gebhart/patrepeval huggingface dataset:
In vivo intraclonal and interclonal kinetic heterogeneity in B-cell chronic lymphocytic leukemia (2009)

Clonal evolution and outgrowth of cellular variants with additional chromosomal abnormalities are major causes of disease progression in chronic lymphocytic leukemia (CLL). Because new DNA lesions occur during S phase, proliferating cells are at the core of this problem. In this study, we used in vivo deuterium ((2)H) labeling of CLL cells to better understand the phenotype of proliferating cells in 13 leukemic clones. In each case, there was heterogeneity in cellular proliferation, with a higher fraction of newly produced CD38+ cells compared with CD38- counterparts. On average, there were 2-fold higher percentages of newly born cells in the CD38+ fraction than in CD38- cells; when analyzed on an individual patient basis, CD38+ (2)H-labeled cells ranged from 6.6% to 73%. Based on distinct kinetic patterns, interclonal heterogeneity was also observed. Specifically, 4 patients exhibited a delayed appearance of newly produced CD38+ cells in the blood, higher leukemic cell CXC chemokine receptor 4 (CXCR4) levels, and increased risk for lymphoid organ infiltration and poor outcome. Our data refine the proliferative compartment in CLL based on CD38 expression and suggest a relationship between in vivo kinetics, expression of a protein involved in CLL cell retention and trafficking to solid tissues, and clinical outcome.
Vitreoretinal instruments: vitrectomy cutters, endoillumination and wide-angle viewing systems (2016)

There have been many advances in vitreoretinal surgery since Machemer introduced the concept of pars plana vitrectomy, in 1971. Of particular interest are the changes in the vitrectomy cutters, their fluidics interaction, the wide-angle viewing systems and the evolution of endoillumination through the past decade and notably in the last few years. The indications of 27-gauge surgery have expanded, including more complex cases. Cut rates of up to 16,000 cuts per minute are already available. New probe designs and pump technology have allowed duty cycle performances of near 100% and improved flow control. The smaller vitrectomy diameter can be positioned between narrow spaces, allowing membrane dissection and serving as a multifunctional instrument. Enhanced endoillumination safety can be achieved by changing the light source, adding light filters, increasing the working distance and understanding the potential interactions between light and vital dyes commonly used to stain the retina. Wide-angle viewing systems (contact, non-contact or a combination of both) provide a panoramic view of the retina. Non-contact systems are assistant-independent, while contact systems may be associated with better image resolution. This review will cover some current aspects on vitrectomy procedures, mainly assessing vitrectomy cutters, as well as the importance of endoillumination and the use of wide-angle viewing systems.
DEM Analysis on Flow Patterns of Geldart's Group A Particles in Fluidized Bed (2002)

A discrete particle model for flows of Geldart's Group A particles is investigated. It is known that Group A particles have a characteristic flow regime (homogeneous regime) in fluidized beds. It is found that the present simulation predicts the homogeneous regime and the hysteresis behavior in the bed pressure drop. By analyzing the stress chain in the particles bed, it is shown that the hysteresis behavior is caused by a change in the stress distribution in the particles bed.
Studies on the structures of udosaponins A,B,C,D,E and F from Aralia cordata THUNB. (1989)

Six new triterpenoid saponins, named udosaponins A, B, C, D, E, and F, were isolated as methyl esters, 2, 6, 7, 8, 9 and 11, respectively, along with five kinown saponins as methyl esters, 1, 3, 4, 5 and 10, from the aerial parts of Aralia cordata THUNB. (Araliaceae). On the basis of 13C-nuclear magnetic resonance spectra and chemical evidence, these saponins were established to be oleanane-type saponins having a glucuronopyranosyl residue at the C-3 position of oleanolic acid and hederagenin.
Moving pictures of the human microbiome (2011)

DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.
diffX: an algorithm to detect changes in multi-version XML documents (2005)

This paper presents the diffX algorithm for detecting changes between two versions of an XML document. The identified changes are reported as a script of edit operations. The script, when applied to the first version of the XML document, will produce the second version. The goal is to optimize the runtime of mapping the nodes between the two versions and to minimize the size of the edit script. To achieve this goal an isolated tree fragment mapping technique is used, in order to iteratively identify the largest matching tree fragments between the tree representations, of the two versions of the document. The mapping technique is robust enough to handle differences in both the structure and the content of the two trees. The generated edit script from the mapping acknowledges the different order sensitiveness of element and attributes of XML data model. The primitives for the edit script comprise both the atomic (node) and non-atomic (subtree) edit operations natural to XML document modification. The runtime of the algorithm is O(n2).
Mechanically Responsive Molecular Crystals (2015)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMechanically Responsive Molecular CrystalsPanče Naumov*†, Stanislav Chizhik‡§, Manas K. Panda†, Naba K. Nath†, and Elena Boldyreva*‡§View Author Information† New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates‡ Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of Russian Academy of Sciences, ul. Kutateladze, 18, Novosibirsk 630128, Russia§ Novosibirsk State University, ul. Pirogova, 2, Novosibirsk 630090, Russia*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 22, 12440–12490Publication Date (Web):November 4, 2015Publication History Received7 July 2015Published online4 November 2015Published inissue 25 November 2015https://doi.org/10.1021/acs.chemrev.5b00398Copyright © 2015 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views18773Altmetric-Citations599LEARN 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 InReddit PDF (23 MB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Crystal structure,Crystals,Deformation,Energy,Stress Get e-Alerts
An Advanced Hierarchical Motion Estimation Scheme With Lossless Frame Recompression and Early-Level Termination for Beyond High-Definition Video Coding (2011)

In this paper, we present a hardware-efficient fast algorithm with a lossless frame recompression scheme and early-level termination strategy for large search range (SR) motion estimation (ME) utilized in beyond high-definition video encoder. To achieve high ME quality for hierarchical motion search, we propose an advanced hierarchical ME scheme which processes the multiresolution motion search with an efficient refining stage. This enables high data and hardware reuse for much lower bandwidth and memory cost, while achieving higher ME quality than previous works. In addition, a lossless frame recompression scheme based on this ME algorithm is presented to further reduce bandwidth. A hierarchical memory organization as well as a leveling two-step data fetching strategy is applied to meet constraint of random access for hierarchical motion search structure. Also, the leveling compression strategy by allowing a lower level to refer to a higher one for compression is proposed to efficiently reduce the bandwidth. Furthermore, an early-level termination method suitable for hierarchical ME structure is also applied. This method terminates high-level redundant motion searches by establishing thresholds based on current block mode and motion search level; it also applies the early refinement termination in order to avoid unnecessary refinement for high levels. Experimental results show that the total scheme has a much lower bit rate increasing compared with previous works especially for high motion sequences, while achieving a considerable saving of memory and bandwidth cost for large SR of [-128,127].
Supermolecular structure of the enteropathogenic <i>Escherichia coli</i> type III secretion system and its direct interaction with the EspA-sheath-like structure (2001)

Enteropathogenic Escherichia coli (EPEC) secretes several Esp proteins via the type III secretion system (secreton). EspA, EspB, and EspD are required for translocation of the effector proteins into host cells, in which EspB and EspD are thought to form a pore in the host membrane. Recent study has shown that EspA forms a filamentous structure that assembles as a physical bridge between bacteria and host cell surfaces, which then functions as a conduit for the translocation of bacterial effectors into host cells. To investigate the supermolecular structure of the type III secreton in EPEC, we partially purified it from the bacteria membrane and observed it via transmission electron microscopy. The EPEC type III secreton was composed of a basal body and a needle part and was similar to those of Salmonella and Shigella, except for a sheath-like structure at the tip of the needle. The length of sheath-like structures varied; it extended more than 600 nm and was 10 times longer than the Shigella needle part. The putative major needle component, EscF, was required for both secretion of Esp proteins and needle complex formation. Interestingly, elongation of the sheath-like structure was observed under constitutive expression of EspA but not of EscF. Furthermore, the transmission electron microscopy view with immunogold labeled anti-EspA antibodies clearly showed that EspA is a component of the sheath-like structure. This study revealed, to our knowledge for the first time, the supermolecular structure of the EPEC type III secreton and its direct association with the EspA-sheath-like structure.
Database systems : design, implementation, and management (2000)

From the Publisher:
Database Systems: Design, Implementation, and Management, Fifth Edition is the only book that takes students step-by-step through the entire process of database development and creation. This text provides the most comprehensive, detailed, and clear coverage of database basics, with ample exercises and problems at the end of each chapter to encourage hands-on learning. After completing this text, users will gain the marketable skills and technical background necessary to compete in tomorrow's competitive database administration marketplace.
Enhanced islet expansion by β‐cell proliferation in young diabetes‐prone rats fed a protective diet (2010)

Type 1 diabetes is inhibited in diabetes-prone BioBreeding (BBdp) rats fed a low-antigen hydrolyzed casein (HC) diet. In cereal-fed BBdp rats, islet expansion is defective accompanied by a futile upregulation of islet neogenesis without increased islet mass, due to a subtle blockage in islet cell cycle. We hypothesized that islet growth is enhanced before insulitis in HC-fed young BBdp rats and that islet neogenesis could be stimulated by a trophic factor, islet neogenesis-associated protein (INGAP). beta-Cell homeostasis was analyzed using immunohistochemistry, morphometry, laser capture microdissection and RT-PCR in BBdp rats fed HC or cereal diets. beta-cell proliferation in small and medium islets, and the number and area fraction of medium and large islets were increased in HC-fed animals. In situ islet cell cycle analysis revealed an increased proportion of proliferating S + G2 cells in medium and large islets of 25-45 day HC-fed rats. Expression of the cell cycle inhibitor, p16(INK4a) correlated with islet size and the percentage of p16(INK4a+) beta-cells increased in HC-fed BBdp rats, likely reflecting an increase in large islet area fraction. In HC-fed rats, extra-islet insulin(+) clusters (EIC), insulin(+) duct cells, large islet area fraction, and beta-cell mass were increased. Neurogenin-3 and Pdx-1, markers of beta-cell progenitors, were increased in EIC of weanling HC-fed rats. Daily injection of INGAP (30-45 days) increased the number of small islets, total islets, and insulin(+) cells in small ducts. Thus, in BBdp rats fed a protective HC diet, beta-cell expansion is enhanced through increased beta-cell proliferation and stimulation of islet neogenesis.
Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens (2009)

Models of mammalian regulatory networks controlling gene expression have been inferred from genomic data but have largely not been validated. We present an unbiased strategy to systematically perturb candidate regulators and monitor cellular transcriptional responses. We applied this approach to derive regulatory networks that control the transcriptional response of mouse primary dendritic cells to pathogens. Our approach revealed the regulatory functions of 125 transcription factors, chromatin modifiers, and RNA binding proteins, which enabled the construction of a network model consisting of 24 core regulators and 76 fine-tuners that help to explain how pathogen-sensing pathways achieve specificity. This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells.
Growth of diamond thin films by dc plasma chemical vapor deposition (1987)

Diamond thin films have been formed by dc plasma chemical vapor deposition with a high growth rate (∼20 μm/h). The diamond has been grown from methane (CH4) and hydrogen (H2) mixed gases on Si and α-Al2O3 substrates at a pressure of 200 Torr without surface scratching by diamond or c-BN powder. The obtained films have good crystallinity in the sense of electron and x-ray diffraction. Vicker’s hardness of the film is the same as that of natural diamond (∼10 000 kg/mm2). The influence of the dc discharge in a low vacuum (∼200 Torr) on diamond synthesis will be discussed briefly.
A Journey through Torah: A Critique of the Documentary Hypothesis (2014)

A Journey Through Torah: A Critique of the Documentary Hypothesis by Ben Zion Katz, Jerusalem: Urim Publications, 2012, 144 pp. How is a traditional Jew supposed to deal with the Documentary Hypothesis (DH)? These days, the entire academic world of biblical scholarship seems to agree that Mosaic authorship of the Bible is untenable, that multiple authors over many time periods are responsible for different parts of the Five Books of the Torah, and that a redactor put them all together, leaving in many repetitions, differences in style, and contradictions. The approach taken by many traditional Jews is to ignore the DH, branding it apikorsut (heresy) and a corrupting influence that undermines faith. There have certainly been critiques of the DH, but many of these are by now outdated or not comprehensive enough (e.g., R. David Zvi Hoffmann's commentary on the Torah, Umberto Cassuto's The Documentary Hypothesis). Most traditional Jews try to live according to the statement made by Rav Soloveitchik in the first chapter of The Lonely Man of Faith, I have not even been troubled by the theories of Biblical criticism which contradict the very foundations upon which the sanctity and integrity of the Scriptures rest, mainly by not investigating the matter too deeply, or ignoring it altogether. In this short book, Ben Zion Katz confronts the DH head on, in an honest and open way. He first indicates various flaws in the approach (the orthographic argument, pointing out that the Bible uses the more ancient forms of certain words, e.g., na'arah without a final letter he, was particularly intriguing, p. 40), but also notes where certain conclusions must be taken seriously. He then amasses sources from the Talmud through the medieval Sages who, at least partially, accept certain aspects of both lower criticism (textual emendation) and higher criticism (authorship). The Talmud (TB Bava Batra 15a) famously discusses the last eight verses of the Bible, detailing the death of Moses, and offers the opinion of R. that they were written by Joshua. Later, Ibn Ezra (d. 1164) discussed the secret of the twelve, verses that he believes were added to the Bible after the death of Moses. R. the Pious (d. 1217), in comments that would later be censored, similarly notes passages that are post-Mosaic (the book's author first discussed this in a 1997 article in the Jewish Bible Quarterly, Judah HaHasid: Three Controversial Commentaries, 25:1). …
Thermal management challenges in forced convection tablets (2015)

Handheld devices with computing capabilities that match laptops and desktops have recently emerged as market drivers in the consumer electronics industry. To accommodate such high performance in small form-factors like that of a tablet is a thermal management challenge. In touch-interactive electronics devices like tablets, skin temperature is as important as the processor temperature. Cooling by natural convection alone is insufficient to address the higher power density found in this class of high-performance tablet. Therefore, these devices require forced convection solutions. This study presents the thermal management challenges of a forced convection tablet using experimental and computational techniques. One such thermal challenge stems from the blower speed versus ergonomic requirements of acoustics. To understand more about this relation, the tablet is experimentally characterized for acoustics for several controlled blower speeds. The tablet is also characterized using airflow bench tests, infrared thermography and thermocouple measurements. The system-level thermal model of the tablet is constructed using FloTHERM XT®. The validated model serves as a test vehicle to study alternate thermal management strategies and understand their impact on the overall product design.
<title>Evaluation of multiple quantum well SLM</title> (2000)

Poor performance in key components has limited the development of optical target recognition systems. New components are now available, however, that exhibit size and speed characteristics compatible with image processing applications. The U.S. Army Aviation and Missile Command is well known for acquiring and testing a variety of spatial light modulators for image processing applications. We have recently acquired a pair of Sanders Multiple Quantum Well Spatial Light Modulators. These modulators will be evaluated in a manner similar to that used with previous modulators to determine contrast ratio, switching characteristics, optical efficiency, and residual phase modulation. The results of these measurements will be presented.
Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase (1993)

Rational ligand design is a complex problem that can be divided into three parts: the search for optimal positions and orientations of functional groups in the binding site, the connection of such positions to form candidate ligands, and the estimation of their binding constants. Approaches for addressing the first two parts of the problem are described in the present work. They are applied to the construction of peptide ligands in the binding site of the human immunodeficiency virus 1 (HIV-1) proteinase. The primary objective is to test the method by comparison of the results with the MVT-101 complex structure for which coordinates are available; the results obtained with the liganded and unliganded proteinase structure are used to examine the utility of the latter for binding studies. A secondary objective is to show how to find new inhibitor candidates. The multiple copy simultaneous search (MCSS) method is utilized to search for optimal positions and orientations of a set of functional groups. For peptide ligands, functional groups corresponding to the protein main chain (N-methylacetamide) and to protein side chains (e.g., methanol, ethyl guanidinium) are used. The resulting N-methylacetamide minima are connected to form hexapeptide main chains with a simple pseudoenergy function that permits a complete search of all possible ways of connecting the minima. Side chains are added to the main-chain candidates by application of the same pseudoenergy function to the appropriate functional group minima. A set of 15 hexapeptides with the sequence of MVT-101 is then minimized by a Monte Carlo scheme, which allows for escape from local minima. Comparison of the MCSS results with the structure of MVT-101 in the HIV-1 binding site showed that all of its functional group positions correspond (within 2.4 A) to some (usually more than one) MCSS minima. There were also many other low-energy MCSS minima which do not appear in any known inhibitors, e.g., methyl ammonium minima in the neighborhood of the catalytic aspartates. Among the 15 lowest minima are seven hexapeptides with the same main-chain orientation as the one found by X-ray crystallography for the inhibitor MVT-101 in the binding site and eight with the main chain oriented in the opposite direction; the latter tend to be more stable. [Addendum: These results are in agreement with recent high-resolution crystallographic data provided after the study was completed.(ABSTRACT TRUNCATED AT 400 WORDS)
Power Saving Mechanism Based on Simple Moving Average for 802.3ad Link Aggregation (2009)

Abstract- In this paper, we propose a power saving mechanism based on a simple moving average of the traffic rate in 802.3ad link aggregation. Two key components comprise the proposed mechanism: (1) a negotiation protocol for both nodes connected to an 802.3ad aggregated link and (2) an algorithm to estimate an appropriate number of active links to comprise the aggregated link in accordance with the current rate of traffic outbound on the link. We present an evaluation of the characteristics of the algorithm and its performance through simulation with real traffic trace data. Our simulations demonstrate that under certain conditions the proposed algorithm is capable of reducing the average number of active links by as much as 25.4% (6.7 W out of 26.4 W).
After Columbine: A Schoolplace Violence Prevention Manual. (1999)

This study highlights a potential source of androcentric bias which could be addressed to improve equity for women surgeons.
The impact of chromatin remodelling on cellulase expression in Trichoderma reesei (2015)

The regulation of xylanase and cellulase expression in T. reesei is not only restricted to the action of transcription factors but is clearly related to changes in the chromatin packaging. Both the applied condition and the presence of Xyr1 influence chromatin status.