bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new online detector for estimation of peripheral neutron equivalent dose in organ
Authors: Irazola L. , Lorenzoli M. , Bedogni R. , Pola A. , Terrón J. A. , Sanchez‐Nieto B. , Expósito M. R. , Lagares J. I. , Sansaloni F. , Sanchez‐Doblado F. 
Published: October 2014

Purpose:Peripheral dose in radiotherapy treatments represents a potential source of secondary neoplasic processes. As in the last few years, there has been a fast‐growing concern on neutron collateral effects, this work focuses on this component. A previous established methodology to estimate peripheral neutron equivalent doses relied on passive (TLD, CR39) neutron detectors exposed in‐phantom, in parallel to an active [static random access memory (SRAMnd)] thermal neutron detector exposed ex‐phantom. A newly miniaturized, quick, and reliable active thermal neutron detector (TNRD, Thermal Neutron Rate Detector) was validated for both procedures. This first miniaturized active system eliminates the long postprocessing, required for passive detectors, giving thermal neutron fluences in real time.Methods:To validate TNRD for the established methodology, intrinsic characteristics, characterization of 4 facilities [to correlate monitor value (MU) with risk], and a cohort of 200 real patients (for second cancer risk estimates) were evaluated and compared with the well‐established SRAMnd device. Finally, TNRD was compared to TLD pairs for 3 generic radiotherapy treatments through 16 strategic points inside an anthropomorphic phantom.Results:The performed tests indicate similar linear dependence with dose for both detectors, TNRD and SRAMnd, while a slightly better reproducibility has been obtained for TNRD (1.7% vs 2.2%). Risk estimates when delivering 1000 MU are in good agreement between both detectors (mean deviation of TNRD measurements with respect to the ones of SRAMnd is 0.07 cases per 1000, with differences always smaller than 0.08 cases per 1000). As far as the in‐phantom measurements are concerned, a mean deviation smaller than 1.7% was obtained.Conclusions:The results obtained indicate that direct evaluation of equivalent dose estimation in organs, both in phantom and patients, is perfectly feasible with this new detector. This will open the door to an easy implementation of specific peripheral neutron dose models for any type of treatment and facility.
Does administering iodine in radiological procedures increase patient doses?
Authors: He Wenjun , Huda Walter , Mah Eugene , Yao Hai 
Published: October 2014

Purpose:The authors investigated the changes in the pattern of energy deposition in tissue equivalent phantoms following the introduction of iodinated contrast media.Methods:The phantom consisted of a small “contrast sphere,” filled with water or iodinated contrast, located at the center of a 28 cm diameter water sphere. Monte Carlo simulations were performed usingmcnp5codes, validated by simulating irradiations with analytical solutions. Monoenergetic x‐rays ranging from 35 to 150 keV were used to simulate exposures to spheres containing contrast agent with iodine concentrations ranging from 1 to 100 mg/ml. Relative values of energy imparted to the contrast sphere, as well as to the whole phantom, were calculated. Changes in patterns of energy deposition around the contrast sphere were also investigated.Results:Small contrast spheres can increase local absorbed dose by a factor of 13, but the corresponding increase in total energy absorbed was negligible (<1%). The highest localized dose increases were found to occur at incident photon energies of about 60 keV. For a concentration of about 10 mg/ml, typical of clinical practice, localized absorbed doses were generally increased by about a factor of two. At this concentration of 10 mg/ml, the maximum increase in total energy deposition in the phantom was only 6%. These simulations demonstrated that increases in contrast sphere doses were offset by corresponding dose reductions at distal and posterior locations.Conclusions:Adding iodine can result in values of localized absorbed dose increasing by more than an order of magnitude, but the total energy deposition is generally very modest (i.e., <10%). Their data show that adding iodine primarily changes the pattern of energy deposition in the irradiated region, rather than increasing patient doses per se.
A Novel
Anelloviridae
Species Detected in
Tadarida brasiliensis
Bats: First Sequence of a Chiropteran
Anellovirus
Authors: Cibulski Samuel Paulo , Teixeira Thais Fumaco , de Sales Lima Francisco Esmaile , do Santos Helton Fernandes , Franco Ana Claudia , Roehe Paulo Michel 
Published: October 2014

ABSTRACT

Using metagenomic approaches, we identified a novel Torque teno virus from Brazilian free-tailed bats (
Tadarida brasiliensis
) (TT-TbV). The TT-TbV genome and deduced protein sequences share extremely low identity with known anelloviruses. Due to a high degree of phylogenetic divergence, such putative virus could not be allocated into any
Anelloviridae
genera.
Genome Sequence of Bacillus amyloliquefaciens GB03, an Active Ingredient of the First Commercial Biological Control Product
Authors: Choi Soo-Keun , Jeong Haeyoung , Kloepper Joseph W. , Ryu Choong-Min 
Published: October 2014

ABSTRACT

Bacillus amyloliquefaciens
GB03 has been used as a representative commercialized strain of the bacilli for biological control against a broad spectrum of plant pathogens and as a bio-fertilizer to promote growth and yield of field crops for more than two decades. Herein, we present the genome sequence and a brief analysis of strain GB03.
First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak
Authors: Hoffmann Maria , Muruvanda Tim , Pirone Cary , Korlach Jonas , Timme Ruth , Payne Justin , Evans Peter , Meng Jianghong , Brown Eric W. , Allard Marc W. 
Published: October 2014

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Cubana (
Salmonella
serovar Cubana) is associated with human and animal disease. Here, we used third-generation, single-molecule, real-time DNA sequencing to determine the first complete genome sequence of
Salmonella
serovar Cubana CFSAN002050, which was isolated from fresh alfalfa sprouts during a multistate outbreak in 2012.
Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013
Authors: Díaz-Quiñonez José Alberto , Hernández-Monroy Irma , López-Martínez Irma , Ortiz-Alcántara Joanna , González-Durán Elizabeth , Ruiz-Matus Cuitláhuac , Kuri-Morales Pablo , Ramírez-González José Ernesto 
Published: October 2014

ABSTRACT

We present the draft genome sequence of
Vibrio cholerae
InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the
Vibrio
7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXφ and RS1φ.
Patient-centered care, collaboration, communication, and coordination: a report from AMIA's 2013 Policy Meeting
Authors: Flatley Brennan Patti , Valdez Rupa , Alexander Greg , Arora Shifali , Bernstam Elmer V , Edmunds Margo , Kirienko Nikolai , Martin Ross D , Sim Ida , Skiba Diane , Rosenbloom Trent 
Published: October 2014

Abstract
In alignment with a major shift toward patient-centered care as the model for improving care in our health system, informatics is transforming patient–provider relationships and overall care delivery. AMIA's 2013 Health Policy Invitational was focused on examining existing challenges surrounding full engagement of the patient and crafting a research agenda and policy framework encouraging the use of informatics solutions to achieve this goal. The group tackled this challenge from educational, technical, and research perspectives. Recommendations include the need for consumer education regarding rights to data access, the need for consumers to access their health information in real time, and further research on effective methods to engage patients. This paper summarizes the meeting as well as the research agenda and policy recommendations prioritized among the invited experts and stakeholders.
Evaluation of swabbing methods for estimating the prevalence of bacterial carriage in the upper respiratory tract: a cross sectional study
Authors: Coughtrie A L , Whittaker R N , Begum N , Anderson R , Tuck A , Faust S N , Jefferies J M , Yuen H M , Roderick P J , Mullee M A , Moore M V , Clarke S C 
Published: October 2014

ObjectivesBacterial carriage in the upper respiratory tract is usually asymptomatic but can lead to respiratory tract infection (RTI), meningitis and septicaemia. We aimed to provide a baseline measure ofStreptococcus pneumoniae,Moraxella catarrhalis,Pseudomonas aeruginosa,Staphylococcus aureus,Haemophilus influenzaeandNeisseria meningitidiscarriage within the community. Self-swabbing and healthcare professional (HCP) swabbing were compared.DesignCross-sectional study.SettingIndividuals registered at 20 general practitioner practices within the Wessex Primary Care Research Network South West, UK.Participants10 448 individuals were invited to participate; 5394 within a self-swabbing group and 5054 within a HCP swabbing group. Self-swabbing invitees included 2405 individuals aged 0–4 years and 3349 individuals aged ≥5 years. HCP swabbing invitees included 1908 individuals aged 0–4 years and 3146 individuals aged ≥5 years.Results1574 (15.1%) individuals participated, 1260 (23.4%, 95% CI 22.3% to 24.5%) undertaking self-swabbing and 314 (6.2%, 95% CI 5.5% to 6.9%) undertaking HCP-led swabbing. Participation was lower in young children and more deprived practice locations. Swab positivity rates were 34.8% (95% CI 32.2% to 37.4%) for self-taken nose swabs (NS), 19% (95% CI 16.8% to 21.2%) for self-taken whole mouth swabs (WMS), 25.2% (95% CI 20.4% to 30%) for nasopharyngeal swabs (NPS) and 33.4% (95% CI 28.2% to 38.6%) for HCP-taken WMS. Carriage rates ofS. aureuswere highest in NS (21.3%).S. pneumoniaecarriage was highest in NS (11%) and NPS (7.4%).M. catarrhaliscarriage was highest in HCP-taken WMS (28.8%).H. influenzaeandP. aeruginosacarriage were similar between swab types.N. meningitidiswas not detected in any swab. Age and recent RTI affected carriage ofS. pneumoniaeandH. influenzae. Participant costs were lower for self-swabbing (£41.21) versus HCP swabbing (£69.66).ConclusionsHigher participation and lower costs of self-swabbing as well as sensitivity of self-swabbing favour this method for use in large population-based respiratory carriage studies.
Safety and efficacy of antenatal milk expressing for women with diabetes in pregnancy: protocol for a randomised controlled trial
Authors: Forster Della A , Jacobs Susan , Amir Lisa H , Davis Peter , Walker Susan P , McEgan Kerri , Opie Gillian , Donath Susan M , Moorhead Anita M , Ford Rachael , McNamara Catharine , Aylward Amanda , Gold Lisa 
Published: October 2014

IntroductionMany maternity providers recommend that women with diabetes in pregnancy express and store breast milk in late pregnancy so breast milk is available after birth, given (1) infants of these women are at increased risk of hypoglycaemia in the first 24 h of life; and (2) the delay in lactogenesis II compared with women without diabetes that increases their infant's risk of receiving infant formula. The Diabetes and Antenatal Milk Expressing (DAME) trial will establish whether advising women with diabetes in pregnancy (pre-existing or gestational) to express breast milk from 36 weeks gestation increases the proportion of infants who require admission to special or neonatal intensive care units (SCN/NICU) compared with infants of women receiving standard care. Secondary outcomes include birth gestation, breastfeeding outcomes and economic impact.Methods and analysisWomen will be recruited from 34 weeks gestation to a multicentre, two arm, unblinded randomised controlled trial. The intervention starts at 36 weeks. Randomisation will be stratified by site, parity and diabetes type. Women allocated to the intervention will be taught expressing and encouraged to hand express twice daily for 10 min and keep an expressing diary. The sample size of 658 (329 per group) will detect a 10% difference in proportion of babies admitted to SCN/NICU (85% power, α 0.05). Data are collected at recruitment (structured questionnaire), after birth (abstracted from medical record blinded to group), and 2 and 12 weeks postpartum (telephone interview).Data analysis:the intervention group will be compared with the standard care group by intention to treat analysis, and the primary outcome compared using χ2and ORs.Ethics and disseminationResearch ethics approval will be obtained from participating sites. Results will be published in peer-reviewed journals and presented to clinicians, policymakers and study participants.Trial registration numberAustralian Controlled Trials Register ACTRN12611000217909.
iContraception®: a software tool to assist professionals in choosing contraceptive methods according to WHO medical eligibility criteria
Authors: Guisado Lopez Ramón , Ramirez Polo Isabel , Arjona Berral Jose Eduardo , Guisado Fernandez Julia , Castelo-Branco Camil 
Published: October 2014

ObjectiveTo design software to assist health care providers with contraceptive counselling.MethodsThe Model-View-Controller software architecture pattern was used. Decision logic was incorporated to automatically compute the safety category of each contraceptive option. Decisions are made according to the specific characteristics or known medical conditions of each potential contraception user. The software is an app designed for the iOS and Android platforms and is available in four languages. iContraception®facilitates presentation of visual data on medical eligibility criteria for contraceptive treatments.ResultsThe use of this software was evaluated by a sample of 54 health care providers. The general satisfaction with the use of the app was over 8 on a 0–10 visual analogue scale in 96.3% of cases.ConclusionsiContraception provides easy access to medical eligibility criteria of contraceptive options and may help with contraceptive counselling.
The Southern Uplands Terrane in Scotland – a notional controversy revisited
Authors: Stone Philip 
Published: October 2014

Synopsis
Development of a regional geological interpretation for the Southern Uplands Terrane has been driven historically by advances in graptolite biostratigraphy, sandstone petrography and turbidite sedimentology (particularly the recognition of reliable way-up criteria), then, more recently, by a growing appreciation of the nature of accretionary processes at active plate margins. The latter has led to the widely held view of the terrane as an archetypal fossil accretionary prism, built up by the accretion at the margin of Laurentia of the sedimentary cover of Iapetus oceanic crust, the cover being stripped from the oceanic crust during its subduction beneath Laurentia. The achievement of this broad consensus has not been without controversy, which still persists in respect of some aspects of the overall model. Suggestions that the northernmost (Ordovician) part of the terrane might have originated in a back-arc basin have been disproved by a combination of mineral dating and basin thermal history analysis utilizing clay mineralogy. Nevertheless, it remains possible for that part of the terrane to have a continental margin, forearc depositional history. The southernmost (mid-Silurian) part of the terrane most probably developed in a foreland basin setting, as a fold-and-thrust belt overriding Avalonia, following the closure of the Iapetus Ocean. Progress in understanding the origins of the Southern Uplands Terrane has been achieved only by the collaborative application of multidisciplinary techniques – biostratigraphic, sedimentary, structural, geochemical and geophysical. This review is a tribute to all those who have contributed.

Supplementary material:

Coloured versions of the maps comprising Figure 1, showing details of the regional lithostratigraphy, are available at
http://www.geolsoc.org.uk/SUP18769
.
Metabentonites from the Sandbian Stage, Upper Ordovician, in Scotland – a geochemical comparison with their equivalents in Baltoscandia
Authors: Batchelor Richard A. 
Published: October 2014

Synopsis
Four metabentonites, including three new discoveries, are described from the Sandbian Stage, Upper Ordovician, of southern Scotland. They are compared geochemically with suites of more numerous contemporary metabentonites from Scandinavia. Two correlations are made with the Scandinavian suites that confirm relative stratigraphical age relationships. The Scottish examples represent distal ash falls from a volcanic source between Avalonia and Baltica.
New dinosaur and crocodylomorph material from the Middle Jurassic (Bathonian) Kilmaluag Formation, Skye, Scotland
Authors: Wills S. , Barrett P. M. , Walker A. 
Published: October 2014

Synopsis
Archosaur specimens collected from the Kilmaluag Formation (Great Estuarine Group) of Cladach a’Ghlinne, Skye are described. These comprise crocodylomorph material; a pubis and group of osteoderms with an associated tooth; a theropod tooth; and a dinosaur limb bone. The material is regionally important as the Skye assemblage is dominated by aquatic amphibians and amphibious reptiles with terrestrial taxa being comparatively rare. The crocodylomorph pubis is referable to an indeterminate mesoeucrocodylian; the osteoderms and associated tooth to an indeterminate neosuchian. The Kilmaluag Formation has now yielded the only associated and articulated terrestrial/freshwater Middle Jurassic crocodylomorphs from the UK thus far. The theropod tooth is referable to an indeterminate theropod, and provides the first body fossil evidence of a small theropod taxon from the Bathonian of the Hebridean Basin. The dinosaur limb bone is regarded conservatively as an indeterminate dinosaur although it does possess possible theropod affinities.
Three centuries of open access to the caves in Stoney Middleton Dale Site of Special Scientific Interest, Derbyshire
Authors: Cope Mark A. 
Published: October 2014

Abstract
The limestone caves of Stoney Middleton Dale are a Site of Special Scientific Interest (SSSI) for features of geological interest, but have been open access since at least the eighteenth century and have a documented history of geotourism. Using the examples of Carlswark Cavern and Merlin Cavern, this chapter sets out evidence that 300 years of open access has resulted in significant disturbance to the features of geological interest. In particular, the integrity of the overall site for scientific research was affected by historical removal of speleothem formations long before it became a SSSI, with damage still occurring today. As most cave SSSIs in Derbyshire have historically had similar open-access arrangements, the examples presented highlight that there is potential for the integrity of less well historically documented caves elsewhere to have been disturbed. This article highlights the importance of establishing a baseline of historical disturbance to recognize whether the integrity of cave SSSIs have been affected and help monitor if disturbance is still occurring. For cave SSSIs to be useful for geological research, it is suggested that there is a need for the historical legacy of open access to individual caves elsewhere to be better understood.
Molecular Pathways: Intercellular PTEN and the Potential of PTEN Restoration Therapy
Authors: Hopkins Benjamin D. , Parsons Ramon E. 
Published: October 2014

Abstract
Phosphatase and Tensin homolog deleted on chromosome Ten (PTEN) acts as a tumor suppressor through both PI3K-dependent and -independent mechanisms. Reduced PTEN activity has been shown to affect not only tumor cell proliferation and survival but also the microenvironmental context in which nascent tumors develop. As a result of the multifaceted tumor-suppressive roles of PTEN, tumors evolve by selecting for clones in which PTEN activity is lost. PTEN activity within tumors can be modulated in numerous ways, including direct mutation, epigenetic regulation, and amplification or mutation of other proteins that can regulate or degrade PTEN. These events functionally prevent PTEN protein from acting within tumor cells. Paracrine roles for PTEN gene products (exosomal PTEN and PTEN-L) have recently been identified, through which PTEN gene products produced in one cell are able to enter recipient cells and contribute to PTEN functions. In preclinical models purified PTEN-L protein was able to enter tumor xenografts and downregulate PI3K signaling as well as cause tumor cell death. Here, we review the role of PTEN as a multifaceted tumor suppressor and reflect upon the potential for PTEN restoration therapy. Clin Cancer Res; 20(21); 5379–83. ©2014 AACR.
Ibrutinib for the Treatment of Mantle Cell Lymphoma
Authors: Herrera Alex F. , Jacobsen Eric D. 
Published: October 2014

Abstract
Ibrutinib (PCI-32765)—a potent, covalent inhibitor of Bruton tyrosine kinase (BTK), an important kinase in the B-cell receptor signaling pathway—was recently approved by the FDA for the treatment of relapsed or refractory mantle cell lymphoma (MCL). The drug was granted accelerated approval based on the findings of an international, multicenter, single-arm phase II study that enrolled patients with relapsed or refractory MCL. In the study, ibrutinib (560 mg daily) was well tolerated as a single agent and resulted in an overall response rate of 68% and an estimated median response duration of 17.5 months. Ibrutinib's response rate and duration of response compare favorably with those for other novel agents approved for the treatment of relapsed or refractory MCL, while being less toxic than most chemotherapy or chemoimmunotherapy regimens. Ibrutinib is currently being studied in combination with chemoimmunotherapy, monoclonal antibody therapy, and novel agents in both the initial and the relapsed/refractory treatment settings. We review the mechanism of action, preclinical and clinical development, and the role of ibrutinib in the context of other available treatments. Clin Cancer Res; 20(21); 5365–71. ©2014 AACR.