Miracle-dz/UniFAR-FTUs huggingface dataset:
What is meant by intention to treat analysis? Survey of published randomised controlled trials

Abstract Objectives: To assess the methodological quality of intention to treat analysis as reported in randomised controlled trials in four large medical journals. Design: Survey of all reports of randomised controlled trials published in 1997 in the BMJ, Lancet, JAMA, and New England Journal of Medicine. Main outcome measures: Methods of dealing with deviations from random allocation and missing data. Results: 119 (48%) of the reports mentioned intention to treat analysis. Of these, 12 excluded any patients who did not start the allocated intervention and three did not analyse all randomised subjects as allocated. Five reports explicitly stated that there were no deviations from random allocation. The remaining 99 reports seemed to analyse according to random allocation, but only 34 of these explicitly stated this. 89 (75%) trials had some missing data on the primary outcome variable. The methods used to deal with this were generally inadequate, potentially leading to a biased treatment effect. 29 (24%) trials had more than 10% of responses missing for the primary outcome, the methodsof handling the missing responses were similar in this subset. Conclusions: The intention to treat approach is often inadequately described and inadequately applied. Authors should explicitly describe the handling of deviations from randomised allocation and missing responses and discuss the potential effect of any missing response. Readers should critically assess the validity of reported intention to treat analyses. Key messages Intention to treat gives a pragmatic estimate of the benefit of a change in treatment policy rather than of potential benefit in patients who receive treatment exactly as planned Full application of intention to treat is possible only when complete outcome data are available for all randomised subjects About half of all published reports of randomised controlled trials stated that intention to treat was used, but handling of deviations from randomised allocation varied widely Many trials had some missing data on the primary outcome variable, and methods used to deal with this were generally inadequate, potentially leading to bias Intention to treat analyses are often inadequately described and inadequately applied
The open reading frames UL3, UL4, UL10, and UL16 are dispensable for the replication of herpes simplex virus 1 in cell culture

By means of insertion and deletion mutagenesis, we have constructed four herpes simplex virus 1 recombinants, each lacking most sequences encoding a different open reading frame. The deleted genes are located in the unique sequences of the long component and include those designated UL3, UL4, UL10, and UL16. The recombinant virus R7211 lacks 579 of the 696 bp of UL3. The recombinant virus R7217 lacks 307 of the 597 bp of the UL4 open reading frame. R7216 contains a 972-bp deletion within the 1,419-bp open reading frame of UL10, whereas R7210 lacks 988 bp of the 1,119-bp UL16 open reading frame. Growth curves indicated that the yields of these viruses in Vero and BHK cell cultures were only slightly reduced from or in some instances equivalent to that of the parent virus. The function of the gene products is not known. It is of interest to note that (i) the UL16 open reading frame maps entirely within the single intron of UL15 and (ii) on the basis of the extent and size of hydrophobic domains, the UL3 and UL10 gene products were predicted to be membrane proteins.
Biomechanics of fibrous proteins of the extracellular matrix studied by Brillouin scattering

Brillouin light scattering (BLS) spectroscopy is a technique that is able to detect thermally excited phonons within a material. The speed of propagation of these phonons can be determined from the magnitude of the Brillouin frequency shift between incident and scattered light, thereby providing a measure of the mechanical properties of the material in the gigahertz range. The mechanical properties of the extracellular matrices of biological tissues and their constituent biopolymers are important for normal tissue function and disturbances in these properties are widely implicated in disease. BLS offers the prospect of measuring mechanical properties on a microscopic scale in living tissues, thereby providing insights into structure–function relationships under normal and pathological conditions. In this study, we investigated BLS in collagen and elastin—the fibrous proteins of the extracellular matrix (ECM). Measurements were made on type I collagen in rat tail tendon, type II collagen in articular cartilage and nuchal ligament elastin. The dependence of the BLS spectrum on fibre orientation was investigated in a backscattering geometry using a reflective substrate. Two peaks, a bulk mode arising from phonon propagation along a quasi-radial direction to the fibre axis and a mode parallel to the surface, depending on sample orientation relative to the fibre axis, could be distinguished. The latter peak was fitted to a model of wave propagation through a hexagonally symmetric elastic solid, and the five components of the elasticity tensor were combined to give axial and transverse Young's, shear and bulk moduli of the fibres. These were 10.2, 8.3, 3.2 and 10.9 GPa, and 6.1, 5.3, 1.9 and 8 GPa for dehydrated type I collagen and elastin, respectively. The former values are close to those previously reported. A microfocused BLS approach was also applied providing selection of single fibres. The moduli of collagen and elastin are much higher than those measured at lower frequency using macroscopic strains, and the difference between them is much less. We therefore believe, like previous investigators, that molecular-scale viscoelastic effects are responsible for the frequency dependence of the fibre biomechanics. Combining BLS with larger-scale mechanical testing methods therefore should, in the future, provide a means of following the evolution of mechanical properties in the formation of the complex structures found in the ECM.
An infrastructure for searching, reusing and evolving distributed ontologies

The vision of the Semantic Web can only be realized through proliferation of well-known ontologies describing different domains. To enable interoperability in the Semantic Web, it will be necessary to break these ontologies down into smaller, well-focused units that may be reused. Currently, three problems arise in that scenario. Firstly, it is difficult to locate ontologies to be reused, thus leading to many ontologies modeling the same thing. Secondly, current tools do not provide means for reusing existing ontologies while building new ontologies. Finally, ontologies are rarely static, but are being adapted to changing requirements. Hence, an infrastructure for management of ontology changes, taking into account dependencies between ontologies is needed. In this paper we present such an infrastructure addressing the aforementioned problems.
Novel Method for Detection of β-Lactamases by Using a Chromogenic Cephalosporin Substrate

A new cephalosporin with a highly reactive β-lactam ring was found to give an immediate color change in the presence of β-lactamases from many bacteria, including staphylococci, Bacillus species, Enterobacteriaceae, and Pseudomonas. The reaction is confined to organisms producing β-lactamases, but it is sufficiently sensitive to indicate the presence of this enzyme is small amounts in strains previously considered not to produce it. The compound has an unusual ultraviolet spectrum, and the color change can be followed quantitatively by measuring changes in absorption which occur in the 380- to 500-nm region, where cephalosporins normally have no absorption. The development of color is thought to be a consequence of the β-lactam ring being unusually highly conjugated with the 3-substituent. Although in the bacteria only β-lactamases produce this color change, it was found that serum and tissues from experimental animals also rapidly produced the colored breakdown product, which was then excreted in the urine. The mechanism of the mammalian breakdown was considered to be different from that found in bacteria.
A Buffered Alcohol-Based Fixative for Histomorphologic and Molecular Applications

Formalin-fixed paraffin-embedded (FFPE) tissue is the predominant preparation for diagnostic histopathological evaluation and increasingly the biospecimen on which molecular diagnostics are performed. However, formalin is carcinogenic and results in cross-linking of proteins and nicking and alterations of nucleic acids. Alternative fixatives, including 70% ethanol, improved biomolecular integrity; however, they have yet to replace neutral-buffered formalin (NBF). Herein, we describe the phosphate-buffered ethanol 70% (BE70) fixative. The histomorphology of BE70-fixed tissue is very similar to that of NBF; however, it is a non-cross-linking fixative and lacks the carcinogenic profile of formaldehyde-based fixatives. RNA isolated from tissue fixed in BE70 was of substantially higher quality and quantity than that was recovered from formalin-fixed tissue. Furthermore, the BE70 fixative showed excellent RNA and DNA integrity compared with that of NBF fixative based on real-time polymerase chain reaction analysis results. Immunohistochemical staining was similar for the antigen tested. In conclusion, BE70 is a non-cross-linking fixative that is superior to NBF and 70% ethanol with reference to biomolecule recovery and quality from paraffin-embedded tissue. Additional studies to compare the histomorphologic and immunohistochemical performance and utility in a clinical setting are required.
Regulation of split anergy in natural killer cells by inhibition of cathepsins C and H and cystatin F

Freshly isolated human primary NK cells induce preferential lysis of Oral Squamous Carcinoma Stem Cells (OSCSCs) when compared to differentiated Oral Squamous Carcinoma Cells (OSCCs), while anti-CD16 antibody and monocytes induce functional split anergy in primary NK cells by decreasing the cytotoxic function of NK cells and increasing the release of IFN-γ. Since NK92 cells have relatively lower levels of cytotoxicity when compared to primary NK cells, and have the ability to increase secretion of regulatory cytokines IL-10 and IL-6, we used these cells as a model of NK cell anergy to identify and to study the upstream regulators of anergy. We demonstrate in this paper that the levels of truncated monomeric cystatin F, which is known to inhibit the functions of cathepsins C and H, is significantly elevated in NK92 cells and in anergized primary NK cells. Furthermore, cystatin F co-localizes with cathepsins C and H in the lysosomal/endosomal vesicles of NK cells. Accordingly, the mature forms of aminopeptidases cathepsins C and H, which regulate the activation of effector granzymes in NK cells, are significantly decreased, whereas the levels of pro-cathepsin C enzyme is increased in anergized NK cells after triggering of the CD16 receptor. In addition, the levels of granzyme B is significantly decreased in anti-CD16mAb and target cell anergized primary NK cells and NK92 cells. Our study provides the cellular and molecular mechanisms by which target cells may utilize to inhibit the cytotoxic function of NK cells.
A 20dB stripline coupler with CPWG transitional structure

Two designs of 20dB directional stripline couplers with high isolation are presented. Each of the couplers consists of a stripline coupler and a transitional structure. Grounded coplanar waveguide (CPWG) and microstrip line are utilized as transitional structures, respectively. The presented designs of coupler have advantages of compact size, high isolation, and simple design procedure. The stripline coupler with CPWG and the one with microstrip line are simulated and the results are compared. The coupler with CPWG transitional structure is fabricated and measured. With the return loss of higher than 23 dB, the isolation of fabricated 20dB stripline coupler with CPWG is higher than 43 dB over the frequency range from 2.6GHz to 4.7 GHz.
Detection of and phylogenetic studies with avian metapneumovirus recovered from feral pigeons and wild birds in Brazil

The aim of the present study was to determine whether avian metapneumovirus (aMPV)-related viruses were present in wild and synanthropic birds in Brazil. Therefore, we analysed samples from wild birds, feral pigeons and domestic chickens in order to perform a phylogenetic comparison. To detect the presence of aMPV, a nested reverse transcriptase-polymerase chain reaction was performed with the aim of amplifying a fragment of 270 bases for subtype A and 330 bases for subtype B, comprising the gene coding the G glycoprotein. Positive samples for aMPV subtypes A and B were found in seven (13.2%) different asymptomatic wild birds and pigeons (50%) that had been received at the Bosque dos Jequitibás Zoo Triage Center, Brazil. Also analysed were positive samples from 15 (12.9%) domestic chickens with swollen head syndrome from several regions of Brazil. The positive samples from wild birds, pigeons and domestic chickens clustered in two major phylogenetic groups: some with aMPV subtype A and others with subtype B. The similarity of the G fragment nucleotide sequence of aMPV isolated from chickens and synanthropic and wild avian species ranged from 100 to 97.5% (from 100 to 92.5% for the amino acids). Some positive aMPV samples, which were obtained from wild birds classified in the Orders Psittaciformes, Anseriformes and Craciformes, clustered with subtype A, and others from the Anas and Dendrocygma genera (Anseriformes Order) with subtype B. The understanding of the epizootiology of aMPV is very important, especially if this involves the participation of non-domestic bird species, which would add complexity to their control on farms and to implementation of vaccination programmes for aMPV.
7T head volume coils: Improvements for rostral brain imaging

To improve the performance of 7T head coils over the rostral head regions. Due to radiofrequency (RF) field/tissue interactions, the RF magnetic field profile produced by 7T volume head coils is very inhomogeneous, with enhanced sensitivity near the center of the human brain and substantially reduced in the periphery.
Expression analysis of a GA 20-oxidase in embryos from two sorghum lines with contrasting dormancy: possible participation of this gene in the hormonal control of germination.

The role of GAs in promoting seed germination is well known and experiments with seeds from different species have suggested the requirement of de novo synthesis of GAs upon imbibition for germination. There are also strong indications that the enhancement of GA synthesis is part of the mechanism through which environmental signals (i.e. light) induce germination. Since along the GA biosynthetic pathway, oxidation at C-20 carried out by GA 20-oxidases is thought to be a site of regulation, a cDNA clone encoding a GA 20-oxidase was isolated from embryos of sorghum (SbGA 20ox). Expression analysis of this gene in embryos within imbibed caryopses with low dormancy showed detectable amounts of the specific mRNA early upon incubation, increasing thereafter. In contrast, it remained barely detectable in embryos from dormant caryopses. Changes in endogenous GA4 levels were in agreement with those of SbGA 20ox mRNA, suggesting that GA production might be regulated differentially at the level of transcription of this gene. The expression of SbGA 20ox was enhanced in incubated embryos isolated from either type of caryopses, illustrating a physiological control exerted by the surrounding seed tissues on gene expression. The results also show that ABA leads to a suppression of transcription of this gene.
Does Prosecutorial Experience “Balance Out” a Judge's Liberal Tendencies?

Conclusive evidence of a relationship between background characteristics such as gender, race, or religion and specific judicial decisions has been hard to come by. Studies that find a correlation between prosecutorial experience and increased support for conservative positions have been an exception to this pattern. The presumption that former prosecutors make more-conservative judges permeates media accounts of judicial nominees and may affect judicial selection processes. After examining forty years of criminal cases from the Supreme Court and the U.S. Courts of Appeals, I find no relationship between prosecutorial background and a propensity for favoring conservative outcomes. Judicial ideology remains the better predictor of future judicial behavior in criminal cases.
The effect of different solvents on the ATP/ADP content and growth properties of HeLa cells

Testing of the effects of xenobiotics in cultured cells often requires the use of organic solvents to effect suspension of the test agents in cell culture media. However, the toxic effects of the solvents themselves may introduce artifacts, which obscure interpretation of the experimental results. In this article, the toxicity of different solvents commonly used for solvation of a variety of xenobiotic agents was studied. We show that ethanol, acetone, isooctane, methanol, and hexane were considerably less toxic than the more commonly used solvent, DMSO, when ATP content and growth rates of HeLa cells exposed to these solvents was measured. © 1998 John Wiley & Sons, Inc. J Biochem Toxicol 13: 11–15, 1999
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework

MOTIVATION Regulatory DNA elements are associated with DNase I hypersensitive sites (DHSs). Accordingly, identification of DHSs will provide useful insights for in-depth investigation into the function of noncoding genomic regions. RESULTS In this study, using the strategy of ensemble learning framework, we proposed a new predictor called iDHS-EL for identifying the location of DHS in human genome. It was formed by fusing three individual Random Forest (RF) classifiers into an ensemble predictor. The three RF operators were respectively based on the three special modes of the general pseudo nucleotide composition (PseKNC): (i) kmer, (ii) reverse complement kmer and (iii) pseudo dinucleotide composition. It has been demonstrated that the new predictor remarkably outperforms the relevant state-of-the-art methods in both accuracy and stability. AVAILABILITY AND IMPLEMENTATION For the convenience of most experimental scientists, a web server for iDHS-EL is established at http://bioinformatics.hitsz. edu.cn/iDHS-EL, which is the first web-server predictor ever established for identifying DHSs, and by which users can easily get their desired results without the need to go through the mathematical details. We anticipate that IDHS-EL: will become a very useful high throughput tool for genome analysis. CONTACT bliu@gordonlifescience.org or bliu@insun.hit. edu.cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Regulation of Insulin Receptor Trafficking by Bardet Biedl Syndrome Proteins

Insulin and its receptor are critical for the regulation of metabolic functions, but the mechanisms underlying insulin receptor (IR) trafficking to the plasma membrane are not well understood. Here, we show that Bardet Biedl Syndrome (BBS) proteins are necessary for IR localization to the cell surface. We demonstrate that the IR interacts physically with BBS proteins, and reducing the expression of BBS proteins perturbs IR expression in the cell surface. We show the consequence of disrupting BBS proteins for whole body insulin action and glucose metabolism using mice lacking different BBS genes. These findings demonstrate the importance of BBS proteins in underlying IR cell surface expression. Our data identify defects in trafficking and localization of the IR as a novel mechanism accounting for the insulin resistance commonly associated with human BBS. This is supported by the reduced surface expression of the IR in fibroblasts derived from patients bearing the M390R mutation in the BBS1 gene.
Transforming mathematics instruction: multiple approaches and practices

approach denies, to some extent, the opportunity for such colonialism, and actively promotes localism. However, as my analysis shows, some evidence of theoretical colonialism remains. So in spite of the challenges in reading this text, in the sense that a reader might be seeking those summaries of similarities and differences across the world, the book provides a rich account of international approaches to teaching and learning algebra. It also highlights some particularities and localised features of practice in the countries examined. As I pointed out at the beginning of this review, this approach to international comparative study of classroom practice is still a relatively new aspect of mathematics education research. The LPS in its five volumes and large number of journal articles provides a framework and articulates the character of this kind of research.
Swarm of Robots Coordination Strategy Based on WSN Packages Transmission and Supervisors' External Commands

The use of Unmanned Aerial Vehicles (UAV) has been quite increased in last years. These devices can be used in a variety of applications: from urban monitoring to even military services and borders patrol. Their use may be directly connected to the concept of Wireless Sensor Networks (WSNs). The behavior of the robots can act as a way to move WSN nodes while assuring the communication between the nodes (robots). These features turn the network able to perform the mentioned tasks. However, as significant as the task to be performed, is the external monitoring of its successful completion or not. It allows the operator to take the most appropriate decision. This paper focuses on the preliminary results of a real-time external vision of a swarm of UAVs acting as a WSN. Quantitative simulation verification from the communication packages flow is extracted.
Channel Re-Assignment in Wireless Mesh Networks based on Link Load Estimation

A channel assignment scheme for multi-radio WMNs (Wireless Mesh Networks) to provide high-throughput paths especially for the highly loaded node with the best connectivity to the gateway(e.g. in terms of highest rate, lowest interference or both) is provided in this paper. We observed the flows on the links and data packets at each wireless access point in an existing wireless mesh backbone from logs files of traffic flows generated at gateway level. After observing, we estimate the traffic load for each network link using load estimation algorithm. We provide the links having maximum load to minimum interference channel i.e. non-interference channel based on IEEE 802.11. The performance evaluation shows that by using the proposed channel assignment, the network performance is improved.