bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating abundance of cryptic but trappable animals using trapping point transects: a case study for Key Largo woodrats
Authors: Potts Joanne M. , Buckland Stephen T. , Thomas Len , Savage Anne 
Published: April 2012

Summary1. Obtaining robust abundance or density estimates is problematic for many rare or cryptic species. We combine elements of capture–recapture and distance sampling, to develop a method called trapping point transects (TPT), and we applied this method to estimate the abundance of the endangered Key Largo woodrat (Neotoma floridana smalli).2. Trapping point transects requires two separate surveys to be held concurrently in space and time. In themain survey, the encounter rate (number of animals caught per trap per session) is measured. In thetrial survey, animals whose locations are known prior to opening traps are used to estimate the detection functiong(r) (the probability of capturing an animal given it is distancerfrom a trap when it is set), so the effective trapping area in the main survey can be estimated. It is assumed animals in the trial survey are a representative sample of all animals in the population. Individual heterogeneity in trappability is accommodated using random effects ing(r).3. Performance of two TPT estimators was assessed by simulation. Generally, when underlying capture probabilities were high [g(0) = 0·8] and between‐individual variation was small, modest survey effort (360 trap nights in the trial survey) generated little bias in estimated abundance (c.5%). Uncertainty and relative bias in population estimates increased with decreasing capture probabilities and increasing between‐individual variation. Survey effort required to obtain unbiased estimates was also investigated.4. Given the challenges of working with cryptic, sparse or nocturnal species, we tested the validity of this method to estimate the abundance of the Key Largo woodrats between 2008 and 2011.5. Trapping point transects was found to be an effective monitoring method yielding annual estimates of the extant wild population of 693, 248, 78 and 256 animals, with CVs of 0·45, 0·55, 0·82 and 0·43, respectively. The TPT method could be adapted to a range of species that are otherwise very difficult to monitor.
Serotonin inhibits low‐threshold spike interneurons in the striatum
Authors: Cains Sarah , Blomeley Craig P. , Bracci Enrico 
Published: April 2012

Key points
The striatum is the largest nucleus of the basal ganglia, a brain structure crucially involved in motor control. Recent results show that nitric oxide plays an important role in striatal pathophysiology.
The activity of the striatum is modulated by extrinsic neurotransmitters such as serotonin, produced by specialised neurons located in the brainstem.
This modulation is exerted through control of striatal interneurons. However, nitric oxide‐producing interneurons (NOS interneurons) have been difficult to investigate due to their rarity.
Using transgenic mice in which NOS interneurons express green fluorescent protein, we found that NOS interneurons are strongly inhibited by serotonin.
This inhibition is mediated by a specific class of serotonin receptors (5‐HT2C) causing an increase in a specific potassium conductance (KCNQ).
These results cast light on the role of serotonin in the striatum, revealing that it tightly controls the activity of the only neuronal type that releases nitric oxide.
The regulation of K‐ and L‐cell activity by GLUT2 and the calcium‐sensing receptor CasR in rat small intestine
Authors: Mace Oliver J. , Schindler Marcus , Patel Sonal 
Published: April 2012

Key points
In intestine, nutrients including glucose and amino acids and non‐nutrients including bile acids increase secretion of anti‐diabetic gut peptides such as gluco‐insulinotropic peptide (GIP), glucagon‐like peptide‐1 (GLP‐1) and peptide tyrosine tyrosine (PYY).
Facilitative glucose transporter pathways in addition to active electrogenic transporter pathways contribute to GIP, GLP‐1 and PYY secretion; in particular, the facilitative glucose transporter 2 (GLUT2) is involved.
Sucralose, in the presence of glucose, can strongly and acutely upregulate GIP, GLP‐1 and PYY secretion in a time scale of minutes.
Amino acid‐stimulated GIP, GLP‐1 and PYY secretion is acutely regulated by the calcium‐sensing receptor (CasR).
The results establish new functions for GLUT2 and CasR as regulators of gut peptide secretion that sense nutrients and provide signalling pathways for the release of GIP, GLP‐1 and PYY.
Voltage‐dependent amplification of synaptic inputs in respiratory motoneurones
Authors: Enríquez Denton M. , Wienecke J. , Zhang M. , Hultborn H. , Kirkwood P. A. 
Published: April 2012

Key points
The processes whereby various excitatory and inhibitory inputs are integrated in spinal motoneurones during naturally occurring motor acts are not well understood, largely because there are amplifying mechanisms within the motoneurone that can control the effective strengths of the inputs.
Knowledge of these processes is important in understanding conditions such as motoneurone disease, or the spasticity that can follow spinal cord injury or stroke
Respiration is a natural motor act that continues normally under experimental conditions, and this study investigated, for the first time, the likely amplifying processes at work in respiratory motoneurones.
In phrenic motoneurones, which control the most important respiratory muscle, the diaphragm, we found that the mechanism most favoured by investigations in other motoneurones, the activation of persistent inward currents via calcium channels, appears to make a very small contribution. Instead, modulation of synaptic currents (through NMDA channels) appears to be more important.
Abstract  The role of persistent inward currents (PICs) in cat respiratory motoneurones (phrenic inspiratory and thoracic expiratory) was investigated by studying the voltage‐dependent amplification of central respiratory drive potentials (CRDPs), recorded intracellularly, with action potentials blocked with the local anaesthetic derivative, QX‐314. Decerebrate unanaesthetized or barbiturate‐anaesthetized preparations were used. In expiratory motoneurones, plateau potentials were observed in the decerebrates, but not under anaesthesia. For phrenic motoneurones, no plateau potentials were observed in either state (except in one motoneurone after the abolition of the respiratory drive by means of a medullary lesion), but all motoneurones showed voltage‐dependent amplification of the CRDPs, over a wide range of membrane potentials, too wide to result mainly from PIC activation. The measurements of the amplification were restricted to the phase of excitation, thus excluding the inhibitory phase. Amplification was found to be greatest for the smallest CRDPs in the lowest resistance motoneurones and was reduced or abolished following intracellular injection of the NMDA channel blocker, MK‐801. Plateau potentials were readily evoked in non‐phrenic cervical motoneurones in the same (decerebrate) preparations. We conclude that the voltage‐dependent amplification of synaptic excitation in phrenic motoneurones is mainly the result of NMDA channel modulation rather than the activation of Ca2+ channel mediated PICs, despite phrenic motoneurones being strongly immunohistochemically labelled for CaV1.3 channels. The differential PIC activation in different motoneurones, all of which are CaV1.3 positive, leads us to postulate that the descending modulation of PICs is more selective than has hitherto been believed.
Lack of an endogenous GABAA receptor‐mediated tonic current in hypoglossal motoneurons
Authors: Numata J. M. , van Brederode J. F. M. , Berger A. J. 
Published: April 2012

Key points
Tonic GABAA receptor‐mediated currents have profound effects on neuronal excitability, yet it is not known whether this current is present in mammalian motoneurons.
This study shows that tonic GABAA receptor‐mediated current can be observed in hypoglossal motoneurons in vitro under certain experimental conditions.
The tonic current was only observed when exogenous GABA was applied and GABA transporters were blocked suggesting that GABA transporters highly regulate extracellular GABA concentration.
Furthermore, we demonstrate that the current probably arises from activation of extrasynaptic GABAA receptors containing a δ subunit.
This tonic current may function to reduce the excitability of hypoglossal motoneurons; these motoneurons are important in many functions including chewing, swallowing, suckling, vocalization and upper airway patency.
Abstract  Tonic GABAA receptor‐mediated current is an important modulator of neuronal excitability, but it is not known if it is present in mammalian motoneurons. To address this question studies were performed using whole‐cell patch‐clamp recordings from mouse hypoglossal motoneurons (HMs) in an in vitro slice preparation. In the presence of blockers of glutamatergic and glycinergic receptor‐mediated transmission application of SR‐95531 or bicuculline, while abolishing GABAA receptor‐mediated phasic synaptic currents, did not reveal a tonic GABAA receptor‐mediated current. Additionally, blockade of both GAT‐1 and GAT‐3 GABA transporters did not unmask this tonic current. In contrast, application of exogenous GABA (1 to 15 μm) resulted in a tonic GABAergic current that was observed when both GAT‐1 and GAT‐3 transporters were simultaneously blocked, and this current was greater than the sum of the current observed when each transporter was blocked individually. We also investigated which GABAA receptor subunits may be responsible for the current. Application of the δ subunit GABAA receptor agonist THIP resulted in a tonic GABAA receptor current. Application of the δ subunit modulator THDOC resulted in an enhanced tonic current. Application of the α5 subunit GABAA receptor inverse agonist L‐655,708 did not modulate the current. In conclusion, these data show that HMs have tonic GABAA receptor‐mediated current. The level of GABA in the vicinity of GABAA receptors responsible for this current is regulated by GABA transporters. In HMs a tonic current in response to exogenous GABA probably arises from activation of GABAA receptors containing δ subunits.
A multichannel, real‐time MRI RF power monitor for independent SAR determination
Authors: El‐Sharkawy AbdEl‐Monem M. , Qian Di , Bottomley Paul A. , Edelstein William A. 
Published: April 2012

Purpose:Accurate measurements of the RF power delivered during clinical MRI are essential for safety and regulatory compliance, avoiding inappropriate restrictions on clinical MRI sequences, and for testing the MRI safety of peripheral and interventional devices at known RF exposure levels. The goal is to make independent RF power measurements to test the accuracy of scanner‐reported specific absorption rate (SAR) over the extraordinary range of operating conditions routinely encountered in MRI.Methods:A six channel, high dynamic range, real‐time power profiling system was designed and built for monitoring power delivery during MRI up to 440 MHz. The system was calibrated and used in two 3 T scanners to measure power applied to human subjects during MRI scans. The results were compared with the scanner‐reported SAR.Results:The new power measurement system has highly linear performance over a 90 dB dynamic range and a wide range of MRI duty cycles. It has about 0.1 dB insertion loss that does not interfere with scanner operation. The measurements of whole‐body SAR in volunteers showed that scanner‐reported SAR was significantly overestimated by up to about 2.2 fold.Conclusions:The new power monitor system can accurately and independently measure RF power deposition over the wide range of conditions routinely encountered during MRI. Scanner‐reported SAR values are not appropriate for setting exposure limits during device or pulse sequence testing.
In vivo dosimetry with radiochromic films in low‐voltage intraoperative radiotherapy of the breast
Authors: Avanzo M. , Rink A. , Dassie A. , Massarut S. , Roncadin M. , Borsatti E. , Capra E. 
Published: April 2012

Purpose:EBT2 radiochromic films were studied and used forin vivo dosimetry in targeted intraoperative radiotherapy (TARGIT), a technique in which the Intrabeam system (Carl Zeiss, Oberkochen, Germany) is used to perform intraoperative partial breast irradiation with x‐rays of 50 kVp.Methods:The energy of the radiation emitted by the Intrabeam with the different spherical applicators, under 1 and 2 cm of solid water, and under the tungsten impregnated rubber used for shielding of the heart in TARGIT of the breast, was characterized with measurements of half‐value layer (HVL). The stability of response of EBT2 was verified inside this range of energies. EBT2 films were calibrated using the red and green channels of the absorption spectrum in the 0–20 Gy dose range delivered by the Intrabeam x‐rays. The dependence of film response on temperature during irradiation was measured. Forin vivo dosimetry, pieces of radiochromic films wrapped in sterile envelopes were inserted after breast conserving surgery and before TARGIT into the excision cavity, on the skin and on the shielded pectoralis fascia for treatments of the left breast.Results:HVLs of the Intrabeam in TARGIT of the breast correspond to effective energies of 20.7–36.3 keV. The response of EBT2 was constant inside this range of energies. We measured the dose to the target tissue and to organs at risk in 23 patients and obtained an average dose of 13.52 ± 1.21 Gy to the target tissue. Dose to the skin in close proximity to the applicator was 2.22 ± 0.97 Gy, 0.29 ± 0.17 Gy at 5–10 cm from the applicator, and 0.08 ± 0.07 Gy at more than 10 cm from the applicator. Dose to the pectoral muscle for left breast treatment was 0.57 ± 0.23 Gy.Conclusions:Our results show that EBT2 films are accurate at the beam energies, dose range, and irradiation temperature found in TARGIT and thatin vivo dosimetry in TARGIT with EBT2 films wrapped in sterile envelopes is a feasible procedure. Measured dose to the organs at risk indicates that the technique is safe from side effects to the skin and the heart.
On the Shifting Balance: the Case of Staphylococcus aureus CC398
Authors: Baquero Fernando 
Published: April 2012

ABSTRACT

The recent study by L. Price et al. [mBio, 3(1):e00305-11, 2012] demonstrating the human origin of the livestock-associated CC398
Staphylococcus aureus
provides an excellent example of how bacterial populations can explore a wide range of potential niches and acquire optimal adaptations for life in alternative hosts. The shifting balance theory proposed by Sewall Wright 80 years ago serves as a perfect model for understanding the observed facts: a possibly large CC398 population optimally positioned on the top of a fitness peak for living in a human host probably began evolving long ago by variation, drift, and migration, until it reached the low fitness edge of a neighboring alternative peak in the fitness landscape, one in a livestock host. The bacterial population then evolved again, moving uphill to reach a novel optimal “top of the peak” position in livestock. In the case of CC398, it is worrisome to think that it might readapt to human hosts without losing fitness in livestock; a double-host-adapted organism could certainly be in an optimal position for increasing its virulence and antibiotic resistance.
Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7
Authors: Kim Chonsaeng , Bergelson Jeffrey M. 
Published: April 2012

ABSTRACT
Enteroviruses invade the host by crossing the intestinal mucosa, which is lined by polarized epithelium. A number of enteroviruses, including echoviruses (EV) and group B coxsackieviruses (CVB), initiate infection by attaching to decay-accelerating factor (DAF), a molecule that is highly expressed on the apical surface of polarized epithelial cells. We previously observed that entry of DAF-binding CVB3 into polarized intestinal epithelial cells occurs by an unusual endocytic mechanism that requires caveolin but does not involve clathrin or dynamin. Here we examined the entry of a DAF-binding echovirus, EV7. We found that drugs, small interfering RNAs (siRNAs), and dominant negative mutants that target factors required for clathrin-mediated endocytosis, including clathrin and dynamin, inhibited both EV7 infection and internalization of virions from the cell surface. Once virus had entered the cell, it colocalized with markers of early endosomes (EEA1) and then late endosomes (LAMP-2). Inhibition of endosomal maturation—with siRNAs or dominant negative mutants targeting Rab5 and Rab7—inhibited infection and prevented release of viral RNA into the cell. These results indicate that EV7 is internalized by clathrin-mediated endocytosis and then moves to early and late endosomes before releasing its RNA. Trafficking through endosomes is known to be important for viruses that depend on low pH or endosomal cathepsin proteases to complete the entry process. However, we found that EV7 infection required neither low pH nor cathepsins.

IMPORTANCE
The results demonstrate that echovirus 7 (EV7), after binding to decay-accelerating factor (DAF) on the cell surface, enters cells by clathrin-mediated endocytosis; this entry mechanism differs markedly from that of another DAF-binding enterovirus, coxsackievirus B3 (CVB3). Thus, after attachment to the same cell surface receptor, these closely related viruses enter the same cells by different mechanisms. The cellular cues required for release of viral RNA from the enterovirus capsid (“uncoating”) remain poorly defined. We found that EV7 moved to late endosomes and that release of RNA depended on endosomal maturation; nonetheless, EV7 did not depend on the endosomal factors implicated in uncoating and entry by other viruses. The results suggest either that an unidentified endosomal factor is essential for uncoating of EV7 or that trafficking through the endosome is an essential step in a pathway that leads to another intracellular organelle where uncoating is completed.
Use of Social Networking Sites Among Shinas College of Technology Students in Oman
Authors: kindi Salim Said Ali Al , Alhashmi Saadat M. 
Published: April 2012

Introduction: Social networking sites (SNSs) have become a popular method for students to share information and knowledge and to express emotions. They enable students to exchange video files, text messages, pictures and knowledge sharing. They provide an opportunity for students to improve social networking and learning processes, which promotes knowledge in society. Purposes: This paper intends to address the factors motivating students at colleges to use SNSs, to identify the factors that motivate them in using SNSs for educational purposes and to identify the most popular SNSs among students. Design/Methodology: The study uses a questionnaire in order to discover the reasons behind the use of SNSs by students at Shinas College of Technology (ShCT) in Oman. Findings: The study found that the major reasons for frequent use of SNSs are finding information and sharing news. The study also indicated that lack of experience as well as insufficient time and IT skills are effective factors of not using SNSs. Finally, the study discovered that Google Groups, Facebook and Yahoo! 360 are the most popular SNSs used by SHCT students. Research Limitation: The study was limited to ShCT students, which is considered a small community, and the focus group was relatively small. A larger focus group in a different environment may possibly yield different results. Additionally, the list of SNSs listed in the questionnaire was based on previous studies discussed in the literature review. Originality/value: This research will be valuable for those interested in the subject of social networks and e-learning. In this area, there is a dearth of research on reasons for student use of SNSs in Oman, giving this particular research great importance to understanding the way that students interact with SNSs.
A Novel Approach using Expert Knowledge on Error based Pruning
Authors: Mahmood Ali Mirza , Kuppa Mrithyumjaya Rao 
Published: April 2012

Many traditional pruning methods assume that all the datasets are equally probable and equally important, so they apply equal pruning to all the datasets. However, in real-world classification problems, all the datasets are not equal and considering equal pruning rate during pruning tends to generate a decision tree with a large size and high misclassification rate.In this paper, we present a practical algorithm to deal with the data specific classification problem when there are datasets with different properties. Another key motivation of the data specific pruning in the paper is "trading accuracy and size". A new algorithm called Expert Knowledge Based Pruning (EKBP) is proposed to solve this dilemma. We proposed to integrate error rate, missing values and expert judgment as factors for determining data specific pruning for each dataset. We show by analysis and experiments that using this pruning, we can scale both accuracy and generalisation for the tree that is generated. Moreover, the method can be very effective for high dimensional datasets. We conduct an extensive experimental study on openly available 40 real world datasets from UCI repository. In all these experiments, the proposed approach shows considerably reduction of tree size having equal or better accuracy compared to several benchmark decision tree methods that are proposed in literature.
Detection of Redundant Fusion Transcripts as Biomarkers or Disease-Specific Therapeutic Targets in Breast Cancer
Authors: Asmann Yan W. , Necela Brian M. , Kalari Krishna R. , Hossain Asif , Baker Tiffany R. , Carr Jennifer M. , Davis Caroline , Getz Julie E. , Hostetter Galen , Li Xing , McLaughlin Sarah A. , Radisky Derek C. , Schroth Gary P. , Cunliffe Heather E. , Perez Edith A. , Thompson E. Aubrey 
Published: April 2012

Abstract
Fusion genes and fusion gene products are widely employed as biomarkers and therapeutic targets in hematopoietic cancers, but their applications have yet to be appreciated in solid tumors. Here, we report the use of SnowShoes-FTD, a powerful new analytic pipeline that can identify fusion transcripts and assess their redundancy and tumor subtype-specific distribution in primary tumors. In a study of primary breast tumors, SnowShoes-FTD was used to analyze paired-end mRNA-Seq data from a panel of estrogen receptor (ER)+, HER2+, and triple-negative primary breast tumors, identifying tumor-specific fusion transcripts by comparison with mRNA-Seq data from nontransformed human mammary epithelial cell cultures plus the Illumina Body Map data from normal tissues. We found that every primary breast tumor that was analyzed expressed one or more fusion transcripts. Of the 131 tumor-specific fusion transcripts identified, 86 were “private” (restricted to a single tumor) and 45 were “redundant” (distributed among multiple tumors). Among the redundant fusion transcripts, 7 were unique to ER+ tumors and 8 were unique to triple-negative tumors. In contrast, none of the redundant fusion transcripts were unique to HER2+ tumors. Both private and redundant fusion transcripts were widely expressed in primary breast tumors, with many mapping to genomic loci implicated in breast carcinogenesis and/or risk. Our finding that some fusion transcripts are tumor subtype-specific suggests that these entities may be critical determinants in the etiology of breast cancer subtypes, useful as biomarkers for tumor stratification, or exploitable as cancer-specific therapeutic targets. Cancer Res; 72(8); 1921–8. ©2012 AACR.