bluuebunny/crossref_metadata_2025_split huggingface dataset:
An argument for increasing TCP's initial congestion window
Authors: Dukkipati Nandita , Refice Tiziana , Cheng Yuchung , Chu Jerry , Herbert Tom , Agarwal Amit , Jain Arvind , Sutin Natalia 
Published: June 2010

TCP flows start with an initial congestion window of at most four segments or approximately 4KB of data. Because most Web transactions are short-lived, the initial congestion window is a critical TCP parameter in determining how quickly flows can finish. While the global network access speeds increased dramatically on average in the past decade, the standard value of TCP's initial congestion window has remained unchanged.
In this paper, we propose to increase TCP's initial congestion window to at least ten segments (about 15KB). Through large-scale Internet experiments, we quantify the latency benefits and costs of using a larger window, as functions of network bandwidth, round-trip time (RTT), bandwidth-delay product (BDP), and nature of applications. We show that the average latency of HTTP responses improved by approximately 10% with the largest benefits being demonstrated in high RTT and BDP networks. The latency of low bandwidth networks also improved by a significant amount in our experiments. The average retransmission rate increased by a modest 0.5%, with most of the increase coming from applications that effectively circumvent TCP's slow start algorithm by using multiple concurrent connections. Based on the results from our experiments, we believe the initial congestion window should be at least ten segments and the same be investigated for standardization by the IETF.
FIE
Authors: Crowcroft Jon 
Published: June 2010

There are so many initiatives to look at the Internet's Future http://www.future-internet.eu/, http://www.nets-find.net/ and similar programs in pretty every any other geo-political arena, anyone would think that there was some tremendous threat like global warming, about to bring about its immediate demise, and that this would bring civilisation crashing down around our ears.
The Internet has a great future behind it, of course. However, my thesis is that the Future Internet is about as relevant as Anthropogenic Global Warming (AGW), in the way it is being used to support various inappropriate activities. Remember that the start of all this was not the exhaustion of IPv4 address space, or the incredibly slow convergence time of BGP routes, or the problem of scaling router memory for FIBs. It was the US research community reacting to a minor (as in parochial) temporary problem of funding in Communications due to slow down within NSF and differing agendas within DARPA.
It is not necessary to invoke all the hype and hysteria - it is both necessary and sufficient to talk about sustainable energy See for example David Mackay's Without Hot Air book, at http://www.withouthotair.com/, and good technical communications research, development, deployment and operations.
To continue the analogy between FI and AGW, what we really do not need is yet more climatologists with dodgy data curation methodologies (or ethnographers studying Internet governance).
What we do need is some solid engineering, to address a number of problems the Internet has. However, this is in fact happening, and would not stop happening if the entire Future Internet flagship was kidnapped by aliens. "We don't need no" government agency doing top down dictats about what to do when. It won't work and it will be a massive waste of time, energy and other resources - i.e. like AGW, it will be a load of hot air:)
On the other hand, there are a number of deeper lessons from the Internet Architecture which might prove useful in other domains, and in the bulk of this opinion piece, I give examples of these, applying the Postel and End-to-end principles to transport, energy, government information/vices.
Advanced applications of the holonomic systems approach
Authors: Koutschan Christoph 
Published: June 2010

The holonomic systems approach was proposed in the early 1990s by Doron Zeilberger. It laid a foundation for the algorithmic treatment of holonomic function identities. Frédéric Chyzak later extended this framework by introducing the closely related notion of ∂-finite functions and by placing their manipulation on solid algorithmic grounds. For practical purposes it is convenient to take advantage of both concepts which is not too much of a restriction: The class of functions that are holonomic and ∂-finite contains many elementary functions (such as rational functions, algebraic functions, logarithms, exponentials, sine function, etc.) as well as a multitude of special functions (like classical orthogonal polynomials, elliptic integrals, Airy, Bessel, and Kelvin functions, etc.). In short, it is composed of functions that can be characterized by sufficiently many partial differential and difference equations, both linear and with polynomial coefficients. An important ingredient is the ability to execute closure properties algorithmically, for example addition, multiplication, and certain substitutions. But the central technique is called creative telescoping which allows to deal with summation and integration problems in a completely automatized fashion.
Part of this thesis is our Mathematica package HolonomicFunctions in which the above mentioned algorithms are implemented, including more basic functionality such as noncommutative operator algebras, the computation of Gröbner bases in them, and finding rational solutions of parameterized systems of linear differential or difference equations.
Besides standard applications like proving special function identities, the focus of this thesis is on three advanced applications that are interesting in their own right as well as for their computational challenge. First, we contributed to translating Takayama's algorithm into a new context, in order to apply it to an until then open problem, the proof of Ira Gessel's lattice path conjecture. The computations that completed the proof were of a nontrivial size and have been performed with our software. Second, investigating basis functions in finite element methods, we were able to extend the existing algorithms in a way that allowed us to derive various relations which generated a considerable speed-up in the subsequent numerical simulations, in this case of the propagation of electromagnetic waves. The third application concerns a computer proof of the enumeration formula for totally symmetric plane partitions, also known as Stembridge's theorem. To make the underlying computations feasible we employed a new approach for finding creative telescoping operators.
Vinflunine: review of a newvincaalkaloid and its potential role in oncology
Authors: Ng John S 
Published: June 2010

Objective: To review the pharmacology, pharmacokinetics, in vitro and in vivo efficacy, and safety profile of vinflunine in the treatment of various solid tumors.Data sources: A literature search was conducted using keywords included vinflunine, vinca alkaloid, Javlor, and solid tumor in PubMed/MEDLINE (1950—January 2009) and International Pharmaceutical Abstracts (1950—January 2009). Study selection and data extraction: Published studies, posters, and meeting abstracts evaluating the in vitro and in vivo efficacy of vinflunine were reviewed.Data synthesis: Vinflunine is the newest member of the vinca alkaloid family. It has the weakest affinity to tubulins, but is shown to have unique receptor-independent antiangiogenesis, and antimetastasis properties. After administration, it is distributed extensively into tissues, metabolized via the CYP3A4 system, and eventually excreted in urine and feces. Phase II/III trials reported activities of vinflunine in advanced stage nonsmall-cell lung cancer, metastatic breast cancer, metastatic renal cell carcinoma, transitional cell carcinomas of the urothelium, small-cell lung cancer, and malignant pleural mesothelioma as monotherapy and in combination with other chemotherapy agents. More ongoing trials are evaluating its use in other solid tumors and in combination regimens. The most common adverse events in these trials were hematological (anemia and neutropenia), constipation, fatigue, abdominal pain, and myalgia.Conclusions: Vinflunine is a new vinca alkaloid for the treatment of advanced staged solid tumors. Available data showed promising activities in various malignancies. Further studies are needed to further define vinflunine’s role in oncology.
Evaluation of surface contamination with cyclophosphamide following simulated hazardous drug preparation activities using two closed-system products
Authors: Zock Matthew D , Soefje Scott , Rickabaugh Keith 
Published: June 2010

Purpose. A preliminary investigation was conducted to evaluate and compare the effectiveness of two closed-system products in preventing contamination of typical pharmacy workplace surfaces with cyclophosphamide during simulated hazardous drug preparation activities in a controlled laboratory setting. Methods. Two separate trials simulating hazardous drug compounding using cyclophosphamide were performed with two different closed-system products. Prior to each trial, work area surfaces of the biological safety cabinet (BSC) workbench, the BSC airfoil and front grill, and the floor below the BSC were cleaned, and wipe samples were collected and analyzed to determine, if present, levels of cyclophosphamide. Following each trial, wipe samples were collected from the work area surfaces to determine the hazardous drug containment effectiveness of each closed-system product. Results. Cyclophosphamide was not detected on work area surfaces prior to each trial. Low levels were detected on the BSC workbench surface following both trials. Discussion. Based on the limited number of samples obtained during this preliminary study and the determination of the presence of the chemical of interest on the drug vials, no statistical evaluation was performed to compare the relative effectiveness of the two systems tested. Work practices and procedures regarding product operation may affect hazardous drug containment and worker safety. Further study and statistical analyses are needed.
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data
Authors: Dittmar John C , Reid Robert JD , Rothstein Rodney 
Published: June 2010

Abstract

Background
Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data points, making data analysis a time consuming and painstaking process. Here we describe ScreenMill, a new software suite that automates image analysis and simplifies data review and analysis for high-throughput biological experiments.

Results
The ScreenMill, software suite includes three software tools or "engines": an open source Colony Measurement Engine (CM Engine) to quantitate colony growth data from plate images, a web-based Data Review Engine (DR Engine) to validate and analyze quantitative screen data, and a web-based Statistics Visualization Engine (SV Engine) to visualize screen data with statistical information overlaid. The methods and software described here can be applied to any screen in which growth is measured by colony size. In addition, the DR Engine and SV Engine can be used to visualize and analyze other types of quantitative high-throughput data.

Conclusions

ScreenMill automates quantification, analysis and visualization of high-throughput screen data. The algorithms implemented in ScreenMill are transparent allowing users to be confident about the results ScreenMill produces. Taken together, the tools of ScreenMill offer biologists a simple and flexible way of analyzing their data, without requiring programming skills.
Nonparametric methods for the analysis of single-color pathogen microarrays
Authors: Jabado Omar J , Conlan Sean , Quan Phenix-Lan , Hui Jeffrey , Palacios Gustavo , Hornig Mady , Briese Thomas , Lipkin W Ian 
Published: June 2010

AbstractBackgroundThe analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.ResultsPositive predictive value and false positive rates were examined to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-WhitneyU, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, the chi-square proved most useful.ConclusionsThe acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.
Detection of quantitative trait loci affecting haematological traits in swine via genome scanning
Authors: Gong Yuan-Fang , Lu Xin , Wang Zhi-Peng , Hu Fang , Luo Yan-Ru , Cai Shao-Qian , Qi Chun-Mei , Li Shan , Niu Xiao-Yan , Qiu Xiao-Tian , Zeng Jian , Zhang Qin 
Published: June 2010

AbstractBackgroundHaematological traits, which consist of mainly three components: leukocyte traits, erythrocyte traits and platelet traits, play extremely important role in animal immune function and disease resistance. But knowledge of the genetic background controlling variability of these traits is very limited, especially in swine.ResultsIn the present study, 18 haematological traits (7 leukocyte traits, 7 erythrocyte traits and 4 platelet traits) were measured in a pig resource population consisting of 368 purebred piglets of three breeds (Landrace, Large White and Songliao Black Pig), after inoculation with the swine fever vaccine when the pigs were 21 days old. A whole-genome scan of QTL for these traits was performed using 206 microsatellite markers covering all 18 autosomes and the X chromosome. Using variance component analysis based on a linear mixed model and the false discovery rate (FDR) test, 35 QTL with FDR < 0.10 were identified: 3 for the leukocyte traits, 28 for the erythrocyte traits, and 4 for the platelet traits. Of the 35 QTL, 25 were significant atFDR< 0.05 level, including 9 significant atFDR< 0.01 level.ConclusionsVery few QTL were previously identified for hematological traits of pigs and never in purebred populations. Most of the QTL detected here, in particular the QTL for the platelet traits, have not been reported before. Our results lay important foundation for identifying the causal genes underlying the hematological trait variations in pigs.
Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates
Authors: DaRe Jeana T , Kouri Drew P , Zimmerman Peter A , Thomas Peter J 
Published: June 2010

Abstract

Background
Diagnosis of infectious diseases now benefits from advancing technology to perform multiplex analysis of a growing number of variables. These advances enable simultaneous surveillance of markers characterizing species and strain complexity, mutations associated with drug susceptibility, and antigen-based polymorphisms in relation to evaluation of vaccine effectiveness. We have recently developed assays detecting single nucleotide polymorphisms (SNPs) in the P. falciparum genome that take advantage of post-PCR ligation detection reaction and fluorescent microsphere labeling strategies. Data from these assays produce a spectrum of outcomes showing that infections result from single to multiple strains. Traditional methods for distinguishing true positive signal from background can cause false positive diagnoses leading to incorrect interpretation of outcomes associated with disease treatment.

Results
Following analysis of Plasmodium falciparum dihydrofolate reductase SNPs associated with resistance to a commonly used antimalarial drug, Fansidar (Sulfadoxine/pyrimethamine), and presumably neutral SNPs for parasite strain differentiation, we first evaluated our data after setting a background signal based on the mean plus three standard deviations for known negative control samples. Our analysis of single allelic controls suggested that background for the absent allele increased as the concentration of the target allele increased. To address this problem, we introduced a simple change of variables from customary (X,Y) (Cartesian) coordinates to planar polar coordinates (X = r cos(θ), Y = r sin(θ)). Classification of multidimensional fluorescence signals based on histograms of angular and radial data distributions proved more effective than classification based on Cartesian thresholds. Comparison with known diallelic dilution controls suggests that histogram-based classification is effective for major:minor allele concentration ratios as high as 10:1.

Conclusion
We have observed that the diallelic SNP data resulting from analysis of P. falciparum mutations is more accurately diagnosed when a simple polar transform of the (X,Y) data into (r,θ) is used. The development of high through-put methods for genotyping P. falciparum SNPs and the refinement of analytical approaches for evaluating these molecular diagnostic results significantly advance the evaluation of parasite population diversity and antimalarial drug resistance.
A novel allele of FILAMENTOUS FLOWER reveals new insights on the link between inflorescence and floral meristem organization and flower morphogenesis
Authors: Lugassi Nitsan , Nakayama Naomi , Bochnik Rachel , Zik Moriyah 
Published: June 2010

Abstract

Background
The Arabidopsis
FILAMENTOUS FLOWER (FIL) gene encodes a YABBY (YAB) family putative transcription factor that has been implicated in specifying abaxial cell identities and thus regulating organ polarity of lateral organs. In contrast to double mutants of fil and other YAB genes, fil single mutants display mainly floral and inflorescence morphological defects that do not reflect merely a loss of abaxial identity. Recently, FIL and other YABs have been shown to regulate meristem organization in a non-cell-autonomous manner. In a screen for new mutations affecting floral organ morphology and development, we have identified a novel allele of FIL, fil-9 and characterized its floral and meristem phenotypes.

Results
The fil-9 mutation results in highly variable disruptions in floral organ numbers and size, partial homeotic transformations, and in defective inflorescence organization. Examination of meristems indicates that both fil-9 inflorescence and floral meristems are enlarged as a result of an increase in cell number, and deformed. Furthermore, primordia emergence from these meristems is disrupted such that several primordia arise simultaneously instead of sequentially. Many of the organs produced by the inflorescence meristems are filamentous, yet they are not considered by the plant as flowers. The severity of both floral organs and meristem phenotypes is increased acropetally and in higher growth temperature.

Conclusions
Detailed analysis following the development of fil-9 inflorescence and flowers throughout flower development enabled the drawing of a causal link between multiple traits of fil-9 phenotypes. The study reinforces the suggested role of FIL in meristem organization. The loss of spatial and temporal organization of fil-9 inflorescence and floral meristems presumably leads to disrupted cell allocation to developing floral organs and to a blurring of organ whorl boundaries. This disruption is reflected in morphological and organ identity aberrations of fil-9 floral organs and in the production of filamentous organs that are not perceived as flowers. Here, we show the role of FIL in reproductive meristem development and emphasize the potential of using fil mutants to study mersitem organization and the related effects on flower morphogenesis.
Comparison of the chloroplast peroxidase system in the chlorophyte Chlamydomonas reinhardtii, the bryophyte Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana
Authors: Pitsch Nicola T , Witsch Benjamin , Baier Margarete 
Published: June 2010

Abstract

Background
Oxygenic photosynthesis is accompanied by the formation of reactive oxygen species (ROS), which damage proteins, lipids, DNA and finally limit plant yield. The enzymes of the chloroplast antioxidant system are exclusively nuclear encoded. During evolution, plastid and mitochondrial genes were post-endosymbiotically transferred to the nucleus, adapted for eukaryotic gene expression and post-translational protein targeting and supplemented with genes of eukaryotic origin.

Results
Here, the genomes of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana were screened for ORFs encoding chloroplast peroxidases. The identified genes were compared for their amino acid sequence similarities and gene structures. Stromal and thylakoid-bound ascorbate peroxidases (APx) share common splice sites demonstrating that they evolved from a common ancestral gene. In contrast to most cormophytes, our results predict that chloroplast APx activity is restricted to the stroma in Chlamydomonas and to thylakoids in Physcomitrella. The moss gene is of retrotransposonal origin.
The exon-intron-structures of 2CP genes differ between chlorophytes and streptophytes indicating an independent evolution. According to amino acid sequence characteristics only the A-isoform of Chlamydomonas 2CP may be functionally equivalent to streptophyte 2CP, while the weakly expressed B- and C-isoforms show chlorophyte specific surfaces and amino acid sequence characteristics. The amino acid sequences of chloroplast PrxII are widely conserved between the investigated species. In the analyzed streptophytes, the genes are unspliced, but accumulated four introns in Chlamydomonas. A conserved splice site indicates also a common origin of chlorobiont PrxQ.
The similarity of splice sites also demonstrates that streptophyte glutathione peroxidases (GPx) are of common origin. Besides a less related cysteine-type GPx, Chlamydomonas encodes two selenocysteine-type GPx. The latter were lost prior or during streptophyte evolution.

Conclusion
Throughout plant evolution, there was a strong selective pressure on maintaining the activity of all three investigated types of peroxidases in chloroplasts. APx evolved from a gene, which dates back to times before differentiation of chlorobionts into chlorophytes and streptophytes, while Prx and presumably also GPx gene patterns may have evolved independently in the streptophyte and chlorophyte branches.