bluuebunny/crossref_metadata_2025_split huggingface dataset:
Branchiopoda
Authors: Fritsch Martin , Richter Stefan 
Published: March 2016

AbstractIn over 150 years of nervous system research on Branchiopoda, numerous detailed descriptions are available. Branchiopods constitute one of the morphologically most disparate taxa in Crustacea, but the nervous system architecture appears to be fairly homogeneous across the taxon. As in all other crustaceans, the branchiopod brain consists of a proto-, deuto-, and tritocerebrum and is connected posteriorly to the ventral nerve cord. Proto- and deutocerebra are often completely confluent and are both connected posteriorly with the tritocerebrum by circumoral connectives. Each brain part is connected to sensory or mechanosensory organs by nerves (antennule, antenna) or tracts (compound eyes), and possesses a discrete centre for integrative processing (central body, optical neuropils, deutocerebral lobes). The presence of olfactory glomeruli is still uncertain; hemiellipsoid bodies, however, appear to be absent. The ventral nerve cord consists of a well-separated pair of ganglia in each appendage-bearing segment, which are interconnected by two parallel longitudinal connectives and two transversal commissures. Laterally, each ganglion projects nerves into the appendages and also sends nerves into the integument and the visceral body cavity. At the posterior end, two longitudinal neurite bundles extend into the telson and innervate the proctodaeum and the dorsal setae. Investigations into neuro-active substances have revealed a uniform distribution pattern of individually identifiable neurons (e.g. serotonin-like immunoreactive neurons). Although the phylogenetic position of Branchiopoda within Tetraconata is still uncertain, it appears more likely that the branchiopod brain is secondarily simplified instead of being primitive. It is uncertain whether or not this also concerns the ventral nerve cord.
Perspective—The Origin Of Vertebrate Neural Organization
Authors: Lacalli Thurston 
Published: March 2016

Abstract
The closest invertebrate relatives of vertebrates have brains that are smaller and organizationally much simpler that those of vertebrates, but there are similarities in basic architecture from which an evolutionary trajectory from simple to complex can be inferred. The molecular data show that many of the patterning signals are common to a range of taxa, including insects and annelids, indicating that some features are ancient and widely shared. Among protochordates, amphioxus provides the best model for the basic circuitry of the basal brainstem, including the hypothalamus and reticular formation. These have key roles in homeostasis and locomotory control, using circuits where paracrine transmission, neuropeptides, and open tract organization predominate. What is missing from amphioxus are the expanded dorsal centres, used by vertebrates for processing inputs from the paired sense organs of the head, which are themselves vertebrate innovations. Signals from these are routed through stacked arrays of cells in cortex and related structures that act as parallel array processors. In pallial derivatives in the forebrain, this has led to the emergence of primary consciousness, exemplified by awareness of the visual field, which is probably widespread in vertebrates. The function of consciousness is suggested here to relate to the adaptive advantage of generating a searchable display of sensory data, i.e. a searchable database.
Testing the ‘microbubble effect’ using the Cavitron technique to measure xylem water extraction curves
Authors: Pivovaroff Alexandria L. , Burlett Régis , Lavigne Bruno , Cochard Hervé , Santiago Louis S. , Delzon Sylvain 
Published: March 2016

Abstract
Plant resistance to xylem cavitation is a major drought adaptation trait and is essential to characterizing vulnerability to climate change. Cavitation resistance can be determined with vulnerability curves. In the past decade, new techniques have increased the ease and speed at which vulnerability curves are produced. However, these new techniques are also subject to new artefacts, especially as related to long-vesselled species. We tested the reliability of the ‘flow rotor’ centrifuge technique, the so-called Cavitron, and investigated one potential mechanism behind the open vessel artefact in centrifuge-based vulnerability curves: the microbubble effect. The microbubble effect hypothesizes that microbubbles introduced to open vessels, either through sample flushing or injection of solution, travel by buoyancy or mass flow towards the axis of rotation where they artefactually nucleate cavitation. To test the microbubble effect, we constructed vulnerability curves using three different rotor sizes for five species with varying maximum vessel length, as well as water extraction curves that are constructed without injection of solution into the rotor. We found that the Cavitron technique is robust to measure resistance to cavitation in tracheid-bearing and short-vesselled species, but not for long-vesselled ones. Moreover, our results support the microbubble effect hypothesis as the major cause for the open vessel artefact in long-vesselled species.
Radiation therapy for localized duodenal low-grade follicular lymphoma
Authors: Harada Arisa , Oguchi Masahiko , Terui Yasuhito , Takeuchi Kengo , Igarashi Masahiro , Kozuka Takuyo , Harada Ken , Uno Takashi , Hatake Kiyohiko 
Published: March 2016

Abstract
The aim of this study was to evaluate the initial treatment results and toxicities of radiation therapy for patients with early stage low-grade follicular lymphoma (FL) arising from the duodenum. We reviewed 21 consecutive patients with early stage duodenal FL treated with radiation therapy between January 2005 and December 2013 at the Cancer Institute Hospital, Tokyo. The characteristics of patients were: median age 62 years (range, 46–79 years), gender (male, 6; female, 15), clinical stage (I, 20; II 1, 1), histological grade (I, 17; II, 4). All patients were treated with radiation therapy alone. The median radiation dose was 30.6 Gy (range, 30.6–39.6) in 17 fractions. The involved-site radiation therapy was delivered to the whole duodenum. The median follow-up time was 43.2 months (range 21.4–109.3). The 3-year overall survival (OS), relapse-free survival (RFS) and local control (LC) rates were 94.7%, 79.3% and 100%, respectively. There were four relapses documented outside the treated volumes: two in the gastrointestinal tract (jejunum, terminal ileum), one in an abdominal lymph node (mesenteric lymph node) and one in the bone marrow. None died of the disease; one death was due to acute myeloid leukemia. No toxicities greater than Grade 1 were observed during treatment and over the follow-up time. The 30.6 Gy of involved-site radiation therapy provided excellent local control with very low toxicities. Radiation therapy could be an effective and safe treatment option for patients with localized low grade FL arising from the duodenum.
The “Rise–Peak–Fall” Pattern of Time Dependency of the Cardiovascular Pleiotropic Effects of Treatment With Low-dose Atorvastatin, Losartan, and a Combination Thereof in Rats
Authors: Janic Miodrag , Lunder Mojca , Cerne Darko , Marc Janja , Jerin Ales , Skitek Milan , Drevensek Gorazd , Sabovic Miso 
Published: March 2016

Abstract:
Treatment with low, subtherapeutic doses of statins and sartans expresses beneficial pleiotropic effects on the arterial wall. The present study explored whether these effects depend on treatment duration. Wistar rats were randomly divided into 4 groups and received low-dose atorvastatin, low-dose losartan, their combination, or saline (control) daily. After 4, 6, 8, and 10 weeks of treatment, the animals were anesthetized, blood samples taken, and hearts and thoracic aortas isolated. Thoracic aorta endothelium–dependent relaxation and parameters of the isolated heart exposed to ischemic–reperfusion injury were assessed along with blood serum parameters and vasoactive genes expression. Low-dose atorvastatin, losartan, and especially their combination showed the characteristic time dependency of all studied parameters (thoracic aorta relaxation, isolated heart parameters, C-reactive protein values, genes encoding endothelial nitric oxide synthase, and CD40). The peak in efficacy was observed after 6 weeks of treatment and subsequently steadily declined. The peak versus control values were significant for all measured parameters. Only a combination of atorvastatin and losartan increased nitric oxide and decreased asymmetric dimethylarginine. A characteristic time-dependent “rise–peak–fall” pattern of the cardiovascular pleiotropic effects of statins and sartans in subtherapeutic low doses was revealed. Evidently, resistance to the explored treatment occurs after a certain period.
Single-Cell Gene Expression Profiling and Cell State Dynamics: Collecting Data, Correlating Data Points and Connecting the Dots
Authors: Marr Carsten , Zhou Joseph X. , Huang Sui 
Published: March 2016

AbstractSingle-cell analyses of transcript and protein expression profiles – more precisely, single-cell resolution analysis of molecular profiles of cell populations – have now entered the center stage with widespread applications of single-cell qPCR, single-cell RNA-Seq and CyTOF. These high-dimensional population snapshot techniques are complemented by low-dimensional time-resolved, microscopy-based monitoring methods. Both fronts of advance have exposed a rich heterogeneity of cell states within uniform cell populations in many biological contexts, producing a new kind of data that has stimulated a series of computational analysis methods for data visualization, dimensionality reduction, and cluster (subpopulation) identification. The next step is now to go beyond collecting data and correlating data points: to connect the dots, that is, to understand what actually underlies the identified data patterns. This entails interpreting the “clouds of points” in state space as a manifestation of the underlying molecular regulatory network. In that way control of cell state dynamics can be formalized as a quasi-potential landscape, as first proposed by Waddington. We summarize key methods of data acquisition and computational analysis and explain the principles that link the single-cell resolution measurements to dynamical systems theory.
Light sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development
Authors: Girstmair Johannes , Zakrzewski Anne , Lapraz François , Handberg-Thorsager Mette , Tomancak Pavel , Pitrone Peter Gabriel , Simpson Fraser , Telford Maximilian J. 
Published: March 2016

ABSTRACTBACKGROUNDSelective plane illumination microscopy (SPIM a type of light-sheet microscopy) involves focusing a thin sheet of laser light through a specimen at right angles to the objective lens. As only the thin section of the specimen at the focal plane of the lens is illuminated, out of focus light is naturally absent and toxicity due to light (phototoxicity) is greatly reduced enabling longer term live imaging. OpenSPIM is an open access platform (Pitrone et al. 2013 andOpenSPIM.org) created to give new users step-by-step instructions on building a basic configuration of a SPIM microscope, which can in principle be adapted and upgraded to each laboratory’s own requirements and budget. Here we describe our own experience with the process of designing, building, configuring and using an OpenSPIM for our research into the early development of the polyclad flatwormMaritigrella crozieri– a non-model animal.RESULTSOur OpenSPIM builds on the standard design with the addition of two colour laser illumination for simultaneous detection of two probes/molecules and dual sided illumination, which provides more even signal intensity across a specimen. Our OpenSPIM provides high resolution 3d images and time lapse recordings, and we demonstrate the use of two colour lasers and the benefits of two color dual-sided imaging. We used our microscope to study the development of the embryo of the polyclad flatwormMaritigrella crozieri. The capabilities of our microscope are demonstrated by our ability to record the stereotypical spiral cleavage pattern ofMaritigrellawith high-speed multi-view time lapse imaging. 3D and 4D (3D + time) reconstruction of early development from these data is possible using image registration and deconvolution tools provided as part of the open source Fiji platform. We discuss our findings on the pros and cons of a self built microscope.CONCLUSIONSWe conclude that home-built microscopes, such as an OpenSPIM, together with the available open source software, such as MicroManager and Fiji, make SPIM accessible to anyone interested in having continuous access to their own light-sheet microscope. However, building an OpenSPIM is not without challenges and an open access microscope is a worthwhile, if significant, investment of time and money. Multi-view 4D microscopy is more challenging than we had expected. We hope that our gained experience during this project will help future OpenSPIM users with similar ambitions.
Human mismatch repair system corrects errors produced during lagging strand replication more effectively
Authors: Andrianova Maria A. , Bazykin Georgii A. , Nikolaev Sergey I. , Seplyarskiy Vladimir B. 
Published: March 2016

AbstractMismatch repair (MMR) is one of the main systems maintaining fidelity of replication. Different effectiveness in correction of errors produced during replication of the leading and the lagging DNA strands was reported in yeast, but this effect is poorly studied in humans. Here, we use MMR-deficient (MSI) and MMR-proficient (MSS) cancer samples to investigate properties of the human MMR. MSI, but not MSS, cancers demonstrate unequal mutation rates between the leading and the lagging strands. The direction of strand asymmetry in MSI cancers matches that observed in cancers with mutated exonuclease domain of polymerase δ, indicating that polymerase δ contributes more mutations than its leading-strand counterpart, polymerase ε. As polymerase δ primarily synthesizes DNA during the lagging strand replication, this implies that mutations produced in wild type cells during lagging strand replication are repaired by the MMR ~3 times more effectively, compared to those produced on the leading strand.
Deep mutational scanning reveals characteristics important for targeting of the tail-anchored protein Fis1
Authors: Keskin Abdurrahman , Akdoğan Emel , Dunn Cory D. 
Published: March 2016

ABSTRACTProteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of theSaccharomyces cerevisiaeFis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl-terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening the Fis1 TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs at specific organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong,in vivoevidence that lysine and arginine can “snorkel,” or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.AbbreviationsTAtail anchorOMouter membraneMADmembrane-anchoring domain3-AT3-aminotriazoleCHXcycloheximide
Factors affecting the implementation of Web 2.0 applications in Omani academic libraries
Authors: Al-Kharousi Rahma , Jabur Naeema H , Bouazza Abdelmajed , Al-Harrasi Nabhan 
Published: March 2016

Purpose– The purpose of this paper is to investigate the different factors that affect using Web 2.0 applications in Omani academic libraries (OALs).Design/methodology/approach– In all, 29 interviews with directors and library staff of five OALs were conducted for the purpose of collecting data for the current research.Findings– The results indicated that there are nine internal factors and four external factors that affect using Web 2.0 applications in OALs. Internal factors include the low motivation of directors and library staff regarding using of Web 2.0 applications, lack of training and constant changes in the management structure. Meanwhile, the external factors are related to lack of policy and regulations and weakness and low speed of the internet.Practical implications– Most academic libraries in Oman have not yet adopted Web 2.0 applications to enhance their services. Therefore, this study intends to open insight into the state of Web 2.0 adoption in academic libraries and will help library managers to understand factors facing the use of Web 2.0 applications in their libraries, and this could signal a basis for policy shift in the internet infrastructure especially in the institutions of the higher education.Originality/value– This research is the first study in the field of Web 2.0 applications in OALs that investigates the factors affecting the use of Web 2.0 applications in academic libraries in general and in OALs specifically.
Integrated library management systems
Authors: Madhusudhan Margam , Singh Vikas 
Published: March 2016

Purpose
– The purpose of this paper is to analyze the various features and functions of Koha, Libsys, NewGenLib and Virtua with the help of specially designed evaluation checklist and rank them based on features/functions of integrated library management system (ILMS).

Design/methodology/approach
– The evaluation approach taken in this paper is similar to that of Singh and Sanaman (2012) and Madhusudhan and Shalini (2014) with minor modifications, comprising 306 features/functions and categorized as ten broad categories.

Findings
– The paper explores different features of open source (OS) and commercial ILMS, which reveals that Virtua got the highest total score of 218 (77.86 per cent), followed by Koha ILMS with 204 score (72.86 per cent). Interestingly, NewGenLib got the lowest total score, that is, 163 (58.21 per cent). ILMS under study are lagging behind in exploiting the full potential of the Web 2.0 features, including cloud computing features, and needs to be addressed in their future development.

Practical implications
– It is hoped that both the OS and commercial software will attend to the lacunae and soon develop fully functional Web 2.0/3.0 and cloud-based technologies.

Originality/value
– The findings of this paper will not only guide the librarians in the selection of a good ILMS, which can cater to the needs of their libraries, but also abreast the knowledge of evaluation of ILMS for the students of Library and Information Science. And the findings will help the ILMS vendors to know the limitations of their ILMS, so that they can overcome the limitations faced by users and improve their products.
Applying the DEMATEL approach to identify the focus of library service quality
Authors: Chen Yen-Ting 
Published: March 2016

Purpose
– This paper aims to apply the decision-making trial and evaluation laboratory (DEMATEL) to validate the service factors of an academic library.

Design/methodology/approach
– First, the service criteria were extracted from the SERVQUAL model and then their values were examined in the user’s mind. Second, the DEMATEL was applied to estimate the importance of the criteria and identify the causal factors. Next, an empirical study was conducted to demonstrate and validate the proposed approach. Finally, this paper offers some practical suggestions for academic libraries based on the analysis.

Findings
– According to the analysis’ results, “Empathy” is the causal factor in the cause–effect diagram; i.e. the library should pay more attentions to “Empathy” rather than “Reliability”, “Responsiveness” and “Assurance” factors.

Originality/value
– DEMATEL is a useful tool to identify the prominence and relationship of service factors; the evaluation is easy to apply and has not been used before in the discussion of library service. This paper provides an alternative for libraries to sort out the priorities of service improvement. The correspondence improvement can be addressed based on the causal analysis to make notable enhancement in service quality.
Use of social media by science students in public universities in Southwest Nigeria
Authors: Fasae Joseph Kehinde , Adegbilero-Iwari Idowu 
Published: March 2016

Purpose
– The purpose of this paper is to investigate the use of social media for academic practices by science students of public universities in Southwest Nigeria.

Design/methodology/approach
– Descriptive design was used for the study. Research instrument used was questionnaire where 140 copies were administered to science students, using purposive sampling technique. Three institutions in southwest of Nigeria were selected for the study. Copies of the questionnaire were distributed to students in their lecture rooms and laboratories during practical classes with the permission and assistance of their lecturers. The data collected were analysed using frequency and simple percentage.

Findings
– The results reveal that among the various social media networks available, Facebook (93.48 per cent) is the most recognized and most famous, followed by Google+ (63.77 per cent) and Twitter (47.83 per cent). Two-third of the students make use of social media daily to remain up-to-date with trending events/news and to occupy free time when they are bored, among other reasons. The findings show that Google+ (52.17 per cent) is the most beneficial social media network followed by Facebook (29.7 per cent) and Wikia (23.91 per cent). Most of the science students are knowledgeable in the usage and application of social media, while majority of them considered poor Internet connectivity, receiving of unwanted messages/pictures and electricity failure as the leading problems encountered while using social media.

Originality/value
– The study was necessary to identify the use and application of social media by science students in public universities in Southwest Nigeria.