newly designed 9a derivatives should be higher-affinity agonists of 5-HT1AR. The computational predictions on the new 9a derivatives have been confirmed by our wet-experimental studies as chemical synthesis, binding affinity assays, and agonistic-function assays. The consistency between our computational design and wet-experimental measurements has led to our discovery of higher-affinity agonists of 5-HT1AR, with ∼50-fold increase in receptor-binding affinity and ∼25-fold improvements in agonistic function. In addition, our newly designed 5-HT1AR agonists showed very high selectivity of 5-HT1AR over subtype 5-HT2AR and also over three subtypes of dopamine receptors (D1, D2, and D3).
A Vicarious Technique for Understanding and Diagnosing Hyperspectral Spatial Misregistration (2023)

Pushbroom hyperspectral imaging (HSI) systems intrinsically measure our surroundings by leveraging 1D spatial imaging, where each pixel contains a unique spectrum of the observed materials. Spatial misregistration is an important property of HSI systems because it defines the spectral integrity of spatial pixels and requires characterization. The IEEE P4001 Standards Association committee has defined laboratory-based methods to test the ultimate limit of HSI systems but negates any impacts from mounting and flying the instruments on airborne platforms such as unmanned aerial vehicles (UAV's) or drones. Our study was designed to demonstrate a novel vicarious technique using convex mirrors to bridge the gap between laboratory and field-based HSI performance testing with a focus on extracting hyperspectral spatial misregistration. A fast and simple extraction technique is proposed for estimating the sampled Point Spread Function's width, along with keystone, as a function of wavelength for understanding the key contributors to hyperspectral spatial misregistration. With the ease of deploying convex mirrors, off-axis spatial misregistration is assessed and compared with on-axis behavior, where the best performance is often observed. In addition, convex mirrors provide an easy methodology to exploit ortho-rectification errors related to fixed pushbroom HSI systems, which we will show. The techniques discussed in this study are not limited to drone-based systems but can be easily applied to other airborne or satellite-based systems.
Optical Pseudo-Color Processing of Height and Flow Velocity (1979)

An optical technique is introduced for pseudo-color representation of height or deformation of a solid object, a flow velocity distribution of fluid and so on. First, a photograph is taken in which parts of movement, height, etc. are coded into their own center frequency of spatial bandpass processes. For example, a photograph of a flow of fluid carrying aluminium powder on its surface is taken under periodical illumination of a flashing stroboscope. Then the frequency-coded transparency is converted into a colored image by an optical spatial filtering processor being illuminated by spatially coherent white light and having an off-axis slit as the spatial filter.A simple mathematical procedure is derived for estimating an output color of the processor from the spatial power spectral density of the input transparency. In the derivation the tristimulus values are expressed respectively by the output powers of the three linear systems whose power transfer functions are easily calculated under the given slit configuration. It is shown that the small-signal resolution of the processor is approximately equal to that of an incoherently illuminated optical system of the same configuration and size having an on-axis slit of the same width. It is recommended that the slit width is approximately 1/5 of the slit offset from the optical axis for optimally compromising the excitation purity with the resolution, and that the bandwidth vs. center frequency ratio should be less than 1/5 to make chromaticity determined mostly by the center frequency and little affected by the spectral shape of input signals.Experimental results are shown in colored figures. The rangeability of input frequency is roughly 1:1.5, but it can be adjusted using a prism if necessary.
Long-Term Efficacy of Biofeedback Therapy for Dyssynergic Defecation: Randomized Controlled Trial (2010)

Biofeedback therapy provided sustained improvement of bowel symptoms and anorectal function in constipated subjects with dyssynergic defecation, whereas standard therapy was largely ineffective.
Sample Size Requirements for Association Studies of Gene-Gene Interaction (2002)

In the study of complex diseases, it may be important to test hypotheses related to gene-gene (G x G) interaction. The success of such studies depends critically on obtaining adequate sample sizes. In this paper, the author investigates sample size requirements for studies of G x G interaction, focusing on four study designs: the matched-case-control design, the case-sibling design, the case-parent design, and the case-only design. All four designs provide an estimate of interaction on a multiplicative scale, which is used as a unifying theme in the comparison of sample size requirements. Across a variety of genetic models, the case-only and case-parent designs require fewer sampling units (cases and case-parent trios, respectively) than the case-control (pairs) or case-sibling (pairs) design. For example, the author describes an asthma study of two common recessive genes for which 270 matched case-control pairs would be required to detect a G x G interaction of moderate magnitude with 80% power. By comparison, the same study would require 319 case-sibling pairs but only 146 trios in the case-parent design or 116 cases in the case-only design. A software program that computes sample size for studies of G x G interaction and for studies of gene-environment (G x E) interaction is freely available (http://hydra.usc.edu/gxe).
Chemical strategies to understand the language of ubiquitin signaling (2013)

Ubiquitin (Ub) is a small 76 amino acid long protein that is highly conserved in all eukaryotes studied to date. In humans, more than 600 ligases are involved in the reversible modification of specific lysine side-chain amines in substrate proteins by conjugation with the C-terminal carboxylate of Ub. Initially monoubiquitylated proteins can undergo repetitive ubiquitylation starting from one of seven lysine residues or the α-amine in the first Ub to generate a variety of polyUb chains with different topologies and functions. The most well known role for protein ubiquitylation is in targeting substrates for proteolytic destruction by 26S proteasomes. However, a growing body of evidence indicates that both mono- and polyubiquitylation play proteasome-independent roles in modulating the structure, function, and localization of protein substrates. Understanding the complexity of Ub-mediated functions in our cells is a major challenge for modern biology. In addition to well-established in vivo genetic methods, biochemical and biophysical investigations of ubiquitylated proteins in vitro can shed light on the direct mechanistic roles for Ub in different contexts. Such studies have traditionally been limited by the ability to obtain sufficient quantities of homogenously ubiquitylated proteins with precisely defined linkages. This review focuses on recent advances in both synthetic and recombinant protein-based methods that have yielded access to homogenously site-specifically ubiquitylated proteins. Mechanistic studies of the roles for protein ubiquitylation and of the enzymes involved in protein deubiquitylation that are enabled by these chemical tools are highlighted.
Characteristic of Langerhans cell histiocytosis in oral and maxillofacial regions (2020)

Abstract Langerhans cell histiocytosis (LCH） is a rare disease caused by excessive proliferation of Langerhans cells in various regions of the body. Previous studies have reported that 10% of LCH occurs in the oral and maxillofacial regions. In the oral and maxillofacial regions, swelling and pain are the typical symptoms, and jaw fracture and tooth loss are often seen in advanced cases. In this study, we present the results of a literature review of LCH that developed in the oral and maxillofacial regions. The history, pathological conditions, diagnosis, treatment, and progress of LCH are discussed.