gebhart/patrepeval huggingface dataset:
Tumors Associated With Oncogenic Osteomalacia Express Genes Important in Bone and Mineral Metabolism (2002)

Oncogenic osteomalacia (OOM) is associated with primitive mesenchymal tumors that secrete phosphaturic factors resulting in low serum concentrations of phosphate and calcitriol, phosphaturia, and defective bone mineralization. To identify overexpressed genes in these tumors, we compared gene expression profiles of tumors resected from patients with OOM and histologically similar control tumors using serial analysis of gene expression (SAGE). Three hundred and sixty-four genes were expressed at least twofold greater in OOM tumors compared with control tumors. A subset of 67 highly expressed genes underwent validation with an extended set of OOM and control tumors using array analysis or reverse-transcription polymerase chain reaction (RT-PCR). Ten of these validated genes were consistently overexpressed in all OOM tumors relative to control tumors. Strikingly, genes with roles in bone matrix formation, mineral ion transport, and bone mineralization were highly expressed in the OOM tumors.
Rethinking the Objectives of Decision Aids: A Call for Conceptual Clarity (2007)

Health decision aids are a potentially valuable adjunct to patient-physician communication and decision making. Although the overarching goal of decision aids--to help patients make informed, preference-sensitive choices--is widely accepted, experts do not agree on the means to achieve this end. In this article, the authors critically examine the theoretical basis and appropriateness of 2 widely accepted criteria used to evaluate decision aids: values clarification and reduction of decisional conflict. First, they argue that although clarifying values is central to decision making under uncertainty, it is not clear that decision aids--as they have been conceived and operationalized so far--can and should be used to achieve this goal. The pursuit of clarifying values, particularly values clarification exercises, raises a number of ethical, methodological, and conceptual issues, and the authors suggest research questions that should be addressed before values clarification is routinely endorsed. Second, the authors argue that the goal of reducing decisional conflict is conceptually untenable and propose that it be eliminated as an objective of decision aids.
High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes (2020)

ABSTRACT Isothermal nucleic acid amplification tests (iNAT), such as loop-mediated isothermal amplification (LAMP), are good alternatives to polymerase chain reaction (PCR)-based amplification assays, especially for point-of-care and low resource use, in part because they can be carried out with relatively simple instrumentation. However, iNATs can generate spurious amplicons, especially in the absence of target sequences, resulting in false positive results. This is especially true if signals are based on non-sequence-specific probes, such as intercalating dyes or pH changes. In addition, pathogens often prove to be moving, evolving targets, and can accumulate mutations that will lead to inefficient primer binding and thus false negative results. Internally redundant assays targeting different regions of the target sequence can help to reduce such false negatives. Here we describe rapid conversion of three previously described SARS-CoV-2 LAMP assays that relied on non-sequence-specific readout into assays that can be visually read using sequence-specific fluorogenic oligonucleotide strand exchange (OSD) probes. We evaluate one-pot operation of both individual and multiplex LAMP-OSD assays and demonstrate detection of SARS-CoV-2 virions in crude human saliva.
Artifact properties of carbon nanotube yarn electrode in magnetic resonance imaging (2013)

Employing the CNTY electrode may generate much less field distortion in the vicinity, improve local MR image quality and possibly be beneficial in various aspects.
Teaching Statistical Principles with a Roulette Simulation (2013)

This paper uses the game of roulette in a simulation setting to teach students in an introductory Stats course some basic issues in theoretical and empirical probability. Using an Excel spreadsheet with embedded VBA (Visual Basic for Applications), one can simulate the empirical return and empirical standard deviation for a range of bets in Roulette over some predetermined number of plays. In particular, the paper illustrates the difference between different playing strategies by contrasting a low payout bet (say a bet on âredâ) and a high payout bet (say a bet on a particular number) by considering the expected return and volatility associated with the bets. The paper includes an Excel VBA based simulation of the Roulette wheel where students can make bets and monitor the return on the bets for one play or multiple plays. In addition it includes a simulation of the casino house advantage for repeated multiple plays; that is, it allows students to see how casinos may derive a new certain return equal to the house advantage by entertaining large numbers of bets which will systematically drive the volatility of the house advantage down to zero. This simulation has been shown to be especially effective at theUniversityofCape Townfor teaching first year Statistics students the subtler points of probability, as well as encouraging discussions around the risk-return trade-off facing gamblers. The program has also been shown to be useful for teaching students the principles of theoretical and empirical probabilities as well as an understanding of volatility.
OPTIMIZATION OF LOCAL PARALLEL INDEX (LPI) IN PARALLEL/DISTRIBUTED DATABASE SYSTEMS (2016)

The widespread growth of data has created many problems for businesses, such as delay requests; in this paper, we propose several methods of partitioning an index B*Tree in multi-processor machines in parallel/distributed database systems and collaboration between processors when executing multi-queries. When optimizing, indexing automatically comes to mind; we distinguish two types of indexing: B*Tree and Bitmap. Since the advent of multicore computers (multi processors) parallelism becomes an indispensable part of optimization. Our work will focus on partitioning each table on three parts following indexing key partitioning; each processor will host a partition of the index, and the first processor that will finish will immediately take another partition of the index pending according to the priority. The parallelism will reduce the CPU cost then reduces execution time; collaboration between processors will further reduce these costs.
Structure–Activity Relationship Studies of Orally Active Antimalarial 2,4-Diamino-thienopyrimidines (2015)

Based on the initial optimization of orally active antimalarial 2,4-diamino-thienopyrimidines and with the help of metabolite identification studies, a second generation of derivatives involving changes at the 2- and 4-positions of the thienopyrimidine core were synthesized. Improvements in the physiochemical properties resulted in the identification of 15a, 17a, 32, and 40 as lead molecules with improved in vivo exposure. Furthermore, analogue 40 exhibited excellent in vivo antimalarial activity when dosed orally at 50 mg/kg once daily for 4 days in the Plasmodium berghei mouse model, which is superior to the activity seen with previously reported compounds, and with a slightly improved hERG profile.
Multi-Gb/s multi-mode LDPC decoder architecture for IEEE 802.11ad standard (2014)

This paper presents an area-efficient multi-Gbps multi-mode LDPC decoder architecture for 60GHz wireless gigabit communications. A novel, low-complexity local switch is proposed to implement the multi-mode dynamic column-shifting scheme. Furthermore, the usage of a one's-complement instead of a two's-complement number system is explored. Moreover, an efficient quantization method is also presented to reduce the memory and area requirement of the decoder. The synthesis and layout is performed using TSMC 65-nm CMOS technology. Post layout results show that the proposed decoder requires only 0.575 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of area to achieve a throughput of 9.25 Gb/s for all code rates defined under IEEE 802.11ad. The proposed architecture shows much better throughput, as well as better area- and energy-efficiency, compared to other multi-mode LDPC architectures.
Java Data Objects (2002)

From the Publisher:
Java Data Objects is a standardized Java API for object persistence. It facilitates the storage and retrieval of complex object models with various storage mechanisms, including both object and relational databases. Analysts agree that JDO's transparent persistence will accelerate software development and yield more flexible applications and object models.

According to Infoworld, The JDO standard promises to be a winner for business leaders and corporate developers alike. Unifying data accessthat is, using familiar Java constructs to access information housed in relational databases, object databases, file systems, or even flash RAMmeans that corporate applications will experience an increase in usability, portability and integration.

This book is for Java developers, designers and architects with a good understanding of the Java language who wish to write applications that use JDO for persistence. Prior knowledge of JDBC and J2EE is not specifically required, but would help to accelerate the reader's understanding of JDO's relationship with these technologies.

The companion CD-ROM includes the following JDO implementations:FastObjects, Kodo JDO, LiDO and OpenFusion JDO.
Preferential transfer of the complete glycan is determined by the oligosaccharyltransferase complex and not by the catalytic subunit (2006)

Most eukaryotic cells show a strong preference for the transfer in vivo and in vitro of the largest dolichol-P-P-linked glycan (Glc(3)Man(9)GlcNAc(2)) to protein chains over that of biosynthetic intermediates that lack the full complement of glucose units. The oligosaccharyltransferase (OST) is a multimeric complex containing eight different proteins, one of which (Stt3p) is the catalytic subunit. Trypanosomatid protozoa lack an OST complex and express only this last protein. Contrary to the OST complex from most eukaryotic cells, the Stt3p subunit of these parasites transfers in cell-free assays glycans with Man(7-9)GlcNAc(2) and Glc(1-3)Man(9)GlcNAc(2) compositions at the same rate. We have replaced Saccharomyces cerevisiae Stt3p by the Trypanosoma cruzi homologue and found that the complex that is formed preferentially transfers the complete glycan both in vivo and in vitro. Thus, preference for Glc(3)Man(9)GlcNAc(2) is a feature that is determined by the complex and not by the catalytic subunit.
Detection of apnoeas, hypopnoeas and arousals by the AutoSet in the sleep apnoea/hypopnoea syndrome (1998)

Limited sleep study systems are increasingly being used to diagnose the sleep apnoea/hypopnoea syndrome, but validation is essential and detection of arousal's desirable. One such system (AutoSet) was validated on an event-by-event basis, and the hypothesis that sudden large breaths detected by this system mark arousal from sleep was also examined. Twenty consecutive patients (apnoea/hypopnoea index (AHI) 39+/-6 (SEM)) underwent polysomnography (PSG), which included real-time signals of AutoSet (Version 3.03) scored events. PSG respiratory events were defined using airflow and thoracoabdominal movement and AutoSet events using nasal pressure. All apnoeas were scored by both systems, but 41% more hypopnoeas were scored on PSG and these were clinically significant, with 78% ending in cortical arousal. Twenty per cent of apnoeas and hypopnoeas scored by the AutoSet occurred during wakefulness. Large breaths, defined as a two-thirds increase in ventilation, marked 77% of respiratory-associated but only 9% of spontaneous arousals. Large breaths also marked 48% of "autonomic" arousals following respiratory events without visible electroencephalographic changes. Twenty-seven per cent of large breaths occurred during wakefulness. This study shows that the AutoSet and the standard polysomnographic approach differ in their detection of hypopnoeas. The AutoSet underdetected hypopnoeas during sleep, but also included some hypopnoeas occurring during wakefulness. Detection of large breaths may potentially be useful for identifying respiratory arousals. Detection of periods of wakefulness may improve the accuracy of the system.
A fingerprinting method for chondroitin/dermatan sulfate and hyaluronan oligosaccharides (2000)

A previously published method for the analysis of glycosaminoglycan disaccharides by high pH anion exchange chromatography (Midura,R.J., Salustri,A., Calabro,A., Yanagishita,M. and Hascall,V.C. (1994), Glycobiology,4, 333-342) has been modified and calibrated for chondroitin and dermatan sulfate oligosaccharides up to hexasaccharide in size and hyaluronan oligosaccharides up to hexadecasaccharide. For hyaluronan oligosaccharides chain length controls elution position; however, for chondroitin and dermatan sulfate oligosaccharides elution times primarily depend upon the level of sulfation, although chain length and hence charge density plays a role. The sulfation position of GalNAc residues within an oligosaccharide is also important in determining its elution position. Compared to 4-sulfation a reducing terminal 6-sulfate retards elution; however, when present on an internal GalNAc residue it is the 4-sulfate containing oligosaccharide which elutes later. These effects allow discrimination between oligosaccharides differing only in the position of GalNAc sulfation. Using this simple methodology, a Dionex CarboPac PA-1 column with NaOH/NaCl eluents and detection by absorbance at 232 nm, a quantitative analytical fingerprint of a chondroitin/dermatan sulfate chain may be obtained, allowing a determination of the abundance of chondroitin sulfate, dermatan sulfate, and hyaluronan along with an analysis of structural features with a linear response to approximately 0.1 nmol. The method may readily be calibrated using either commercial disaccharides or the di- and tetrasaccharide products of a limit digest of commercial chondroitin sulfate by chondroitin ABC endolyase. Commercially available and freshly prepared shark, whale, bovine, and human cartilage chondroitin sulfates have been examined by this methodology and we have confirmed that freshly isolated shark cartilage CS contains significant amounts of the biologically important GlcA2Sbeta(1-3)GalNAc6S structure.
Synthesis of Some New (Nα-Dipicolinoyl)-bis-L-leucyl-DL-norvalyl Linear tetra and Cyclic octa Bridged Peptides as New Antiinflammatory Agents (2003)

In continuation to our search for new amino acid and peptide based anti-inflammatory agents, the suggestion, synthesis, structure elucidation of some N α -bis-dipicolinoyl amino acids, linear tetra and cyclic octa bridged peptides 1-9, of which four are new compounds 6-9, were herein realized. Accordingly, N α -bis-dipicolinoyl-L-leucine methyl ester 1, the corresponding acid 2, its bis-DL-norvalyl methyl ester homologue 3, the acid 4 and hydrazide 5 analogues were conventionally prepared. The tetrachlorophthalic acid hydrazine conjugate 6, anisaldehyde hydrazone 7, the benzenetetracarboxylic acid and naphthalenetetracarboxylic acid bis-L-leucyl-DL-norvalyl cyclic octa bridged peptides 8 and 9 respectively, were newly synthesized via condensation of the hydrazide 5 with the corresponding aldehyde or anhydride. The chromatographic, IR, NMR and mass spectral analysis confirmed the identities of the synthesized compounds. Comparable to the two reference antiinflammatory drugs indomethacin ® and voltaren ® (100%), the determined antiinflammatory potency of the candidates (carrageenan ® induced paw edema in rats) revealed a general significant activity (66 - 94%), except for the practically inactive 6 (∼1.5 % activity). In particular, the potency of the (N α -dipicolinoyl)-bis-L-leucyl-DL-norvalyl anisaldehyde hydrazone 7 was of 94 and 87%, comparable to the reference drugs. However, 7 also showed 58% protection against ulcer formation, comparable to null for indomethacin ® . Additionally, an acceptable acute toxicity was observed (LD 50 : 2833 mg/kg, comparable to 2700 and 2850 for indomethacin ® and voltaren ® respectively).
Effect of Superheat and Cavity Size on Frequency of Bubble Departure in Boiling (1977)

A theoretical model has been developed to predict the effect of cavity size (both radius and depth), and superheat on frequency of bubble departure by considering the effect on waiting time (time between the last bubble departure and appearance of the next one on the surface) and bubble growth time. An increase in cavity size or decrease in surface superheat results in longer waiting time and bubble growth time, thus causing a lower frequency. The model explains qualitatively the observed effect of superheat and cavity size on bubble departure frequency during pool boiling experiments with water on artificial cavities drilled by laser.
Solvothermal and surfactant-free synthesis of crystalline Nb2O5, Ta2O5, HfO2, and Co-doped HfO2 nanoparticles (2010)

A simple route to niobium, hafnium and tantalum oxide nanocrystals using a nonaqueous sol-gel route based on the solvothermal reaction of the corresponding metal chlorides with benzyl alcohol is presented. This approach can easily be extended to the preparation of high quality Co-doped HfO(2) nanoparticles of uniform size and shape and with a homogenous distribution of the magnetic ions. The structural characterization of all these nanomaterials as well as the magnetic properties of pure and doped hafnia, with special attention to the doping efficiency, are discussed. The obtained Co-doped hafnia exhibits paramagnetic properties with very weak antiferromagnetic interactions between Co ions moments.
Statistics on Adoption in the United States (1993)

Adoption is a topic of crucial importance both to those directly involved and to society. Yet, at this writing, the federal government collects no comprehensive national statistics on adoption. The purpose of this article is to address what we do know, what we do not know, and what we need to know about the statistics on adoption. The article provides an overview of adoption and describes data available regarding adoption arrangements and the characteristics of parents who relinquish children, of children who are adopted or in substitute care, and of adults who seek to adopt. Recommendations for future data collection are offered, including the establishment of a national data collection system for adoption statistics.
Adaptive rheology and ordering of cell cytoskeleton govern matrix rigidity sensing (2015)

Matrix rigidity sensing regulates a large variety of cellular processes and has important implications for tissue development and disease. However, how cells probe matrix rigidity, and hence respond to it, remains unclear. Here, we show that rigidity sensing and adaptation emerge naturally from actin cytoskeleton remodelling. Our in vitro experiments and theoretical modelling demonstrate a biphasic rheology of the actin cytoskeleton, which transitions from fluid on soft substrates to solid on stiffer ones. Furthermore, we find that increasing substrate stiffness correlates with the emergence of an orientational order in actin stress fibres, which exhibit an isotropic to nematic transition that we characterize quantitatively in the framework of active matter theory. These findings imply mechanisms mediated by a large-scale reinforcement of actin structures under stress, which could be the mechanical drivers of substrate stiffness-dependent cell shape changes and cell polarity.
High Efficiency Thermoacoustic Loudspeaker Made with a Silica Aerogel Substrate (2018)

Abstract The extremely low thermal effusivity of the silica aerogel is exploited to develop a high efficiency thermoacoustic (TA) loudspeaker with solid substrate. The deposition of the electrically conductive, low heat capacity active film on the silica aerogel surface is achieved with both the spray coating of silver nanowires and the sputter coating of gold films. The uniform spray coating of the hydrophobic silica aerogel is enabled by a low pressure plasma treatment, which however impairs its robustness. The spray‐coated samples prove to be fragile when subjected to elevated temperatures and thus not suitable for TA applications. Sputter coating, not requiring any treatment of the aerogel surface, allows the fabrication of working TA loudspeaker samples with a 100 nm gold active film. The electroacoustic response of the gold‐sputtered silica aerogel TA loudspeaker is characterized at different input power levels. The experimental results are compared with those present in literature, showing an improved efficiency with respect to the other TA loudspeakers with solid substrate.
Design of a novel Artificial Magnetic Conductor plane and its application for low-profile dipole (2010)

Artificial Magnetic Conductor (AMC) surface can be used as reflector or ground plane for low-profile antennas. In this paper, a novel AMC unit cell which is printed on grounded dielectric substrate is proposed; whose overall size is 10 mm × 10 mm (0.19λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5.8GHz</sub> ×0.19λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5.8GHz</sub> ). S11, reflection phase and surface impedance of the proposed AMC unit cell can be obtained by simulation. Two dipoles parallel placed over the proposed AMC structure and conversional PEC respectively. The overall height of the dipole with proposed AMC ground plane is 0.08λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5.8GHz</sub> , less than one tenth of operating wavelength, and the dipole backward radiation can be reduced. However, the overall height of dipole with PEC ground plane is 0.25λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5.8GHz</sub> . Simulation results verify the proposed AMC unit cell can be used as ground plane for low-profile antennas. The proposed unit cell is easily fabricated than mushroom type structure and has smaller size than UC-PBG structure and square patch structure.
ALK Inhibitor Response in Melanomas Expressing <i>EML4-ALK</i> Fusions and Alternate <i>ALK</i> Isoforms (2017)

Abstract Oncogenic ALK fusions occur in several types of cancer and can be effectively treated with ALK inhibitors; however, ALK fusions and treatment response have not been characterized in malignant melanomas. Recently, a novel isoform of ALK (ALKATI) was reported in 11% of melanomas but the response of melanomas expressing ALKATI to ALK inhibition has not been well characterized. We analyzed 45 melanoma patient-derived xenograft models for ALK mRNA and protein expression. ALK expression was identified in 11 of 45 (24.4%) melanomas. Ten melanomas express wild-type (wt) ALK and/or ALKATI and one mucosal melanoma expresses multiple novel EML4-ALK fusion variants. Melanoma cells expressing different ALK variants were tested for response to ALK inhibitors. Whereas the melanoma expressing EML4-ALK were sensitive to ALK inhibitors in vitro and in vivo, the melanomas expressing wt ALK or ALKATI were not sensitive to ALK inhibitors. In addition, a patient with mucosal melanoma expressing ALKATI was treated with an ALK/ROS1/TRK inhibitor (entrectinib) on a phase I trial but did not respond. Our results demonstrate ALK fusions occur in malignant melanomas and respond to targeted therapy, whereas melanomas expressing ALKATI do not respond to ALK inhibitors. Targeting ALK fusions is an effective therapeutic option for a subset of melanoma patients, but additional clinical studies are needed to determine the efficacy of targeted therapies in melanomas expressing wt ALK or ALKATI. Mol Cancer Ther; 17(1); 222–31. ©2017 AACR.