gebhart/patrepeval huggingface dataset:
The 20 S proteasome core, active within apoptotic exosome-like vesicles, induces autoantibody production and accelerates rejection (2015)

Autoantibodies to components of apoptotic cells, such as anti-perlecan antibodies, contribute to rejection in organ transplant recipients. However, mechanisms of immunization to apoptotic components remain largely uncharacterized. We used large-scale proteomics, with validation by electron microscopy and biochemical methods, to compare the protein profiles of apoptotic bodies and apoptotic exosome-like vesicles, smaller extracellular vesicles released by endothelial cells downstream of caspase-3 activation. We identified apoptotic exosome-like vesicles as a central trigger for production of anti-perlecan antibodies and acceleration of rejection. Unlike apoptotic bodies, apoptotic exosome-like vesicles triggered the production of anti-perlecan antibodies in naïve mice and enhanced anti-perlecan antibody production and allograft inflammation in mice transplanted with an MHC (major histocompatibility complex)-incompatible aortic graft. The 20S proteasome core was active within apoptotic exosome-like vesicles and controlled their immunogenic activity. Finally, we showed that proteasome activity in circulating exosome-like vesicles increased after vascular injury in mice. These findings open new avenues for predicting and controlling maladaptive humoral responses to apoptotic cell components that enhance the risk of rejection after transplantation.
Mechanical Behaviors and Raman Shifts of Apatite and Collagen Phases in Bone Tissue (2016)

Bone is often regarded as a composite material consisting of mineral particles and organic matrix of mainly Type I collagen in microscopic scale. The mechanical properties of bone tissues in macroscopic scale depend on the structural organization and properties of constituents in the microscopic scale. Raman spectroscopy is known as useful tool for the analysis of material at ultra-structural level. The aim of this study are to observe the mechanical behaviors of mineral and collagen phases in bone tissues by using Raman imaging system and to investigate the effect of structural anisotropy of cortical bone on the mechanical responses. Cortical bone of bovine femoral diaphyses were used for specimen, where the longer edges of specimens were aligned to the parallel or perpendicular to the femoral axis. Raman microscope system was used for the analysis of mechanical response of bone tissue under tensile loading by the micro-tensile device. Imaging area was 30×30 μm and measurement points were 21×21 at 1.5 μm intervals. Raman shifts of specific Raman peaks were calculated from apatite crystal and collagen molecule in bone matrix. As the results, Raman shift decreased with increasing tensile stress. It was confirmed that the Raman shift was correlated to the lattice strain of apatite crystal measured by X-ray diffraction.
Bglbrick strategy for the construction of single domain antibody fusions (2017)

Single domain antibodies, recombinantly expressed variable domains derived from camelid heavy chain antibodies, are often expressed as multimers for detection and therapeutic applications. Constructs in which several single domain antibodies are genetically fused serially, as well as those in which single domain antibodies are genetically linked with domains that naturally form multimers, yield improvement in apparent binding affinity due to avidity. Here, using a single domain antibody that binds envelope protein from the Dengue virus, we demonstrated the construction of single domain antibody dimers using the Bglbrick cloning strategy. Constructing single domain antibodies and multimerization domains as Bglbrick parts enables the easy mixing and matching of parts. The dimeric constructs provided enhanced fluorescent signal in assays for detection of Dengue virus like particles over the monomeric single domain antibody.
Transition Metal‐Catalyzed Regio‐ and Stereoselective Aminobromination of Olefins with TsNH2 and NBS as Nitrogen and Bromine Sources. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Measurement report: Altitudinal variation of cloud condensation nuclei activation across the Indo-Gangetic Plain prior to monsoon onset and during peak monsoon periods: results from the SWAAMI field campaign (2021)

Abstract. Vertical distributions (altitude profiles) of condensation nuclei (CN) and cloud condensation nuclei (CCN) and their spatial variations across the Indo-Gangetic Plain (IGP) have been investigated based on airborne measurements carried out during the SWAAMI field campaign (June to July 2016) capturing the contrasting phases of the Indian monsoon activity in 2016 just prior to its onset and during its active phase. Prior to the monsoon onset, high concentrations of CN and CCN prevailed across the IGP, and the profiles revealed frequent occurrence of elevated layers (in the altitude range 1–3 km). Highest concentrations and elevated peaks with high values occurred over the central IGP. The scenario changed dramatically during the active phase of the monsoon, when the CN and CCN concentrations dropped (CN by 20 % to 30 % and CCN by 6 % to 25 %) throughout the IGP with more pronounced changes at altitudes higher than 3 km where decreases as high as &gt; 80 % were observed. These reductions have an east-to-west decreasing gradient, being most remarkable in the eastern IGP and very weak over the western IGP where the CN concentrations above 3 km increased during the monsoon. The activation ratios (ARs) showed contrasting features, increasing with increase in altitude, prior to the onset of monsoon, reversing the trend to decrease with increase in altitude during the active phase of the monsoon. The supersaturation spectrum became flatter during the active phase of the monsoon, indicating an increase in the hygroscopicity of aerosols following the mixing of surface-based emissions with the advected marine air mass.
Adhesive Interactions Regulate Transcriptional Diversity in Malignant B Cells (2010)

The genetic profiling of B-cell malignancies is rapidly expanding, providing important information on the tumorigenic potential, response to treatment, and clinical outcome of these diseases. However, the relative contributions of inherent gene expression versus microenvironmental effects are poorly understood. The regulation of gene expression programs by means of adhesive interactions was studied here in ARH-77 human malignant B-cell variants, derived from the same cell line by selective adhesion to a fibronectin matrix. The populations included cells that adhere to fibronectin and are highly tumorigenic (designated "type A" cells) and cells that fail to adhere to fibronectin and fail to develop tumors in vivo ("type F" cells). To identify genes directly affected by cell adhesion to fibronectin, type A cells deprived of an adhesive substrate (designated "AF cells") were also examined. Bioinformatic analyses revealed a remarkable correlation between cell adhesion and both B-cell differentiation state and the expression of multiple myeloma (MM)-associated genes. The highly adherent type A cells expressed higher levels of NFkappaB-regulated genes, many of them associated with MM. Moreover, we found that the transcription of several MM-related proto-oncogenes is stimulated by adhesion to fibronectin. In contrast, type F cells, which display poor adhesive and tumorigenic properties, expressed genes associated with higher levels of B-cell differentiation. Our findings indicate that B-cell differentiation, as manifested by gene expression profiles, is attenuated by cell adhesion to fibronectin, leading to upregulation of specific genes known to be associated with the pathogenesis of MM.
Automated Specimen Inspection, Quality Analysis, and Its Impact on Patient Safety: Beyond the Bar Code (2014)

Reduction in medical errors is a major focus of the US health system as it faces its largest restructuring in history. The emphasis on error reduction follows several revealing reports from the Institute of Medicine estimating the number of errors and resulting morbidity and mortality in US hospitals. The motivation for reducing medical errors is increased patient satisfaction as well as large reduction in healthcare costs. Therefore, automation (i.e., integrating, streamlining, and coordinating through technology) of the many processes within medical institutions should be a national priority.

Within laboratories, there are many sequential processes that must occur flawlessly to prevent errors. However, error rates in clinical laboratories have been estimated to be around 1%, which doesn't come close to an ideal goal of 1 error per million events, or a well-known quality concept called Six Sigma, which is 3.4 errors per million events. Many clinical laboratory errors occur in the sample receipt and preparation process, also known as accessioning (1, 2). Specimen accessioning errors may be attributed to many factors including improper labeling at the time of collection, inadequate vial filling, or selection of an inappropriate vial (e.g., citrate vs EDTA to prevent clotting). Collectively, these are considered phlebotomy errors. Additional errors may occur when reading the specimen information and determining if the specimen is appropriate for analysis (e.g., if it was transported on ice, if required). Even when all the previous parameters are within acceptable specifications, the specimen may have inherent patient-specific issues such as excessive icterus, lipemia, or hemolysis. Well-trained accessioners can identify most of these quality issues by careful inspection and by …
Single-monolayer inkjetted oligothiophene organic TFTs exhibiting high performance and low leakage (2004)

Through the use of a novel oligothiophene precursor, we have demonstrated organic TFTs exhibiting relatively high mobility while simultaneously retaining ultra-low leakage and excellent on-off ratios. The unique tendency of this material to self-assemble into a crystalline morphology allows non-uniform printed droplets to reorganize into high-quality monolayers. The resulting structure provides excellent electrostatic characteristics, ideal for low power analog applications.
A versatile method to fabricate particle-in-cavity plasmonic nanostructures (2011)

We have developed a versatile method to fabricate gold particle-in-ring and magnetic particle-in-nanobowl plasmonic nano-structures, which are of great potential for the investigation of the surface enhanced Raman scattering spectroscopy and the magneto-optical effect, respectively.
Recursive Fact-Finding: A Streaming Approach to Truth Estimation in Crowdsourcing Applications (2013)

This paper presents a streaming approach to solve the truth estimation problem in crowdsourcing applications. We consider a category of crowdsourcing applications where a group of individuals volunteer (or are recruited to) share certain observations or measurements about the physical world. Examples include reporting locations of gas stations that remain operational after a natural disaster or reporting locations of potholes on city streets. We call such applications social sensing. Ascertaining the correctness of reported observations is a key challenge in such applications, referred to as the truth estimation problem. This problem is made difficult by the fact that the reliability of individual sources is usually unknown a priori, since any concerned citizen may, in principle, participate. Moreover, the timescales of crowdsourcing campaigns of interest can be as small as a few hours or days, which does not offer enough history for a reputation system to converge. Instead, recent prior work, including our own, developed fact-finding algorithms to solve this problem by iteratively assessing the credibility of sources and their claims in the absence of reputation scores. Such algorithms, however, operate on the entire dataset of reported observations in a batch fashion, which makes them less suited to applications where new observations arrive continually. In this paper, we describe a streaming fact-finder that recursively updates previous estimates based on new data. The recursive algorithm solves an expectation maximization (EM) problem to determine the odds of correctness of different observations. We compare the performance of our recursive EM algorithm to a batch EM algorithm, as well as to several state-of-art fact-finders through extensive simulations. We also demonstrate convergence of the recursive algorithm to the results of the batch version through a real social sensing experiment. Our evaluation shows that the proposed approach can process data streams much more efficiently while keeping the truth estimation accuracy close to that of the (much slower) batch algorithm. Ours is therefore the first fact-finder developed with explicit consideration to the continuous update needs of crowd-sourcing applications.
Synthesis and Biological Evaluation of Methoxylated Analogues of the Newer Generation Taxoids IDN5109 and IDN5390 (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Structure Modification in Chemical Databases (2005)

This chapter contains sections titled: Introduction Permute Protonation and Formal Charges Tautomerism Nitrogen Configurations Duplicate Removal Nested Loop Application Statistics Impact on Docking Leatherface Protonation and Formal Charges Tautomerism Ionization and Tautomer Model Relationships between Structures Substructural Searching and Analysis Concluding Remarks
Thermal Erasure in Heat-Assisted Magnetic Recording (2020)

Finite-size scaling is utilized to study the erasure mechanism in heat-assisted magnetic recording (HAMR). Predicted scaling equations are evaluated both numerically and experimentally by using the write current-assist percentage (WCAP) method. The method estimates the erasing temperature of an external magnetic field by writing and erasing magnetization patterns at different frequencies. In particular, WCAP modeling shows that the Curie temperature scales according to the time scale that the recording grain is exposed to the elevated temperature. The deviation of the erase temperature from T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> for different values of the applied field is also used to estimate the scaling behavior of the anisotropy field H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sub> and the critical exponent β. In addition, the Stoner-Wohlfarth model is shown to be an accurate approximation for field angle dependence of the erasing process for the FePt media. Faster roll-off in the effective field is observed at small angles for the thermal ECC media.
AnArabidopsisgene network based on the graphical Gaussian model (2007)

We describe a gene network for the Arabidopsis thaliana transcriptome based on a modified graphical Gaussian model (GGM). Through partial correlation (pcor), GGM infers coregulation patterns between gene pairs conditional on the behavior of other genes. Regularized GGM calculated pcor between gene pairs among approximately 2000 input genes at a time. Regularized GGM coupled with iterative random samplings of genes was expanded into a network that covered the Arabidopsis genome (22,266 genes). This resulted in a network of 18,625 interactions (edges) among 6760 genes (nodes) with high confidence and connections representing approximately 0.01% of all possible edges. When queried for selected genes, locally coherent subnetworks mainly related to metabolic functions, and stress responses emerged. Examples of networks for biochemical pathways, cell wall metabolism, and cold responses are presented. GGM displayed known coregulation pathways as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included.
Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling (2015)

Infections and inflammation can lead to cachexia and wasting of skeletal muscle and fat tissue by as yet poorly understood mechanisms. We observed that gut colonization of mice by a strain of Escherichia coli prevents wasting triggered by infections or physical damage to the intestine. During intestinal infection with the pathogen Salmonella Typhimurium or pneumonic infection with Burkholderia thailandensis, the presence of this E. coli did not alter changes in host metabolism, caloric uptake, or inflammation but instead sustained signaling of the insulin-like growth factor 1/phosphatidylinositol 3-kinase/AKT pathway in skeletal muscle, which is required for prevention of muscle wasting. This effect was dependent on engagement of the NLRC4 inflammasome. Therefore, this commensal promotes tolerance to diverse diseases.
The Proto-Oncogene c- myc Is a Direct Target Gene of Epstein-Barr Virus Nuclear Antigen 2 (1999)

Epstein-Barr virus (EBV) infects and transforms primary B lymphocytes in vitro. Viral infection initiates the cell cycle entry of the resting B lymphocytes. The maintenance of proliferation in the infected cells is strictly dependent on functional EBNA2. We have recently developed a conditional immortalization system for EBV by rendering the function of EBNA2, and thus proliferation of the immortalized cells, dependent on estrogen. This cellular system was used to identify early events preceding induction of proliferation. We show that LMP1 and c-myc are directly activated by EBNA2, indicating that all cellular factors essential for induction of these genes by EBNA2 are present in the resting cells. In contrast, induction of the cell cycle regulators cyclin D2 and cdk4 are secondary events, which require de novo protein synthesis.
Poliovirus snapback double-stranded RNA isolated from infected HeLa cells is deficient in poly(A) (1987)

A portion of poliovirus double-stranded RNA (25 to 50%) isolated from infected HeLa cells contains hairpin loops at one end of the duplex structure. These structures rapidly reformed double-stranded molecules after denaturation and appeared as molecules of up to two times genome length upon electrophoresis in denaturing agarose gels. A second form of poliovirus double-stranded RNA was readily denaturable into genome length strands. When the hairpin RNA was treated with S1 nuclease, subsequent denaturation resulted in formation of strands of up to genome length. Hairpin molecules contained very little, if any, poly(A) sequences, suggesting that the hairpin forms after nucleolytic removal of the 3' end of plus-strand templates. We conclude that the hairpin double-stranded RNA found in infected cells is likely generated by intracellular nicking and self-priming and that it does not represent an intermediate in the process of RNA replication.
Targeting a Common Collaborator in Cancer Development (2010)

In this issue of Science Translational Medicine, Wallin et al. have identified a subset of breast and ovarian cancer cell lines that show synergistic response to the combination of doxorubicin and GDC-0941, a class IA phosphatidylinositol 3-kinase (PI3K) inhibitor. Here, we discuss the potential implications of these data on the clinical development of PI3K pathway inhibitors as cancer therapeutics.
Nicotine Population Pharmacokinetics in Healthy Adult Smokers: A Retrospective Analysis (2017)

The population model was able to describe in different populations the nicotine pharmacokinetics after single product use and after 4 days of ad libitum use of Tobacco Heating System, cigarettes, and of different nicotine replacement therapies with various routes of administration.
Failure of Physicians to Consider the Diagnosis of Pertussis in Children (1999)

To determine the ability of physicians to make a diagnosis of pertussis and factors associated with improved diagnosis, 8,235 children from 88 child care centers and 14 elementary schools from Quebec City, Quebec, Canada, were evaluated by using a questionnaire completed by parents and a medical record review. Children must have consulted a physician to be included in the evaluation. There were 558 children meeting the surveillance case definition and 416 meeting a modified World Health Organization case definition who consulted a physician. A diagnosis of pertussis was considered in 24%-26% of children meeting either case definition, made in 12%-14%, and reported for 6%. Pertussis diagnosis was significantly associated with having a history of pertussis exposure (P < or = .003), four pertussis-related symptoms (P < .001), and a cough for > or = 5 weeks (P < or = .05) and consulting in a hospital setting (P < or = .03). The proportion of cases of pertussis diagnosed and reported is low even when children present with classical symptoms.
Synchronization Issues for Smart Grids (2011)

The loss of time synchronization across a Smart Grid due to local A/D and D/A conversion processes between the digital domain and the analogue control domain is considered. It is shown that a local calibration can be implemented to enable a determination of clock skew in individual analog sub-systems. Given this information two correction strategies are explained, one based entirely on network-side modification of the control signal data stream. A second approach is based on modification of the control signal on individual client sub-systems allows use of a multi-cast control signal and facilitates both local and global synchronization of the control signals.
Scaling Trends in NAND Flash (2018)

As the 2D NAND Flash scaling plateaued due to physical and electrical scaling limitations, 3D NAND emerged as a strong successor to continue the scaling trend. 3D NAND has rapidly achieved maturity and is already in the 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> and 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> generation of technology with the total number of layers reaching 96 active layers. The improved cell characteristics of 3D NAND have enabled 4bits/cell capability, allowing for further bit density scaling. This paper describes some of the recent innovations in the 3D NAND technology and the key challenges ahead for continued scaling.