gebhart/patrepeval huggingface dataset:
Detection of the MYD88 L265P mutation in Waldenström’s macroglobulinemia using a highly sensitive allele-specific PCR assay. (2012)

8042 Background: Waldenström’s macroglobulinemia (WM) is a B-cell malignancy characterized by bone marrow (BM) infiltration with lymphoplasmacytic cells and production of an IgM paraprotein. By whole genome sequencing, we recently identified a somatic mutation (L265P) in the MYD88 gene in 27/30 (90%) WM patients (Treon et al, ASH 2011). To expand this finding for possible diagnostic testing, we developed an allele-specific PCR assay for MYD88 L265P and evaluated this assay in a large cohort of WM patients. Methods: An allele-specific PCR assay was developed with a threshold of detection of 0.125% for MYD88 L265P. DNA from bone marrow aspirates from 99 patients with the clinicopathological diagnosis of WM was used for assessment of MYD88 L265P expression by both allele-specific PCR and Sanger sequencing. Findings were correlated with clinical parameters using ANOVA. Results: We observed that 85/99 (86%) WM patients were positive for MYD88 L265P using the allele-specific PCR assay. Of the 85 allele-specific PCR positive patients, 81 demonstrated a detectable mutation peak by Sanger sequencing. All 14 allele-specific PCR negative patients remained negative by Sanger sequencing. By the allele-specific PCR assay, MYD88 L265P positive patients showed greater bone marrow involvement, higher serum IgM and lower serum IgA and IgG levels versus MYD88 L265P negative patients (p<0.008). Conclusions: MYD88 L265P is highly expressed in BM samples of WM patients using an allele-specific PCR assay, and is associated with greater bone marrow disease burden and serum IgM levels. Use of allele-specific PCR provides a simple and sensitive diagnostic tool for detection of the MYD88 L265P mutation.
Dynamic Surface Site Activation: A Rate Limiting Process in Electron Beam Induced Etching (2013)

We report a new mechanism that limits the rate of electron beam induced etching (EBIE). Typically, the etch rate is assumed to scale directly with the precursor adsorbate dissociation rate. Here, we show that this is a special case, and that the rate can instead be limited by the concentration of active sites at the surface. Novel etch kinetics are expected if surface sites are activated during EBIE, and observed experimentally using the electron sensitive material ultra nanocrystalline diamond (UNCD). In practice, etch kinetics are of interest because they affect resolution, throughput, proximity effects, and the topography of nanostructures and nanostructured devices fabricated by EBIE.
Compressed encoding for rank modulation (2011)

Rank modulation has been recently proposed as a scheme for storing information in flash memories. While rank modulation has advantages in improving write speed and endurance, the current encoding approach is based on the “push to the top” operation that is not efficient in the general case. We propose a new encoding procedure where a cell level is raised to be higher than the minimal necessary subset -instead of all - of the other cell levels. This new procedure leads to a significantly more compressed (lower charge levels) encoding. We derive an upper bound for a family of codes that utilize the proposed encoding procedure, and consider code constructions that achieve that bound for several special cases.
Spin-Transfer-Torque MRAM: the Next Revolution in Memory (2022)

This paper introduces the operation and features of Spin-Transfer-Torque Magnetoresistive Random Access Memory (STT-MRAM), and provides a brief history of the field. Then the four main applications of STT-MRAM are described. A review is given of the initial demonstration of perpendicular STT-MRAM and the subsequent development of this technology at IBM. Finally, several potential paths forward to more advanced applications are described.
Investigations of Polarization Dependent Loss in Polarization Modulated Analog Optical Links (2015)

Abstract : This report describes a polarization modulated link and the associated polarization dependent loss, including theory. The general system is discussed as well as the details for measuring and calculating polarization dependent loss in the system. A set of experiments are presented that looks at non-ideal alignment of the polarization modulation arc. In addition to the theory for polarization distortion and a compensation technique, the system is investigated when only partially compensated for polarization dependent loss induced nonlinearity. Finally, the polarization modulator nonlinearities are investigated, with the results showing the tradeoffs for using either the DC bias of a rotating half-wave plate for bias phase control. The report also details the code that contains the model used to analyze the system.
60-dB SNDR 100-MS/s SAR ADCs With Threshold Reconfigurable Reference Error Calibration (2017)

This paper presents a reference error calibration scheme for successive approximation register (SAR) analog-to-digital converters (ADCs) verified with two prototypes. Such a reference error often occurs in high-speed SAR ADCs due to the signal dependent fast switching transient, and leads to a large differential nonlinearity and missing codes, eventually degrading conversion accuracy. The calibration concept aims to differentiate the error outputs and correct them by simply performing a subtraction in the digital domain. It runs in the background with a little hardware overhead, and does not depend on the type of the input signal or reduce the dynamic range. Two prototypes were measured which are made up of different reference generation circuits. Design #1 has the reference voltage from off-chip and a 3-pF decoupling capacitor on-chip, while design #2 includes an on-chip reference buffer. Both designs were fabricated in 65-nm CMOS and achieve at least 9-dB improvement on signal-to-(Noise + Distortion) ratio (SNDR) after calibration. The total core area is around 0.012 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for both chips and the Nyquist SNDR of designs #1 and #2 is 59.03 and 57.93 dB, respectively.
Expression Profiling Identifies Novel Genetic Subgroups with Distinct Clinical Features and Outcome in High-Risk Pediatric Precursor B Acute Lymphoblastic Leukemia (B-ALL). A Children’s Oncology Group Study. (2007)

Abstract While 80% of children with B-ALL achieve long term survival, a significant number still relapse. In contrast to low and intermediate risk ALL, the biologic and genetic features of high risk disease have not been well characterized. COG P9906, testing an augmented BFM regimen, enrolled 271 B-ALL patients from 2000–2003 who were predicted to have poor outcomes based on prior trials. To study the heterogeneity of high risk B-ALL and to identify novel therapeutic targets, we obtained gene expression profiles (Affymetrix HG-U133Plus2) from the pre-treatment samples of 207/271 children on COG P9906. This cohort had a mean age of 10.9 yrs, a male predominance (66%), and a 4 year event free survival (EFS) of 61%. Patients with favorable (TEL-AML/trisomy 4+10) or very unfavorable (BCR-ABL/hypodiploidy) genetic features were excluded. While the cohort contained 20 cases with MLL rearrangements and 23 with E2A-PBX, the remainder had no known recurring genetic abnormalities. Using two unsupervised clustering methods (VxInsight, Hierarchical Clustering), an established method to identify outlier genes (COPA), and a novel method we developed to find genes tightly associated with recurring genetic abnormalities (ROSE), we identified 7 distinct cluster groups. Two of these clusters contained the MLL and E2A-PBX cases, while a third had cases with expression profiles similar to E2A-PBX but lacked the fusion transcript. Four clusters were completely novel and two of these were further distinguished by unique clinical and outcome features (see Fig.). One novel cluster (MC5) had strikingly favorable EFS (94.7% at 4 yrs.) with older children (mean age 14.1 yr) who were predominantly male (4:1). Highly expressed genes distinguishing this cluster included BRDG1, CABLES1, CENTG2, CHST2, MCAM and PTPRM. This cluster is very similar to the novel cluster previously described by Yeoh et al. (Cancer Cell, 1:133, 2002). A second novel cluster (MC4) had the most unfavorable outcome, with a 4 year EFS of only 21.0%. MC4 cases were notable for the highest mean WBC (196.7K/μL) and a preponderance of Hispanic children (p=0.002), known to have poorer responses to established therapies. Highly expressed genes in MC4 which may represent novel diagnostic and therapeutic targets include CRLF2, GPR110, IFITM1, MUC4 and TNFSF4. Many of these genes have been associated with an adverse response in solid tumors. As part of the NCI TARGET Project, in collaboration with St. Jude Children’s Research Hospital, genome wide copy number changes are being integrated with expression data to identify the initiating genetic lesions in these novel clusters. Gene expression profiling is highly useful in resolving the genetic heterogeneity of high risk ALL and in identifying novel therapeutic targets for this resistant disease. Figure Figure
High Surface Area, sp<sup>2</sup>-Cross-Linked Three-Dimensional Graphene Monoliths (2011)

Developing three-dimensional (3D) graphene assemblies with properties similar to those individual graphene sheets is a promising strategy for graphene-based electrodes. Typically, the synthesis of 3D graphene assemblies relies on van der Waals forces for holding the graphene sheets together, resulting in bulk properties that do not reflect those reported for individual graphene sheets. Here, we report the use of sol-gel chemistry to introduce chemical bonding between the graphene sheets and control the bulk properties of graphene-based aerogels. Adjusting synthetic parameters allows a wide range of control over surface area, pore volume, and pore size, as well as the nature of the chemical cross-links (sp(2) vs sp(3)). The bulk properties of the graphene-based aerogels represent a significant step toward realizing the properties of individual graphene sheets in a 3D assembly with surface areas approaching the theoretical value of an individual sheet.
Shift recompression-based feature mining for detecting content-aware scaled forgery in JPEG images (2012)

Content-aware image resizing, also known as image retargeting, seam carving, content-aware scaling, is originally proposed to automatically remove the paths of least importance, known as seams, to reduce image size or insert seams to extend it, in order to display images without distortion on various media especially on mobile devices, such as smartphones and PDAs. Content-aware scaling also allows removing entire objects from photographs without observed clues, and hence it has been used to tamper images. Due to the ubiquity of JPEG images on various mobile devices, it is increasingly necessary to authenticate these JPEG images for legitimate purposes. To detect the content-aware-based forgery in JPEG images, in this paper, we merge shift-recompression-based characteristic features in spatial domain and shift-recompression-based neighboring joint density in DCT domain together; an ensemble classifier is used to discriminate forged JPEG images from intact JPEG images. We also transfer other popular JPEG-based steganalysis methods to detecting the forgery. Experimental results show that steganalysis methods are effective in detecting context-aware-based JPEG forgery and our method is superior to other compared detection methods.
Linguistically-Adapted Structural Query Annotation for Digital Libraries in the Social Sciences (2012)

Query processing is an essential part of a range of applications in the social sciences and cultural heritage domain. However, outof-the-box natural language processing tools originally developed for full phrase analysis are inappropriate for query analysis. In this paper, we propose an approach to solving this problem by adapting a complete and integrated chain of NLP tools, to make it suitable for queries analysis. Using as a case study the automatic translation of queries posed to the Europeana library, we demonstrate that adapted linguistic processing can lead to improvements in translation quality. 1
Endothelialization of Heart Valve Matrix Using a Computer-Assisted Pulsatile Bioreactor (2009)

Although calcification remains as the main clinical concern associated with bioprosthetic heart valve replacement surgery, there is evidence that tissue deterioration leads to thromboembolism. In such instances, measures that prevent thrombosis may be beneficial. To minimize thrombosis, endothelialization of the valve surface before implantation has been proposed to facilitate coverage. In this study we aimed to define the optimal flow parameters for the endothelialization of decellularized heart valves using endothelial progenitor cell (EPC)-derived endothelial cells (ECs). We assessed the thrombogenic characteristics of the endothelialized heart valve surface using a bioreactor. EPC-derived ECs were seeded on decellularized porcine valve scaffolds. A computer-controlled bioreactor system was used to determine the optimal flow rates. Successful endothelialization was achieved by preconditioning the cell-seeded valves with stepwise increases in volume flow rate up to 2 L/min for 7 days. We show that decellularized valve scaffolds seeded with EPC-derived ECs improved the anti-thrombotic properties of the valve, whereas the scaffolds without ECs escalated the coagulation process. This study demonstrates that preconditioning of ECs seeded on valve matrices using a bioreactor system is necessary for achieving uniform endothelialization of valve scaffolds, which may reduce thrombotic activity after implantation in vivo.
Scheduling Processor Voltage and Frequency in Server and Cluster Systems (2005)

Modern server farm and cluster sites consume large quantities of energy both to power and cool the machines in the site. At the same time, less power supply redundancy is offered and power companies and government officials are requesting power consumption be reduced during certain time periods. These trends lead to the requirement of responding to rapid reductions in the maximum power the site may consume. Each possible solution must respond to the new power budget before a cascading failure occurs. Available techniques include powering down some nodes or slowing all nodes in a system uniformly. This work instead examines the feasibility of slowing nodes non-uniformly in response to their performance demands. This approach provides an opportunity to reduce the performance loss caused by a reduction in the power budget. This paper uses the execution characteristics of the work currently running on each processor of the system or cluster to predict the performance of the work at the available frequency settings. The scheduling mechanism selects the lowest frequency for the processor that provides essentially all of the available performance of the work. It ensures that the frequency fits within the available global power budget and, if not, reduces it so that it does. The paper demonstrates the approach using a simple, synthetic benchmark and then validates it using additional, real-world applications.
Polyurethane waste recycling. 1. Glycolysis and hydroglycolysis of water-blown foams (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolyurethane waste recycling. 1. Glycolysis and hydroglycolysis of water-blown foamsJohn Gerlock, Jacob Braslaw, and Mikio ZinboCite this: Ind. Eng. Chem. Process Des. Dev. 1984, 23, 3, 545–552Publication Date (Print):July 1, 1984Publication History Published online1 May 2002Published inissue 1 July 1984https://pubs.acs.org/doi/10.1021/i200026a023https://doi.org/10.1021/i200026a023research-articleACS PublicationsRequest reuse permissionsArticle Views655Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Three-dimensional tracking of fluorescent particles (2006)

Single molecule measurements are generally made in conditions that depart from physiological conditions, such as with molecules excised from cells or even immobilized on surfaces. Such departures can easily cause measurements on biomolecules to be inexact. A tracking instrument to follow a single molecule's path in three dimensions inside a living cell would be a major step towards enabling single-molecule observations in physiological conditions. We describe an instrument that will extend the state of the art in single-molecule tracking technology, allowing extended observations of single particles as they diffuse and are transported. Computations show that our approach should be capable of tracking a protein-sized object diffusing at intracellular speeds for average times of over two seconds - long enough to track a typical fluorescent molecule from capture to photobleaching.
Development of Rapid Canine Fecal Source Identification PCR-Based Assays (2014)

The extent to which dogs contribute to aquatic fecal contamination is unknown despite the potential for zoonotic transfer of harmful human pathogens. We used genome fragment enrichment (GFE) to identify novel nonribosomal microbial genetic markers potentially useful for detecting dog fecal contamination with PCR-based methods in environmental samples. Of the 679 sequences obtained from GFE, we used 84 for the development of PCR assays targeting putative canine-associated genetic markers. Twelve genetic markers were shown to be prevalent among dog fecal samples and were rarely found in other animals. Three assays, DG3, DG37, and DG72, performed best in terms of specificity and sensitivity and were used for the development of SYBR Green and TaqMan quantitative PCR (qPCR) assays. qPCR analysis of 244 fecal samples collected from a wide geographic range indicated that marker concentrations were below limits of detection in noncanine hosts. As a proof-of-concept, these markers were detected in urban stormwater samples, suggesting a future application of newly developed methods for water quality monitoring.
Abstract WMP43: Neurorestorative Therapy of Stroke in T2DM Mice With Exosomes Derived From Brain Endothelial Cells (2017)

MicroRNA-126 is primarily expressed in endothelial cells (ECs), and is emerging as a key player in the pathogenesis of type two diabetes (T2DM) induced vascular damage. Stroke in T2DM increases vascular and white matter (WM) damage in the ischemic brain, and has a poor prognosis compared to non-DM stroke. In this study, we investigated the neurorestorative effects of exosomes derived from mouse brain ECs (EC-Exo) as a treatment of stroke in T2DM mice. Methods: Adult male BKS.Cg-m+/+Lepr db /J (T2DM) and db/+ (non-DM) control mice (3-4 m) were subjected to right extraluminal permanent distal middle cerebral artery occlusion (dMCAo), and intravenous injection at 3 days after dMCAo with: 1) PBS; 2) Liposome mimic as vehicle control (3X10 10 ); 3): EC-Exo (3x10 10 ); 4) Knockdown of miR-126 in EC-Exo (miR-126-/-EC-Exo, 3X10 10 ); 5) Knock-in miR-126 in EC-Exo (miR-126+/+EC-Exo, 3X10 10 ). Mice were sacrificed at 28 days after dMCAo. Results: 1) T2DM-dMCAo mice exhibit significantly decreased blood serum, brain tissue and brain-EC miR-126 expression compared to non-DM-dMCAo mice. 2) EC-Exo contain higher levels of miR-126 than exosomes derived from other types of cells (smooth muscle cells, neurons, astrocytes and marrow stromal cells); 3) EC-Exo treatment significantly increases axonal outgrowth and increases capillary tube formation in vitro. Compared to PBS or liposome mimic treatment groups, EC-Exo treatment of stroke in T2DM-dMCAo mice: 4) is safe and does not appear to induce adverse side effects in physiological parameters and does not decrease lesion volume, but significantly improves neurological outcome and cognitive function after dMCAo; 5) significantly increases axon, myelin, vessel density and increases artery diameter in the ischemic boundary zone; 6) significantly increases perfused vessel density measured by FITC-dextran injection. 7) miR-126-/-EC-Exo treatment significantly decreases, but miR-126+/+EC-Exo increases miR-126 expression compared to EC-Exo control. 8) miR-126+/+EC-Exo treatment significantly improves functional outcomes when compared to miR-126-/-EC-Exo, or PBS control. Conclusion: Treatment of stroke with EC-Exo increases miR-126 expression and promotes neurorestorative effects after stroke in T2DM mice.
Toll-Like Receptor 21 of Chicken and Duck Recognize a Broad Array of Immunostimulatory CpG-oligodeoxynucleotide Sequences (2020)

CpG-oligodeoxynucleotides (CpG-ODNs) mimicking the function of microbial CpG-dideoxynucleotides containing DNA (CpG-DNA) are potent immune stimuli. The immunostimulatory activity and the species-specific activities of a CpG-ODN depend on its nucleotide sequence properties, including CpG-hexamer motif types, spacing between motifs, nucleotide sequence, and length. Toll-like receptor (TLR) 9 is the cellular receptor for CpG-ODNs in mammalian species, while TLR21 is the receptor in avian species. Mammalian cells lack TLR21, and avian cells lack TLR9; however, both TLRs are expressed in fish cells. While nucleotide sequence properties required for a CpG-ODN to strongly activate mammalian TLR9 and its species-specific activities to different mammalian TLR9s are better studied, CpG-ODN activation of TLR21 is not yet well investigated. Here we characterized chicken and duck TLR21s and investigated their activation by CpG-ODNs. Chicken and duck TLR21s contain 972 and 976 amino acid residues, respectively, and differ from TLR9s as they do not have an undefined region in their ectodomain. Cell-based TLR21 activation assays were established to investigate TLR21 activation by different CpG-ODNs. Unlike grouper TLR21, which was preferentially activated by CpG-ODN with a GTCGTT hexamer motif, chicken and duck TLR21s do not distinguish among different CpG-hexamer motifs. Additionally, these two poultry TLR21s were activated by CpG-ODNs with lengths ranging from 15 to 31 nucleotides and with different spacing between CpG-hexamer motifs. These suggested that compared to mammalian TLR9 and grouper TLR21, chicken and duck TLR21s have a broad CpG-ODN sequence recognition profile. Thus, they could also recognize a wide array of DNA-associated molecular patterns from microbes. Moreover, CpG-ODNs are being investigated as antimicrobial agents and as vaccine adjuvants for different species. This study revealed that there are more optimized CpG-ODNs that can be used in poultry farming as anti-infection agents compared to CpG-ODN choices available for other species.