gebhart/patrepeval huggingface dataset:
Epigenetics as an answer to Darwinâ€™s â€œspecial difficulty,â€ Part 2: natural selection of metastable epialleles in honeybee castes (2015)

In a recent perspective in this journal, Herb (2014) discussed how epigenetics is a possible mechanism to circumvent Charles Darwin's "special difficulty" in using natural selection to explain the existence of the sterile-fertile dimorphism in eusocial insects. Darwin's classic book "On the Origin of Species by Means of Natural Selection" explains how natural selection of the fittest individuals in a population can allow a species to adapt to a novel or changing environment. However, in bees and other eusocial insects, such as ants and termites, there exist two or more castes of genetically similar females, from fertile queens to multiple sub-castes of sterile workers, with vastly different phenotypes, lifespans, and behaviors. This necessitates the selection of groups (or kin) rather than individuals in the evolution of honeybee hives, but group and kin selection theories of evolution are controversial and mechanistically uncertain. Also, group selection would seem to be prohibitively inefficient because the effective population size of a colony is reduced from thousands to a single breeding queen. In this follow-up perspective, we elaborate on possible mechanisms for how a combination of both epigenetics, specifically, the selection of metastable epialleles, and genetics, the selection of mutations generated by the selected metastable epialleles, allows for a combined means for selection amongst the fertile members of a species to increase colony fitness. This "intra-caste evolution" hypothesis is a variation of the epigenetic directed genetic error hypothesis, which proposes that selected metastable epialleles increase genetic variability by directing mutations specifically to the epialleles. Natural selection of random metastable epialleles followed by a second round of natural selection of random mutations generated by the metastable epialleles would allow a way around the small effective population size of eusocial insects.
ChemInform Abstract: Direct Synthesis of Organic Azides from Alcohols Using 2‐Azido‐1,3‐dimethylimidazolinium Hexafluorophosphate. (2012)

Abstract Azide transfer of the title reagent to alcohols proceeds under mild conditions which have to be slightly changed depending on the substrate.
Adaptive antenna selection at mobile stations for SDMA in WiMAX networks (2009)

Abstract The IEEE 802.16/WiMAX standard has fully embraced multi‐antenna technology and can, thus, deliver robust performance and high transmission rates. Nevertheless, due to its inherent cost concerns, a WiMAX mobile station (MS) should preferably contain fewer radio frequency (RF) chains than antenna elements. This is because the former is often substantially more expensive than the latter. Thus, antenna selection, wherein a subset of antennas is dynamically selected to connect to the limited number of RF chains for transceiving, is a highly appealing performance enhancement technique for multi‐antenna WiMAX terminals. In this paper, a novel protocol for antenna selection in space division multiple access (SDMA) transmission is developed for the next‐generation IEEE 802.16 mobile stations. Both locally and globally optimal selection rules are considered together with various linear precoding designs at the base station (BS). The proposed protocol can readily accommodate various channel situations (e.g., reciprocal and non‐reciprocal channels). As demonstrated by analysis and simulation, the proposed protocol delivers considerable performance improvement over conventional IEEE 802.16 terminals that lack antenna selection capability. Moreover, the proposed protocol leverages the existing signaling method defined in IEEE 802.16, thereby incurring a negligible signaling overhead and requiring only minimal modifications of the standard. To the best of our knowledge, this paper represents the first effort to support antenna selection capability for SDMA transmissions in IEEE 802.16 mobile stations. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Untersuchungen zur Struktur und Kinetik von Zwischenstufen in Protonen‐induzierten Kupplungen von Alkylidin‐ und Isocyanidliganden (1993)

Am koordinierenden C‐Atom des Alkylidinliganden werden die Wolframkomplexe 1 zu den Salzen 2 protoniert. Diese können anschließend durch CH 3 OH‐katalysierte Kupplung des Isocyanid‐ mit dem Alkylidinliganden in die Aminoacetylenkomplexe 3 überführt werden. N‐protonierte Isomere treten als direkte Vorstufen bei der Kupplung auf. R, X und Y beispielsweise Ph, Cl − bzw. CF 3 SO 3 − magnified image
Characterization of the antibody response in mice with type II collagen–induced arthritis, using monoclonal anti–type II collagen antibodies (1986)

Abstract Twenty monoclonal antibodies reactive with type II collagen were characterized as to their determinant specificity and their reactivity with cartilage‐derived components. The monoclonal antibodies reacted with 7 different epitopes on the native type II collagen triple helical structure. Antibodies defining 3 of these epitopes occurred more frequently in sera from arthritic mice than in sera from nonarthritic mice. In vivo injection of some selected autoreactive antibodies caused synovitis, but in no case did it give rise to full‐blown arthritis.
Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression (2011)

We describe a new method that allows cloning of double-stranded RNAs (dsRNAs) that are generated in RNase protection experiments. We demonstrate that the mouse C/D box snoRNA MBII-85 (SNORD116) is processed into at least five shorter RNAs using processing sites near known functional elements of C/D box snoRNAs. Surprisingly, the majority of cloned RNAs from RNase protection experiments were derived from endogenous cellular RNA, indicating widespread antisense expression. The cloned dsRNAs could be mapped to genome areas that show RNA expression on both DNA strands and partially overlapped with experimentally determined argonaute-binding sites. The data suggest a conserved processing pattern for some C/D box snoRNAs and abundant expression of longer, non-coding RNAs in the cell that can potentially form dsRNAs.
Initiation of DNA replication by the Escherichia coli dnaG protein: evidence that tertiary structure is involved. (1980)

The dnaG protein of Escherichia coli initiates DNA replication by synthesizing primer oligonucleotides for elongation by DNA polymerae. The experiments reported here probe the nature of the nucleic acid element recognized by the dnaG protein. Three well-separated groups of nucleotides within the negative-strand origin of the single-stranded phage phi K are protected by the dnaG protein against nuclease digestion. DNA as far as 115 bases from the start site of primer synthesis is involved in binding of the dnaG protein to the replication origin. One molecule of dnaG protein could protect all of these nucleotides if the DNA were folded into a higher-order tertiary structure. Protection of the phi K origin by dnaG protein requires DNA binding protein, and it does not occur if the group of protected nucleotides most distant from the start site is removed from the template. There is no binding of dnaG protein to the complementary strand of the phi K origin-region DNA. The observed protection of the positive strand is due to a functional nucleic acid-protein complex.
Gender Differences in End-User Debugging, Revisited: What the Miners Found (2006)

We have been working to uncover gender differences in the ways males and females problem solve in end-user programming situations, and have discovered differences in males' versus females' use of several debugging features. Still, because this line of investigation is new, knowing exactly what to look for is difficult and important information could escape our notice. We therefore decided to bring data mining techniques to bear on our data, with two aims: primarily, to expand what is known about how males versus females make use of end-user debugging features, and secondarily, to find out whether data mining could bring new understanding to this research, given that we had already studied the data manually using qualitative and quantitative methods. The results suggested several new hypotheses in how males versus females go about end-user debugging tasks, the factors that play into their choices, and how their choices are associated with success
Application of wireless electromagnetic resonance technology to rotary transformer used in ultrasonic spindle (2015)

In order to develop a new style drill for the factories, the ultrasonic spindle was designed. Rotary transformer was introduced to solve the design problems existing in the specification and structure. However, rotary transformer's voltage conversion ratio is markedly lower than the inductance ratio, it cannot transmit sufficient electric power to the ultrasonic element. Then, this problem is being solved by using electromagnetism resonance technology in this paper.
Body Size Estimation: The Influence of Visual Perspective (2018)

Previous research on own visual body size estimation has only looked at estimates made by comparing own body size to a test body viewed in third-person perspective. However, people spend relatively little time seeing their body from this perspective as compared to the first-person perspective. Here, we asked whether the visual perspective on the body influences the accuracy of estimating own body dimensions. A 3D virtual test body was presented in life-size in immersive virtual reality either from a first- or a third-person perspective. In a method of adjustment task, participants adjusted a varying number of the test body's dimensions (weight, leg length, arm span, hip width, and upper torso area) to match their own body. Results showed that participants were more accurate in estimating own body dimensions in the third-person perspective condition, suggesting that our mental body image is informed by viewing the own body as a whole, such as in a full-length mirror.
DNA Replication in the Third Domain (of Life) (2000)

DNA replication is the process underlying evolution and the propagation of living organisms. Since the discovery of DNA-dependent DNA polymerases more than 40 years ago, the mechanisms governing DNA replication have been extensively studied in bacteria and eukarya. During the last several years, these studies have been extended to the third domain of life, the archaea. Although archaea are prokaryotes, their replication machinery and the proteins participating in the initiation of DNA replication are more similar to those found in eukarya than bacteria. It appears, however, that replication in archaea is a simpler version of the eukaryotic one as fewer polypeptides participate in each phase of the replication process. The archaeal replication apparatus also has several unique features not found in eukaryotic organisms. Furthermore, like bacteria, members of this domain thrive under a broad range of environmental conditions including extreme temperature, high salt, pH, etc. Thus, the replication machinery had to adapt to these extreme conditions. This article summarizes our current understanding of the mechanisms governing DNA replication in archaea and highlights similarities and differences between archaeal replication and that of bacteria and eukarya.
Semidefinite optimization for transient analysis of queues (2010)

We derive an upper bound on the tail distribution of the transient waiting time for the GI/GI/1 queue from a formulation of semidefinite programming (SDP). Our upper bounds are expressed in closed forms using the first two moments of the service time and the interarrival time. The upper bounds on the tail distributions are integrated to obtain the upper bounds on the corresponding expectations. We also extend the formulation of the SDP, using the higher moments of the service time and the interarrival time, and calculate upper bounds and lower bounds numerically.
Down-to-earth studies of carbon clusters (1990)

Recent advances in supersonic beam experiments with laser-vaporization sources of clusters have provided some interesting new insights into the nature of the small clusters of carbon, and the processes through which carbon condenses. One cluster in particular, C(sub 60), appears to play a central role. It is argued that this cluster takes the shape of a soccerball: a hollow sphere composed of a shell of 60 carbon atoms connected by a lattice of hexagonal and pentagonal rings, in a pattern of overall icosahedral symmetry. Although C(sub 60) appears to be uniquely stable due to its perfect symmetry, all other even-numbered carbon clusters in the 32 to 100+ atom size range seem to favor similar closed spheroidal forms. These species are interpreted as relatively unreactive side products in condensation reactions of carbon vapor involving spiraling graphitic sheets. The prevalence of C(sub 60) in laser-vaporized carbon vapors and sooting flames suggests that it may be formed readily whenever carbon condenses. Such ready formation and extraordinary stability may have substantial astrophysical implications.
Automation and Control of an Imaging Internal Laser Desorption Fourier Transform Mass Spectrometer (I2LD-FTMS) (2002)

This paper describes the automation of an imaging internal source laser desorption Fourier transform mass spectrometer (I2LD-FTMS). The I2LD-FTMS consists of a laser-scanning device [Scott and Tremblay, Rev. Sci. Instrum. 2002, 73, 1108–1116] that has been integrated with a laboratory-built FTMS using a commercial data acquisition system (ThermoFinnigan FT/MS, Bremen, Germany). A new user interface has been developed in National Instrument's (Austin, Texas) graphical programming language LabVIEW to control the motors of the laser positioning system and the commercial FTMS data acquisition system. A feature of the FTMS software that allows the user to write macros in a scripting language is used creatively to our advantage in creating a mechanism to control the FTMS from outside its graphical user interface. The new user interface also allows the user to configure target locations. Automation of the data analysis along with data display using commercial graphing software is also described.
Molecular replacement techniques for high-throughput structure determination (2007)

In the context of structural genomics projects, there are two main routes to consider for solving efficiently and rapidly the three-dimensional (3D) structure of the target gene products by crystallography. The first is the Multiple-wavelength Anomalous Diffraction (MAD) technique, which necessitates growing SeMet-substituted protein crystals. The second is molecular replacement (MR), which requires X-ray data for the native protein as well as the structure of a related homolog. This chapter describes some of the newest developments in MR to get the best possible set of phases to initialize refinement and reconstruction in the best possible conditions.
Gene Expression Profiling of Early-Phase Sjögren's Syndrome in C57BL/6.NOD-Aec1Aec2Mice Identifies Focal Adhesion Maturation Associated with Infiltrating Leukocytes (2011)

For the first time, FA maturations are implicated as initial biomarkers of impending autoimmunity in lacrimal glands of SjS-prone mice. Changes in TJ complex genes support an increased movement of cells through paracellular spaces.
Supplementary Figures 1-4 from MicroRNA Array Analysis Finds Elevated Serum miR-1290 Accurately Distinguishes Patients with Low-Stage Pancreatic Cancer from Healthy and Disease Controls (2023)

&lt;p&gt;PDF file - 818K, Supplemental Figure S1 (A) A 3D Principal component analysis (PCA) plot of the miRNA data that characterizes the trends exhibited by the expression profiles of pancreatic cancer (PC, purple), pancreatic neuroendocrine tumor (NET, green), chronic pancreatitis (CP, red)), healthy controls (N, blue). Each dot represents a sample and each color represents the type of the sample. (B) VENN diagram showing significantly elevated miRNAs (fold-change less than or equal to 2 and p&lt;0.05) in pancreatic cancer (PC) compared to three control groups (NET, CP, and N). Supplemental Figure S2 Reproducibility of Taqman miRNA microarray. (A) A serum sample was analyzed in duplicate and the correlation was determined using Spearman test. (B) The effects of pre-amplification on serum miR-1290 levels by Taqman RT-PCR. Supplemental Figure S3 Validation of elevated miRNAs in serum from patients with pancreatic cancer. Levels of selected serum microRNAs were compared in an independent set of cases and controls including patients with pancreatic cancer (n=41) compared to patients with pancreatic neuroendocrine tumor (NET) (n=18) and chronic pancreatitis (CP) (n=35), normal controls (N) (n=19), and the combined from of non-malignant controls including chronic pancreatitis and normal controls (CN) (n=54), and non-pancreatic cancer control including pancreatic neuroendocrine tumor, chronic pancreatitis, and normal controls (NCN) (n=72) using Taqman real-time PCR. Boxes represent the inter-quartile range and the line indicates the median value. Error bars indicate the 90th and 10th percentiles. MiR-16 was used as reference gene for normalization. Mann-Whitney was used to compare groups. 2 Supplemental Figure S4 The effects of miR-1290 on pancreatic cancer cell proliferation and invasion. (A). The expression levels of miR-1290 were measured in miR-1290 mimic-transfected AsPC1 and Panc5.04 and miR-1290 inhibitor-transfected Panc10.05 and Panc198 cell lines, respectively. (B). Cell lines expressing low levels of miR 1290 (AsPC1 and Panc5.04) were transfected with miR-1290 mimic and cell lines with high miR-1290 (Panc10.05 and Panc198) were transfected with a miR-1290 inhibitor and miRNA controls, and cell growth was determined using MTS assay, respectively. Data are mean +/- SD of 5 replicates and are representative of two independent experiments. (C). The invasive potential of miR-1290 was determined using a chamber matrigel invasion assay in the same cell lines treated in the same way. Data are mean +/- SD of triplicates and are representative of two independent experiments. Representative photographs of invasion assays were shown (D). Original magnification, 20x.&lt;/p&gt;
Type II Collagen Gene Variants and Inherited Osteonecrosis of the Femoral Head (2005)

All the patients with familial ANFH whom we studied carried COL2A1 mutations. In families with ANFH, haplotype and sequence analysis of the COL2A1 gene can be used to identify carriers of the mutant allele before the onset of clinical symptoms, allowing the initiation of measures that may delay progression of the disease.
Asymmetric cross-coupled sense amplifier for small-sized 0.5-V gigabit-DRAM arrays (2010)

A new sense amplifier (SA) and relevant circuits were proposed for low-power, high-speed, and small-sized 0.5-V gigabit DRAM arrays. The SA, consisting of a low-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> NMOS preamplifier and a cross-coupled high-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> PMOS latch, achieved 46% area reduction compared to our previously proposed SA with a low-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> CMOS preamplifier. Separation of the SA and a data-line pair, and overdrive of the latch achieved a restoring time of 13.4 ns and a sensing time of 6 ns. An adaptive leakage control of the preamplifier reduced the leakage current of the SA to 2% of that without the control.
Combined heterogeneous metal/organic catalysts for eco-friendly synthesis (2015)

Abstract The interplay and synergistic cooperation between homogeneous and heterogeneous catalyst systems is of utmost importance in nature. It is also applied in chemical synthesis. Here, it can allow for new reactivity, which is not possible by the employment of a single catalyst, and promote the catalysis of multiple transformations in a one-pot sequence. This could overall lead to novel reactions and the development of sustainable chemistry. In this context, a versatile and broad synergistic strategy for the selective synthesis of valuable molecules with variable complexity and under eco-friendly conditions is disclosed. It is based on integrated heterogeneous metal/organo multiple relay catalysis, which is performed in a single reaction vessel, and allows for the assembly of complex molecules (e.g., heterocycles and carbocycles) with up to three quaternary stereocenters in a highly enantioselective fashion from simple alcohols and air/O 2 .
Range partition adaptors (1996)

Range partition adaptors, a new type of adaptor for the C++ Standard Template Library (STL), can be the basis for a parallel version of the STL.
Equal Area Rule Methods for Ternary Systems (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEqual Area Rule Methods for Ternary SystemsGuor-Shiarn Shyu, Nishawn S. M. Hanif, Juan F. J. Alvarado, Kenneth R. Hall, and Philip T. EubankCite this: Ind. Eng. Chem. Res. 1995, 34, 12, 4562–4570Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ie00039a051https://doi.org/10.1021/ie00039a051research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations19LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Management of Massive and Submassive Pulmonary Embolism, Iliofemoral Deep Vein Thrombosis, and Chronic Thromboembolic Pulmonary Hypertension (2011)

Venous thromboembolism (VTE) is responsible for the hospitalization of >250 000 Americans annually and represents a significant risk for morbidity and mortality. Despite the publication of evidence-based clinical practice guidelines to aid in the management of VTE in its acute and chronic forms, the clinician is frequently confronted with manifestations of VTE for which data are sparse and optimal management is unclear. In particular, the optimal use of advanced therapies for acute VTE, including thrombolysis and catheter-based therapies, remains uncertain. This report addresses the management of massive and submassive pulmonary embolism (PE), iliofemoral deep vein thrombosis (IFDVT),and chronic thromboembolic pulmonary hypertension (CTEPH). The goal is to provide practical advice to enable the busy clinician to optimize the management of patients with these severe manifestations of VTE. Although this document makes recommendations for management, optimal medical decisions must incorporate other factors, including patient wishes, quality of life, and life expectancy based on age and comorbidities. The appropriateness of these recommendations for a specific patient may vary depending on these factors and will be best judged by the bedside clinician.