bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing prediction models from expression profiles for large scale lncRNA–miRNA interaction profiling
Authors: Huang Yu-An , Chan Keith C C , You Zhu-Hong 
Published: October 2017

Abstract

Motivation
The interaction of miRNA and lncRNA is known to be important for gene regulations. However, not many computational approaches have been developed to analyze known interactions and predict the unknown ones. Given that there are now more evidences that suggest that lncRNA–miRNA interactions are closely related to their relative expression levels in the form of a titration mechanism, we analyzed the patterns in large-scale expression profiles of known lncRNA–miRNA interactions. From these uncovered patterns, we noticed that lncRNAs tend to interact collaboratively with miRNAs of similar expression profiles, and vice versa.

Results
By representing known interaction between lncRNA and miRNA as a bipartite graph, we propose here a technique, called EPLMI, to construct a prediction model from such a graph. EPLMI performs its tasks based on the assumption that lncRNAs that are highly similar to each other tend to have similar interaction or non-interaction patterns with miRNAs and vice versa. The effectiveness of the prediction model so constructed has been evaluated using the latest dataset of lncRNA–miRNA interactions. The results show that the prediction model can achieve AUCs of 0.8522 and 0.8447 ± 0.0017 based on leave-one-out cross validation and 5-fold cross validation. Using this model, we show that lncRNA–miRNA interactions can be reliably predicted. We also show that we can use it to select the most likely lncRNA targets that specific miRNAs would interact with. We believe that the prediction models discovered by EPLMI can yield great insights for further research on ceRNA regulation network. To the best of our knowledge, EPLMI is the first technique that is developed for large-scale lncRNA–miRNA interaction profiling.

Availability and implementation
Matlab codes and dataset are available at https://github.com/yahuang1991polyu/EPLMI/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Motion capture systems for jump analysis
Authors: Rojas-Lertxundi Sendoa , Fernández-López J Ramón , Huerta Sergio , García Bringas Pablo 
Published: October 2017

AbstractThis article presents several methods used in motion capture to measure jumps. The traditional systems to acquire jump information are force plates, but they are very expensive to most people. Amateur sports enthusiasts who want to improve their performance, do not have enough money to spend in professional systems ($+/-20.000$EUR). The price reduction of electronic devices, specifically the inertial measurement units (IMU), are generating new methods of motion capture. In this article we present the state-of the-art motion capture systems for this purpose, from the classical force plates to latest released IMUs. Experiments show that the IMU is equally valid for measuring vertical jump.
The discovery of a five-image lensed quasar at z = 3.34 using PanSTARRS1 and Gaia
Authors: Ostrovski Fernanda , Lemon Cameron A , Auger Matthew W , McMahon Richard G , Fassnacht Christopher D , Chen Geoff C-F , Connolly Andrew J , Koposov Sergey E , Pons Estelle , Reed Sophie L , Rusu Cristian E 
Published: October 2017

Abstract
We report the discovery, spectroscopic confirmation and mass modelling of the gravitationally lensed quasar system PS J0630−1201. The lens was discovered by matching a photometric quasar catalogue compiled from Pan-STARRS1 and Wide-field Infrared Survey Explorer photometry to the Gaia data release 1 catalogue, exploiting the high spatial resolution of the latter (full width at half-maximum ∼0.1 arcsec) to identify the three brightest components of the lensed quasar system. Follow-up spectroscopic observations with the William Herschel Telescope confirm the multiple objects are quasars at redshift zq = 3.34. Further follow-up with Keck adaptive optics high-resolution imaging reveals that the system is composed of two lensing galaxies and the quasar is lensed into an ∼2.8 arcsec separation four-image cusp configuration with a fifth image clearly visible, and a 1.0 arcsec arc due to the lensed quasar host galaxy. The system is well modelled with two singular isothermal ellipsoids, reproducing the position of the fifth image. We discuss future prospects for measuring time delays between the images and constraining any offset between mass and light using the faintly detected Einstein arcs associated with the quasar host galaxy.
Systematic Government Access to Private-Sector Data
Authors: Rubinstein Ira S. , Nojeim Gregory T. , Lee Ronald D. 
Published: October 2017

Abstract
There has been an increase worldwide in government demands for data held by the private sector. In most countries studied, the publicly accessible law provides an inadequate foundation for systematic access, both from a human rights perspective and at a practical level. Transparency about systematic access remains weak. Access for national security purposes is more sparingly regulated than is access for criminal investigation purposes. Relying on the country reports prepared for this project, this chapter develops both a descriptive framework for comparing national laws on surveillance and government access to data held by the private sector, and a normative framework based on factors derived from constitutional and human rights law. A robust, global debate is needed on the standards for government surveillance, premised on greater transparency about current practices. International human rights law provides a useful framework for that debate.
Regulating Foreign Surveillance through International Law
Authors: Deeks Ashley S. 
Published: October 2017

Abstract
Regulating how governments conduct foreign electronic surveillance against another state’s citizens poses a complex challenge. In the wake of Edward Snowden’s leaks in 2013, the extent to which governments conduct surveillance of foreign state leaders and citizens became strikingly clear. This chapter argues that, although states traditionally have been loath to regulate their intelligence activities using international law, that body of law offers an important avenue by which states can reduce criticisms stemming from human rights and other groups, help set the agenda for the future of foreign surveillance, and respond to foreign and domestic fears that government surveillance is unconstrained. The chapter describes the variety of pressures states face to modulate their foreign surveillance, explains some of the benefits that states may accrue by doing so, and suggests six procedural norms around which certain Western democracies may be able to coalesce.
The Many Faces of Socioeconomic Change
Authors: Toye John 
Published: October 2017

Abstract
This book provides a survey of different ways in which economic sociocultural and political aspects of human progress have been studied since the time of Adam Smith. Inevitably, over such a long time span, it has been necessary to concentrate on highlighting the most significant contributions, rather than attempting an exhaustive treatment. The aim has been to bring into focus an outline of the main long-term changes in the way that socioeconomic development has been envisaged. The argument presented is that the idea of socioeconomic development emerged with the creation of grand evolutionary sequences of social progress that were the products of Enlightenment and mid-Victorian thinkers. By the middle of the twentieth century, when interest in the accelerating development gave the topic a new impetus, its scope narrowed to a set of economically based strategies. After 1960, however, faith in such strategies began to wane, in the face of indifferent results and general faltering of confidence in economists’ boasts of scientific expertise. In the twenty-first century, development research is being pursued using a research method that generates disconnected results. As a result, it seems unlikely that any grand narrative will be created in the future and that neo-liberalism will be the last of this particular kind of socioeconomic theory.
Development with a human face, 1980–
Authors: Toye John 
Published: October 2017

Abstract
Early attempts to humanize political economy raised two questions—the class interests of owners of land and capital and the politics of moving to a reformed system of wealth valuation. These two problems recurred when Mahbub ul Haq revolted against the conventional techniques of development planning and advocated a reform that included targets for the structure of consumption, expressed in physical and not financial terms. This basic needs approach was criticized for being top-down, state-led, and foundering on the difficult politics of reform. Amartya Sen rejected the metric of both utility and commodities and argued for that of capabilities to function, but declined to propose a set of basic human capabilities—while supporting ul Haq’s simplistic Human Development Index. Poverty has many dimensions, but even the new multiple poverty index needs to justify the dimensions chosen for inclusion.
A Quantitative Analysis of Microcirculation in Skin Defects Covered with Topical Wound Dressings or a Newly Developed Collagen Matrix
Authors: Held Manuel , Medved Fabian , Petersen Wiebke , Tolzmann Dascha Sophie , Rahmanian-Schwarz Afshin , Schaller Hans-Eberhard , Rothenberger Jens 
Published: October 2017

ABSTRACT

OBJECTIVE:
Innovative skin substitutes and temporary wound dressings are frequently used in the treatment of superficial and partial-thickness wounds. The aim of this study was to compare 2 commonly used temporary skin dressings with a newly developed collagen matrix to determine changes in microcirculation as measured by blood flow, hemoglobin oxygenation, and relative hemoglobin values during healing of partial-thickness skin defects.

METHODS:
This animal study involved 28 adult male Lewis rats. On the back of each rat, 2 standardized partial-thickness skin defects were generated through a skin dermatome (n = 56). Then, wounds were treated with polylactide-based copolymer skin substitute (Suprathel, PolyMedics, Denkendorf, Germany; n = 14), biosynthetic skin dressing (Biobrane, Smith & Nephew, Hamburg, Germany; n = 14), or Collagen Cell Carrier (CCC; Naturin Viscofan, Weinheim, Germany; n = 14). The remaining control wounds were left untreated (n = 14).

MAIN OUTCOME MEASURES:
Perfusion dynamics were assessed every 10 days for 80 days with the O2C device (LEA Medizintechnik, Gieβen, Germany) to determine blood flow, hemoglobin oxygenation, and relative amount of hemoglobin.

MAIN RESULTS:
Blood flow was increased in all wounds for at least 30 days after wound generation. The relative amounts of hemoglobin were increased in superficial layers (2 mm) for 10 to 20 days. Hemoglobin oxygenation in the superficial layers decreased in the polylactide-based copolymer skin substitute and biosynthetic skin dressing–treated groups and initially increased in the untreated wounds and CCC groups on day 10; these values also decreased.

CONCLUSIONS:
The presented results demonstrate the complex changes in microcirculation in the course of healing partial-thickness wounds with different wound dressings and contribute to a better understanding of these wounds. However, based on the results of the study, a clear recommendation for a specific substitute is not yet possible.
Oxidized Regenerated Cellulose/Collagen Dressings: Review of Evidence and Recommendations
Authors: Wu Stephanie , Applewhite Andrew J. , Niezgoda Jeffrey , Snyder Robert , Shah Jayesh , Cullen Breda , Schultz Gregory , Harrison Janis , Hill Rosemary , Howell Melania , Speyrer Marcus , Utra Howard , de Leon Jean , Lee Wayne , Treadwell Terry 
Published: October 2017

ABSTRACT

OBJECTIVE:
Healthcare systems are being challenged to manage increasing numbers of nonhealing wounds. Wound dressings are one of the first lines of defense in wound management, and numerous options exist. The oxidized regenerated cellulose (ORC)/collagen dressing may offer healthcare providers a robust and cost-effective tool for use in a variety of wounds.

DESIGN:
A multidisciplinary panel meeting was convened to discuss the use of ORC/collagen dressings in wound care and provide practice recommendations. A literature search was conducted to provide a brief review of the peer-reviewed studies published between January 2000 and March 2016 to inform the meeting.

SETTING:
A 2-day panel meeting convened in February 2017.

PARTICIPANTS:
Healthcare providers with experience using ORC/collagen dressings. This multidisciplinary panel of 15 experts in wound healing included podiatrists, wound care specialists (doctors, certified wound care nurses, and research scientists), and an orthopedist.

RESULTS:
The literature search identified 58 articles, a majority of which were low levels of evidence (69.3% were level 3 or lower). Panel members identified wound types, such as abrasions, burns, stalled wounds, diabetic foot ulcers, and pressure injuries, where ORC/collagen dressing use could be beneficial. Panel members then provided recommendations and technical pearls for the use of ORC/collagen dressings in practice. Barriers to ORC/collagen dressing use were discussed, and potential resolutions were offered.

CONCLUSIONS:
An ORC/collagen dressing can be a critical tool for clinicians to help manage a variety of wounds. Clinical and economic studies comparing standard-of-care dressings and plain collagen dressings to ORC/collagen dressings are needed.
Pharmacomechanical Thrombolysis for Deep Vein Thrombosis in May-Thurner Syndrome
Authors: Roy Mayank , Sasson Morris , Rosales-Velderrain Armando , Moon Savannah , Grove Mark , King Terry 
Published: October 2017

Objective Patients with May-Thurner syndrome presenting with acute deep vein thrombosis benefit from early lysis of clot and endovascular treatment. We evaluated the outcome of patients with May-Thurner syndrome who presented with deep vein thrombosis, managed with pharmacomechanical thrombolysis as the primary mode of intervention, in combination with angioplasty and stent placement. Methods We reviewed all patients with May-Thurner syndrome managed in our institution between January 2009 to December 2015. Patency rate and postthrombotic syndrome were evaluated as primary end points. Results A total of seven patients (6 females, 1 male) with a mean ± SD age of 48 ± 17 years and mean ± SD body mass index of 29.64 ± 7.25 kg/m2 were identified. Six patients presented with acute deep vein thrombosis and one presented with chronic venous insufficiency. Five patients underwent pharmacomechanical thrombolysis (TRELLIS and altepase) with concomitant stenting of the common iliac vein, one had only angioplasty with stent placement, and one had only pharmacomechanical thrombolysis. Median time from presentation to pharmacomechanical thrombolysis was 4 days (range = 1–9). Patency rate and postthrombotic syndrome at 12 months were 100% and 0%, respectively. No patient experienced major bleeding or pulmonary embolism. The median length of stay was 3 days (range = 0–4). There was no mortality associated with the procedure. The mean ± SD follow-up was 26 ± 15 months. Conclusions In patients with May-Thurner syndrome, pharmacomechanical thrombolysis is an effective approach for the management of acute deep vein thrombosis, decreasing thrombus burden, and long-term postthrombotic syndrome when used in conjunction with stenting.
The uncertainty of old aliquots of cell lines: e-CAS or m-CAS?
Authors: Evans Elizabeth , Paillot Romain , López-Álvarez María Rocío 
Published: October 2017

SummaryThe 3Rs principles (Replacement, Reduction and Refinement) are focused on finding alternatives to the use of animals in research. In this regard, cell lines are popular and useful tools for the replacement of primary cells in in vitro studies. However, around 15-30% of cell lines used in research have been misidentified or cross-contaminated generating concerns about the results obtained from experiments that use them. Here we described how old aliquots of an equine macrophage cell line (e-CAS) stored at the Animal Health Trust did not contain equine cells but macrophages of murine origin (m-CAS).
Designing oil palm landscapes to retain biodiversity using insights from a key ecological indicator group
Authors: Gray Claudia L. , Slade Eleanor M. , Mann Darren J. , Lewis Owen T. 
Published: October 2017

ABSTRACTOil palm expansion threatens biodiverse ecosystems across the tropics. However, palm oil is a widely used and profitable crop, so identifying strategies that mitigate the impact of oil palm expansion on biodiversity is important. Riparian reserves (strips of forest along rivers) are protected in many countries for hydrological reasons and also support species that would not otherwise persist in oil palm. However, management guidelines for riparian zones have been informed by relatively few ecological studies. We assessed how the structural features and landscape context of riparian reserves in Sabah, Malaysia affected dung beetle communities. We also tested the use of flight intercept traps to study movement of dung beetles along linear forest corridors. Overall, dung beetle abundance in riparian reserves was 54% lower than in logged forest areas, but all species observed in the logged forest were found in at least one riparian reserve site and both species richness and diversity increased with reserve width. Distance from a large block of continuous forest affected dung beetle community composition but not species richness, abundance, or functional diversity. The amount of forest cover in the surrounding landscape improved the retention of species within riparian reserves, and increases in vegetation complexity corresponded with higher functional richness and functional dispersion. The flight intercept traps did not indicate that there is net movement of individuals out of logged forest areas into the riparian reserves. The species richness of 30 m reserves (the suggested requirement of reserves in Sabah) was only 10% lower than in logged forest, but our data indicate that riparian reserves of at least 50 – 80 m are needed for species richness and diversity to equal that in nearby logged forest. These findings, particularly if they apply more widely to forest-dependent taxa, should be taken into account when setting policy and sustainability guidelines for oil palm plantations, both in areas undergoing conversion from forest and in existing oil palm plantations where forest restoration is required.
Auditory Motion Does Not Modulate Spiking Activity in the Middle Temporal and Medial Superior Temporal Visual Areas
Authors: Chaplin Tristan A. , Allitt Benjamin J. , Hagan Maureen A. , Rosa Marcello G.P. , Rajan Ramesh , Lui Leo L. 
Published: October 2017

AbstractThe integration of multiple sensory modalities is a key aspect of brain function, allowing animals to take advantage of concurrent sources of information to make more accurate perceptual judgments. For many years, multisensory integration in the cerebral cortex was deemed to occur only in high-level “polysensory” association areas. However, more recent studies have suggested that cross-modal stimulation can also influence neural activity in areas traditionally considered to be unimodal. In particular, several human neuroimaging studies have reported that extrastriate areas involved in visual motion perception are also activated by auditory motion, and may integrate audio-visual motion cues. However, the exact nature and extent of the effects of auditory motion on the visual cortex have not been studied at the single neuron level. We recorded the spiking activity of neurons in the middle temporal (MT) and medial superior temporal (MST) areas of anesthetized marmoset monkeys upon presentation of unimodal stimuli (moving auditory or visual patterns), as well as bimodal stimuli (concurrent audio-visual motion). Despite robust, direction selective responses to visual motion, none of the sampled neurons responded to auditory motion stimuli. Moreover, concurrent moving auditory stimuli had no significant effect on the ability of single MT and MST neurons, or populations of simultaneously recorded neurons, to discriminate the direction of motion of visual stimuli (moving random dot patterns with varying levels of motion noise). Our findings do not support the hypothesis that direct interactions between MT, MST and areas low in the hierarchy of auditory areas underlie audiovisual motion integration.
Rapid Agrobacterium-mediated transformation of tobacco cotyledons using toothpicks
Authors: Yau Yuan-Yeu , Easterling Mona , Brennan Lindsey 
Published: October 2017

AbstractTobacco is a model plant for genetic transformation, with leaf-disk transformation being the most commonly used method for its transformation. One disadvantage of leaf-disk transformation is obtaining an adequately sized leaf. Cotyledons from young seedlings are considered too small and fragile to use. In an attempt to overcome this drawback, a protocol was developed using toothpicks as a tool to inoculate cotyledons ~2mm in diameter. Agrobacterium tumefaciens LBA4404 hosting two different plasmids (pC35.BNK.2 or pRB140-Bxb1-op) was used for transformation. Fifty-six putative transgenic shoots (T0) were obtained from pC35.BNK.2 transformation. Among them, 38 (68%) grew roots in kanamycin-containing medium. Approximately, 35% of transgenic lines contained a single-copy transgenic locus based on Mendelian inheritance analysis and chi-square (χ2) test of T1 seedlings from 17 lines. To simplify the protocol, water-prepared Agrobacterium inoculum was used in pRB140-Bxb1-op (containing gus gene) transformation. This resulted in ~35% putative T0 transgenic lines stained strong blue with GUS histochemical staining assay. Both sets of results demonstrate toothpick inoculation to be an effective approach for Agrobacterium-mediated tobacco cotyledon transformation. This reduces wait time required in existing leaf-disk transformation method using mature leaves. Removal of step requiring submersion of explants in Agrobacterium liquid culture, the protocol also has advantages by minimizing Agrobacterium overgrowth and maintaining explant fitness for later tissue-culturing.