gebhart/patrepeval huggingface dataset:
The human TTP protein: sequence, alignment with related proteins, and chromosomal localization of the mouse and human genes (1991)

Journal Article The human TTP protein: sequence, alignment with related proteins, and chromosomal localization of the mouse and human genes Get access Gregory A. Taylor, Gregory A. Taylor Search for other works by this author on: Oxford Academic PubMed Google Scholar Wi S. Lai, Wi S. Lai Search for other works by this author on: Oxford Academic PubMed Google Scholar Rebecca J. Oakey, Rebecca J. Oakey 1Departments of Medicine and Microbiology, Duke University Medical CenterDurham, NC 27710 Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael F. Seldin, Michael F. Seldin 1Departments of Medicine and Microbiology, Duke University Medical CenterDurham, NC 27710 Search for other works by this author on: Oxford Academic PubMed Google Scholar Thomas B. Shows, Thomas B. Shows 2Department of Human Genetics, Reswell Park Memorial InstituteBuffalo, NY 14263, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Roger L. Eddy, Jr, Roger L. Eddy, Jr 2Department of Human Genetics, Reswell Park Memorial InstituteBuffalo, NY 14263, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Perry J. Blackshear Perry J. Blackshear Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 12, 25 June 1991, Page 3454, https://doi.org/10.1093/nar/19.12.3454 Published: 25 June 1991 Article history Accepted: 29 April 1991 Published: 25 June 1991
A Bivariate Mixture Model for Natural Antibody Levels to Human Papillomavirus Types 16 and 18: Baseline Estimates for Monitoring the Herd Effects of Immunization (2016)

Post-vaccine monitoring programs for human papillomavirus (HPV) have been introduced in many countries, but HPV serology is still an underutilized tool, partly owing to the weak antibody response to HPV infection. Changes in antibody levels among non-vaccinated individuals could be employed to monitor herd effects of immunization against HPV vaccine types 16 and 18, but inference requires an appropriate statistical model. The authors developed a four-component bivariate mixture model for jointly estimating vaccine-type seroprevalence from correlated antibody responses against HPV16 and -18 infections. This model takes account of the correlation between HPV16 and -18 antibody concentrations within subjects, caused e.g. by heterogeneity in exposure level and immune response. The model was fitted to HPV16 and -18 antibody concentrations as measured by a multiplex immunoassay in a large serological survey (3,875 females) carried out in the Netherlands in 2006/2007, before the introduction of mass immunization. Parameters were estimated by Bayesian analysis. We used the deviance information criterion for model selection; performance of the preferred model was assessed through simulation. Our analysis uncovered elevated antibody concentrations in doubly as compared to singly seropositive individuals, and a strong clustering of HPV16 and -18 seropositivity, particularly around the age of sexual debut. The bivariate model resulted in a more reliable classification of singly and doubly seropositive individuals than achieved by a combination of two univariate models, and suggested a higher pre-vaccine HPV16 seroprevalence than previously estimated. The bivariate mixture model provides valuable baseline estimates of vaccine-type seroprevalence and may prove useful in seroepidemiologic assessment of the herd effects of HPV vaccination.
Supplementary Data from Lymph Node–Targeted Immunotherapy Mediates Potent Immunity Resulting in Regression of Isolated or Metastatic Human Papillomavirus–Transformed Tumors (2023)

Supplementary Data from Lymph Node–Targeted Immunotherapy Mediates Potent Immunity Resulting in Regression of Isolated or Metastatic Human Papillomavirus–Transformed Tumors
Induction of Porcine Dermatitis and Nephropathy Syndrome in Piglets by Infection with Porcine Circovirus Type 3 (2018)

Porcine circovirus type 3 (PCV3) is an emerging porcine circovirus that has been associated with porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs, reproductive failure, cardiac pathologies, and multisystemic inflammation in piglets and sows. Many aspects of PCV3 infection biology and pathogenesis, however, remain unknown. Here, we used a PCV3 virus stock from the rescue of an infectious PCV3 DNA clone to intranasally inoculate 4- and 8-week-old specific-pathogen-free piglets for evaluation of PCV3 pathogenesis. For 4-week-old piglets, typical clinical signs resembling those of PDNS-like disease were observed when piglets were inoculated with PCV3 alone or PCV3 combined with immunostimulation by keyhole limpet hemocyanin, with a mortality of 40% (2/5) for both types of inoculated piglets during a 28-day observation period postinoculation. Both types of inoculated piglets showed similar progressive increases in viral loads in the sera and had seroconverted to PCV3 capsid antibody after inoculation. Pathological lesions and PCV3-specific antigen were detected in various tissues and organs, including the lung, heart, kidney, lymph nodes, spleen, liver, and small intestine, in both types of inoculated piglets. The levels of proinflammatory cytokines and chemokines, including interleukin 1 beta (IL-1β), IL-6, IL-23α, gamma interferon (IFN-γ), tumor necrosis factor alpha (TNF-α), and chemokine ligand 5 (CCL5), were significantly upregulated in both groups of inoculated piglets. Eight-week-old piglets also exhibited a similar PDNS-like disease but without death after PCV3 inoculation, as evidenced by pathological lesions and PCV3 antigen in various tissues and organs. These results show for the first time successful reproduction of PDNS-like disease by PCV3 infection and further provide significant information regarding the pathogenesis of PCV3 in piglets.<b>IMPORTANCE</b> Porcine circovirus type 3 (PCV3), an emerging porcine circovirus, is considered the cause of porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs and other systemic diseases in piglets and sows. To evaluate the pathogenesis of PCV3 infection <i>in vivo</i>, we used a PCV3 virus stock from the rescue of an infectious PCV3 DNA clone to intranasally inoculate 4- and 8-week-old specific-pathogen-free piglets and demonstrated successful reproduction of PDNS-like disease in animals that were inoculated with PCV3 alone or PCV3 combined with immunostimulation by keyhole limpet hemocyanin. Both 4- and 8-week-old PCV3-inoculated piglets showed similar increases in viral loads in the sera and had seroconverted to PCV3 capsid antibody. Pathological lesions and PCV3-specific antigen were detected in various tissues and organs, while numerous proinflammatory cytokines and chemokines in the sera were significantly upregulated after PCV3 inoculation. These results will provide significant information regarding the pathogenesis of PCV3 in piglets.
Low Density Lipoprotein Receptor Class A Repeats Are O-Glycosylated in Linker Regions (2014)

The low density lipoprotein receptor (LDLR) is crucial for cholesterol homeostasis and deficiency in LDLR functions cause hypercholesterolemia. LDLR is a type I transmembrane protein that requires O-glycosylation for stable expression at the cell surface. It has previously been suggested that LDLR O-glycosylation is found N-terminal to the juxtamembrane region. Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the "SimpleCell" O-glycoproteome shotgun strategy. Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide GalNAc transferases. Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions.
Moisture-Resistant and Superhydrophobic Metal−Organic Frameworks Obtained via Postsynthetic Modification (2010)

Postsynthetic covalent modification of metal-organic frameworks (MOFs) with long alkyl substituents is shown to protect these materials against moisture. These MOFs, which normally display hydrophilic properties, are readily converted into hydrophobic or superhydrophobic materials. Overcoming the inherent sensitivity of MOFs to water represents a major step forward in their widespread use in technology applications.
PARAFAC-based multilinear subspace clustering for tensor data (2016)

Subspace clustering has become an increasingly popular data analysis and machine learning method, whose main assumption is that data are generated from a union of linear subspaces modeling. While successful in many applications these methods do not take into account the multilinear structure of data such as images and video. Prompted by this observation, the present work introduces a multilinear subspace clustering scheme that exploits the structure of the data, and its performance is evaluated on synthetic and real datasets against state-of-the-art subspace clustering algorithms.
Rational design of bleachable nonchemically amplified DUV photoactive compounds (2001)

Photoactive compounds have been designed, synthesized and characterized for deep ultraviolet non-chemically amplified resist applications. These resist materials may have potential use in next generation 257nm mask fabrication. Mask fabrication requires stringent linewidth specifications over long post-coat and post-exposure bake delays. Lithography simulation and imaging experiments have been done to determine the lithographic performance of resists formulated with these new photoactive compounds. Previously studied chromophores, 7 substituted 3-diazo 4- hydroxycoumarin and N-substituted 3-diazo-2, 4-piperidione, both have the transparency, bleaching and exposure rate kinetics in the DUV that are analogous to those exhibited by the diazonaphthoquinone chromophore at 365nm. The sulfonate linkages attached to these photoactive compounds provide dissolution rate inhibition of novolak that is very similar to the diazonaphthoquinone-sulfonates. The trifunctional diazopiperidione that incorporates three sulfonate linkages provides more efficient inhibition per chromophore than the corresponding bisfunctional photoactive compound. The diazocoumarin based novolak resist demonstrates image reversal (negative tone) with the use of a post-exposure bake. The post-exposure bake causes the exposed photoactive compound to decarboxylate, which dramatically reduces its solubility in aqueous base. The trifunctional diazopiperidione provides the best overall imaging results due to almost complete bleaching and high contrast.
5G Field Trials in the Smart City and Medical Service Areas toward Social Implementation of 5G (2018)

In this article, we describe two examples of field trials contracted by the Ministry of Internal Affairs and Communications of Japan concerning application of fifth-generation mobile communications systems (5G).The first example was in the area of smart city/smart area and was focused on providing a safe and secure society.The results of experimental trials confirmed that the transmission and aggregation of high-resolution video to a monitoring center enabled facility monitoring and wide-area monitoring in places where many people gather such as public facilities and sports events.The second example was in the medical area and involved the provision of remote medical services.Video interviews conducted via a high-resolution television conference system and multiple high-resolution videos obtained for diagnosis were simultaneously transmitted between a general hospital in a city and a rural clinic.
A Power Efficiency Metric for Comparing Energy Consumption in Future Wireless Networks in the Millimeter Wave and Terahertz bands (2022)

Future wireless cellular networks will utilize millimeter-wave and sub-THz frequencies and deploy small-cell base stations to achieve data rates on the order of hundreds of Gigabits per second per user. The move to sub-THz frequencies will require attention to sustainability and reduction of power whenever possible to reduce the carbon footprint while maintaining adequate battery life for the massive number of resource-constrained devices to be deployed. This article analyzes power consumption of future wireless networks using a new metric, the power waste factor ($ W $), which shows promise for the study and development of "green G" - green technology for future wireless networks. Using $ W $, power efficiency can be considered by quantifying the power wasted by all devices on a signal path in a cascade. We then show that the consumption efficiency factor ($CEF$), defined as the ratio of the maximum data rate achieved to the total power consumed, is a novel and powerful measure of power efficiency that shows less energy per bit is expended as the cell size shrinks and carrier frequency and channel bandwidth increase. Our findings offer a standard approach to calculating and comparing power consumption and energy efficiency.
Graphene oxide: an efficient and reusable carbocatalyst for aza-Michael addition of amines to activated alkenes (2011)

Graphene oxide was found to be a highly efficient, reusable and cost-effective organocatalyst for the aza-Michael addition of amines to activated alkenes to furnish corresponding β-amino compounds in excellent yields.
Structural features of low-molecular-weight heparins affecting their affinity to antithrombin (2009)

As part of a more extensive investigation on structural features of different low-molecular-weight heparins (LMWHs) that can affect their biological activities, Enoxaparin, Tinzaparin and Dalteparin were characterised with regards to the distribution of different chain length oligosaccharides as determined by size-exclusion (SE) chromatography, as well as their structure as defined by 2D-NMR spectra (HSQC). The three LMWHs were also fractionated into high affinity (HA) and no affinity (NA) pools with regards to their ability to bind antithrombin (AT). The HA fractions were further subfractionated and characterised. For the parent LMWHs and selected fractions, molecular weight parameters were measured using a SE chromatographic system with a triple detector (TDA) to obtain absolute molecular weights. The SE chromatograms clearly indicate that Enoxaparin is consistently richer in shorter oligosaccharides than Tinzaparin and Dalteparin. Besides providing the content of terminal groups and individual glucosamine and uronic acid residues with different sulfate substituents, the HSQC-NMR spectra permitted us to evaluate and correlate the content of the pentasaccharide, AT-binding sequence A-G-A*-I-A (AT-bs) through quantification of signals of the disaccharide sequence G-A*. Whereas the percent content of HA species is approximately the same for the three LMWHs, substantial differences were observed for the chain distribution of AT-bs as a function of length, with the AT-bs being preferentially contained in the longest chains of each LMWH. The above information will be useful in establishing structure-activity relationships currently under way. This study is therefore critical for establishing correlations between structural features of LMWHs and their AT-mediated anticoagulant activity.
Data-bearing halftone image alignment and assessment on 3D surface (2020)

An alignment approach for data-bearing halftone images, which are a visually pleasant alternative to barcodes, is proposed in this paper. In this paper, we address the alignment problem of data-bearing halftone images on a 3D surface. Different types of surfaces have been tested , using our proposed approach, and high accuracy results have been achieved. Additionally, we also develop a data retrieval tool from an aligned image, in order to decode the data embedded in the original image. A system to assess the accuracy of alignment is introduced to quantify the effectiveness of the proposed alignment approach.
Up‐regulated neuronal COX‐2 expression after cortical spreading depression is involved in non‐REM sleep induction in rats (2007)

Cortical spreading depression is an excitatory wave of depolarization spreading throughout cerebral cortex at a rate of 2-5 mm/min and has been implicated in various neurological disorders, such as epilepsy, migraine aura, and trauma. Although sleepiness or sleep is often induced by these neurological disorders, the cellular and molecular mechanism has remained unclear. To investigate whether and how the sleep-wake behavior is altered by such aberrant brain activity, we induced cortical spreading depression in freely moving rats, monitoring REM and non-REM (NREM) sleep and sleep-associated changes in cyclooxygenase (COX)-2 and prostaglandins (PGs). In such a model for aberrant neuronal excitation in the cerebral cortex, the amount of NREM sleep, but not of REM sleep, increased subsequently for several hours, with an up-regulated expression of COX-2 in cortical neurons and considerable production of PGs. A specific inhibitor of COX-2 completely arrested the increase in NREM sleep. These results indicate that up-regulated neuronal COX-2 would be involved in aberrant brain excitation-induced NREM sleep via production of PGs.
Resist evauation at 50 nm in the EUV using interferometric spatial-frequency-doubled imaging (2003)

By using a spatial frequency doubling method, our 10x Schwarzschild optic can print high-contrast features at 50 nm with low line-edge roughness (LER). In this paper, we also present new techniques for evaluating photoresist at EUV wavelengths using our system. One method is used to determine the ultimate resolution of a resist through linewidth vs. dose measurements. Another is to investigate line-edge roughness properties by varying the aerial image contrast of a pattern. A novel filtering method is proposed that would allow multiple contrasts to be printed in a single exposure. This is achieved by varying the duty cycle and line/space transmission levels of the object grating. Since this is a single exposure technique it would allow for mroe controlled contrast tests when evaluating resists.
An automated integrated platform for rapid and sensitive multiplexed protein profiling using human saliva samples (2020)

During the last decade, saliva has emerged as a potentially ideal diagnostic biofluid for noninvasive testing. In this paper, we present an automated, integrated platform useable by minimally trained personnel in the field for the diagnosis of respiratory diseases using human saliva as a sample specimen. In this platform, a saliva sample is loaded onto a disposable microfluidic chip containing all the necessary reagents and components required for saliva analysis. The chip is then inserted into the automated analyzer, the SDReader, where multiple potential protein biomarkers for respiratory diseases are measured simultaneously using a microsphere-based array via fluorescence sandwich immunoassays. The results are read optically, and the images are analyzed by a custom-designed algorithm. The fully automated assay requires as little as 10 μL of saliva sample, and the results are reported in 70 min. The performance of the platform was characterized by testing protein standard solutions, and the results were comparable to those from the 3.5-h lab bench assay that we have previously reported. The device was also deployed in two clinical environments where 273 human saliva samples collected from different subjects were successfully tested, demonstrating the device’s potential to assist clinicians with the diagnosis of respiratory diseases by providing timely protein biomarker profiling information. This platform, which combines non-invasive sample collection and fully automated analysis, can also be utilized in point-of-care diagnostics.
Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan (2004)

Two actinomycete strains isolated from two patients with lung nocardiosis between 1995 and 1997 in Japan were assigned to novel species of the genus Nocardia based on morphological and chemical criteria. Comparative 16S rRNA gene sequence analysis of the two strains revealed that they belong to the genus Nocardia and are most closely related to the species Nocardia beijingensis. Determination of DNA-DNA relatedness indicated that these strains could be assigned to two novel species. Based on their phenotypic and phylogenetic characters, two novel species of the genus Nocardia are proposed: Nocardia araoensis sp. nov. for IFM 0575(T) (=NBRC 100135(T)=JCM 12118(T)=DSM 44729(T)) and Nocardia pneumoniae sp. nov. for IFM 0784(T) (=NBRC 100136(T)=JCM 12119(T)=DSM 44730(T)).
On the DoF of Parallel MISO BCs with Partial CSIT: Total Order and Separability (2017)

We study the degrees of freedom (DoF) of a K-user parallel MISO broadcast channel with arbitrary levels of partial CSIT over each subchannel. We derive a sum-DoF upperbound which depends on the average CSIT quality of each user. This upperbound is shown to be tight under total order, i.e. when the order of users with respect to their CSIT qualities is preserved over all subchannels. In this case, it is shown that separate coding over each subchannel is optimum in a sum-DoF sense.