bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and energy distributions of X‐ray emissions from leaders in natural and rocket triggered lightning
Authors: Schaal M. M. , Dwyer J. R. , Saleh Z. H. , Rassoul H. K. , Hill J. D. , Jordan D. M. , Uman M. A. 
Published: June 2012

Energetic radiation is known to be produced by lightning. To investigate these emissions, ground‐based observations are being conducted at the International Center for Lightning Research and Testing (ICLRT) at Camp Blanding, FL where measurements of energetic radiation from both natural and rocket‐triggered lightning discharges are recorded. In the present study, data from two natural negative cloud‐to‐ground stepped leaders and one rocket‐triggered “chaotic” dart leader are analyzed in detail to investigate X‐ray energy spectra and spatial X‐ray distributions around the source. These measurements are compared with Monte Carlo simulations of runaway electron propagation with the goal of understanding the underlying mechanism of runaway electron production and their role in lightning initiation and propagation. We show that the energetic electrons that produce X‐rays exhibit a characteristic energy less than 3 MeV for two natural and one rocket‐triggered leaders investigated. In addition to studying these three leaders, energetic electron luminosity, total energy, and energetic electron per meter are compared to the following return stroke currents for 28 leaders from 12 different triggered flashes. Electron luminosity is found to increase exponentially with return stroke current up to about 10 kA and to be roughly constant for larger currents. The maximum electron luminosity, which is determined indirectly through X‐ray luminosities, is on the order of 1017 electrons/s, which is less than the value found from theoretical calculations.
Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life
Authors: Thole Sebastian , Kalhoefer Daniela , Voget Sonja , Berger Martine , Engelhardt Tim , Liesegang Heiko , Wollherr Antje , Kjelleberg Staffan , Daniel Rolf , Simon Meinhard , Thomas Torsten , Brinkhoff Thorsten 
Published: June 2012

Abstract
Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
Ser262 determines the chloride-dependent colour tuning of a new halorhodopsin from Haloquadratum walsbyi
Authors: Fu Hsu-Yuan , Chang Yung-Ning , Jheng Ming-Jin , Yang Chii-Shen 
Published: June 2012

Light is an important environmental signal for all organisms on earth because it is essential for physiological signalling and the regulation of most biological systems. Halophiles found in salt-saturated ponds encode various archaeal rhodopsins and thereby harvest various wavelengths of light either for ion transportation or as sensory mediators. HR (halorhodopsin), one of the microbial rhodopsins, senses yellow light and transports chloride or other halides into the cytoplasm to maintain the osmotic balance during cell growth, and it exists almost ubiquitously in all known halobacteria. To date, only two HRs, isolated from HsHR (Halobacterium salinarum HR) and NpHR (Natronomonas pharaonis HR), have been characterized. In the present study, two new HRs, HmHR (Haloarcula marismortui HR) and HwHR (Haloquadratum walsbyi HR), were functionally overexpressed in Escherichia coli, and the maximum absorbance (λmax) of the purified proteins, the light-driven chloride uptake and the chloride-binding affinity were measured. The results showed them to have similar properties to two HRs reported previously. However, the λmax of HwHR is extremely consistent in a wide range of salt/chloride concentrations, which had not been observed previously. A structural-based sequence alignment identified a single serine residue at 262 in HwHR, which is typically a conserved alanine in all other known HRs. A Ser262 to alanine replacement in HwHR eliminated the chloride-independent colour tuning, whereas an Ala246 to serine mutagenesis in HsHR transformed it to have chloride-independent colour tuning similar to that of HwHR. Thus Ser262 is a key residue for the mechanism of chloride-dependent colour tuning in HwHR.
Parent-Implemented Enhanced Milieu Teaching With Preschool Children Who Have Intellectual Disabilities
Authors: Kaiser Ann P. , Roberts Megan Y. 
Published: June 2012

Purpose
The purpose of this study was to compare the effects of enhanced milieu teaching (EMT) implemented by parents and therapists versus therapists only on the language skills of preschool children with intellectual disabilities (IDs), including children with Down syndrome and children with autism spectrum disorders.

Method
Seventy-seven children were randomly assigned to 2 treatments (parent + therapist EMT or therapist-only EMT) and received 36 intervention sessions. Children were assessed before, immediately after, 6 months after, and 12 months after intervention. Separate linear regressions were conducted for each standardized and observational measure at each time point.

Results

Parents in the parent + therapist group demonstrated greater use of EMT strategies at home than untrained parents in the therapist-only group, and these effects maintained over time. Effect sizes for observational measures ranged from
d
= 0.10 to
d
= 1.32 favoring the parent + therapist group, with the largest effect sizes found 12 months after intervention.

Conclusion
Findings from this study indicate generally that there are benefits to training parents to implement naturalistic language intervention strategies with preschool children who have ID and significant language impairments.
Speech Perception in Noise by Children With Cochlear Implants
Authors: Caldwell Amanda , Nittrouer Susan 
Published: June 2012

PurposeCommon wisdom suggests that listening in noise poses disproportionately greater difficulty for listeners with cochlear implants (CIs) than for peers with normal hearing (NH). The purpose of this study was to examine phonological, language, and cognitive skills that might help explain speech-in-noise abilities for children with CIs.MethodThree groups of kindergartners (NH, hearing aid wearers, and CI users) were tested on speech recognition in quiet and noise and on tasks thought to underlie the abilities that fit into the domains of phonological awareness, general language, and cognitive skills. These last measures were used as predictor variables in regression analyses with speech-in-noise scores as dependent variables.ResultsCompared to children with NH, children with CIs did not perform as well on speech recognition in noise or on most other measures, including recognition in quiet. Two surprising results were that (a) noise effects were consistent across groups and (b) scores on other measures did not explain any group differences in speech recognition.ConclusionsLimitations of implant processing take their primary toll on recognition in quiet and account for poor speech recognition and language/phonological deficits in children with CIs. Implications are that teachers/clinicians need to teach language/phonology directly and maximize signal-to-noise levels in the classroom.
HELPING VALUES AND CIVIC ENGAGEMENT
Authors: Purdam K. , Tranmer M. 
Published: June 2012

ABSTRACT
In this article we examine generalised helping and specifically the importance people attach to helping other people, the extent to which they help in practice and their perceptions of how much people living locally help each other. We consider the extent to which the value of help is associated with other civic engagement activities such as, for example, volunteering, signing a petition and contacting a politician. Our findings suggest that the importance people attach to helping others and the extent to which they help in practice (in terms of helping with or attending activities in their local area) varies considerably across Europe. People are more likely to see helping other people as important than actually help in practice. However, helping in practice is more strongly associated than helping as a value, with other civic engagement activities. It seems that the value of help is detached from what people do in their everyday lives. Both the value of help and helping in practice are associated with the extent to which people in their local area are perceived to help each other. Our findings concerning generalised helping have important implications for the understanding of civic society and the contribution citizens can make.
A bioimage informatics approach to automatically extract complex fungal networks
Authors: Obara Boguslaw , Grau Vicente , Fricker Mark D. 
Published: June 2012

Abstract
Motivation: Fungi form extensive interconnected mycelial networks that scavenge efficiently for scarce resources in a heterogeneous environment. The architecture of the network is highly responsive to local nutritional cues, damage or predation, and continuously adapts through growth, branching, fusion or regression. These networks also provide an example of an experimental planar network system that can be subjected to both theoretical analysis and experimental manipulation in multiple replicates. For high-throughput measurements, with hundreds of thousands of branches on each image, manual detection is not a realistic option, especially if extended time series are captured. Furthermore, branches typically show considerable variation in contrast as the individual cords span several orders of magnitude and the compressed soil substrate is not homogeneous in texture making automated segmentation challenging.
Results: We have developed and evaluated a high-throughput automated image analysis and processing approach using Phase Congruency Tensors and watershed segmentation to characterize complex fungal networks. The performance of the proposed approach is evaluated using complex images of saprotrophic fungal networks with 105–106 edges. The results obtained demonstrate that this approach provides a fast and robust solution for detection and graph-based representation of complex curvilinear networks.
Availability and implementation: The Matlab toolbox is freely available through the Oxford e-Research Centre website: http://www.oerc.ox.ac.uk/research/bioimage/software
Contacts: boguslaw.obara@oerc.ox.ac.uk
Review article: non‐malignant haematological complications of anti‐tumour necrosis factor alpha therapy
Authors: Bessissow T. , Renard M. , Hoffman I. , Vermeire S. , Rutgeerts P. , Van Assche G. 
Published: June 2012

SummaryBackgroundTumour necrosis factor‐alpha (TNF‐α) is an important mediator of the molecular cascade leading to chronic inflammation. TNF‐α inhibitors have proven their safety and efficacy in the treatment of inflammatory diseases.AimTo review the non–malignant haematological adverse events, such as thrombocytopaenia, neutropaenia, hypercoagulability, pancytopaenia and aplastic anaemia in patients receiving TNF‐α inhibitors.MethodsWe reviewed the literature by searching MEDLINE and EMBASE databases as well as references of all retrieved articles for the following terms: anti‐tumour necrosis factor, anti‐TNF, infliximab, adalimumab, certolizumab, etanercept, haematological complications, thrombocytopaenia, neutropaenia, anaemia, bone marrow and thrombosis.ResultsThombocytopaenia is a very rare phenomenon and was associated with no serious adverse events. However, transient neutropaenia developed in up to 16% of cases. Patients with a previous history of neutropaenia on other therapies or baseline neutrophil count <4 × 109/L are at a particularly higher risk. The association between anti‐TNF‐α therapy and thrombosis is very nebulous due to the multitude of potential confounders. Only one case of primary eosinophilia has been reported with anti‐TNF‐α therapy.ConclusionRegular monitoring of the white blood cell count at baseline and with each infusion is recommended for patients on anti‐TNF‐α. Further studies to elucidate their interaction with the immune system are warranted.
Clinical trial design in haemophilia
Authors: DIMICHELE D. M. , BLANCHETTE V. , BERNTORP E. 
Published: June 2012

Summary. Progress in the evidence‐based care of haemophilia A and B worldwide has been historically challenged by the dearth of evaluable outcome data, including but not limited to the safety and effectiveness of therapeutic interventions. These challenges are partially rooted in the inherent difficulty of conducting prospective clinical trials and observational studies with statistically meaningful endpoints in a rare disease such as haemophilia. Despite the logistical barriers, the need for outcome data has never been more critical than in this time of expansive therapeutic advance tempered by the shrinking economic capacity to fund the rapidly increasing cost of treatment. Given that systematic analyses of published literature have been largely unsuccessful in compensating for the lack of rigorous and purposeful data collection, new approaches to clinical study design and statistical modelling are urgently needed. However, even as these are considered, the lack of broadly accepted and well‐defined clinical outcome endpoints poses an additional barrier to progress. The three presentations encompassed by this paper highlight the timely need for quality data from the perspectives of the clinicians, regulatory agencies and health care funders, and describe the ongoing coordinated efforts by the international haemophilia community to further understand and dismantle the barriers to harmonized and standardized data collection on a global scale using well‐defined clinical outcome endpoints.
Discordance between anaplastic lymphoma kinase status in primary non‐small‐cell lung cancers and their corresponding metastases
Authors: Kim Hyojin , Xu Xianhua , Yoo Seol‐Bong , Sun Ping‐Li , Jin Yan , Paik Jin Ho , Choe Gheeyoung , Jheon Sanghoon , Lee Choon‐Taek , Chung Jin‐Haeng 
Published: June 2012

Aims:  The anaplastic lymphoma kinase gene (ALK) has attracted considerable attention as a potential molecular target in non‐small‐cell lung cancer (NSCLC). However, it is unclear whether ALK alterations are acquired during the metastatic progression of NSCLC.Methods and results:  ALK status and ALK expression were evaluated in a series of 67 primary NSCLCs and their corresponding metastatic lesions using fluorescence in‐situ hybridization and immunohistochemistry. ALK rearrangement was detected in 7.5% (5/67) of the primary tumours and in 9.0% (6/67) of the metastases (P < 0.001). ALK copy number gain (CNG) was detected in 1.5% (1/67) of the primary tumours and in 35.8% (24/67) of the metastases. Whereas ALK rearrangement was detected only in adenocarcinomas, CNG was identified in various histological subtypes of NSCLC. ALK expression was detected in 11.9% (8/67) of the primary tumours and in 25.4% (17/67) of the metastatic lesions.Conclusions:  ALK alteration and ALK expression can be acquired during metastatic progression in NSCLC, and ALK CNG is associated with ALK expression.
Population pharmacokinetics of transdermal fentanyl solution following a single dose administered prior to soft tissue and orthopedic surgery in dogs
Authors: FREISE K. J. , LINTON D. D. , NEWBOUND G. C. , TUDAN C. , CLARK T. P. 
Published: June 2012

Freise, K. J., Linton, D. D., Newbound, G. C., Tudan, C., Clark, T. P. Population pharmacokinetics of transdermal fentanyl solution following a single dose administered prior to soft tissue and orthopedic surgery in dogs.J. vet. Pharmacol. Therap.35(Suppl. 2), 65–72.A novel, long‐acting transdermal fentanyl solution (TFS) that delivers sustained plasma fentanyl concentrations following a single application for the control of postoperative pain has recently been approved for use in dogs. The pharmacokinetics (PKs) of this formulation have been evaluated in healthy laboratory dogs, but they have not been reported in a clinical population of dogs for which it is indicated. Plasma fentanyl concentrations were determined from 215 dogs following a single, small‐volume (∼50 μL/kg) dose of TFS administered 2–4 h prior to orthopedic or soft tissue surgery. A population PK model was fit, and a 1‐compartment open PK model with first‐order absorption and an absorption lag‐time best described the data. No tested clinical covariates had a significant effect on the PKs. The final model adequately described the population PKs and gave results consistent with laboratory PK studies in healthy dogs. The PKs were primarily characterized by a rapid initial increase in plasma fentanyl concentrations and a long terminal half‐life of 74.0 (95% C.I. [54.7–113]) h governed by flip‐flop kinetics for the typical subject. The plasma fentanyl concentrations were sustained over days in the range considered to be analgesic for postoperative pain in dogs.
The history of decoquinate in the control of coccidial infections in ruminants
Authors: TAYLOR M. A. , BARTRAM D. J. 
Published: June 2012

Taylor, M. A., Bartram, D. J. The history of decoquinate in the control of coccidial infections in ruminants. J. vet. Pharmacol. Therap. 35, 417–427.Decoquinate is a quinolone derivative that has been used for over 20 years in the control of coccidiosis in domestic ruminants. Decoquinate treats coccidiosis in lambs and calves and prevents coccidiosis in lambs when administered in feed at a dosage of 1 mg decoquinate/kg bodyweight (b.w.) daily for at least 28 days. It prevents coccidiosis in calves and aids in the prevention of coccidiosis in lambs when administered in calf and ewe feed, respectively, at a dosage of 0.5 mg/kg b.w. daily for at least 28 days. Decoquinate also aids in the prevention of abortions and perinatal losses owing to toxoplasmosis by medication of ewe feed at a dosage of 2 mg/kg b.w. daily, fed continuously for 14 weeks prior to lambing. Several field studies have reported reductions in cryptosporidial oocyst shedding. Decoquinate acts early in the life cycle of Eimeria on sporozoites, released from ingested oocysts, and on first‐generation meronts, arresting development and release of merozoites and thus preventing further damage to the intestines owing to the gametocyte stages. Production benefits associated with the use of decoquinate are due mainly to its action as a coccidiostat rather than any effects on diet utilization or ruminal fermentation.
Localizing the contractile deceleration point (CDP) in patients with abnormal esophageal pressure topography
Authors: Lin Z. , Pandolfino J. E. , Xiao Y. , Carlson D. , Bidari K. , Escobar G. , Kahrilas P. J. 
Published: June 2012

AbstractBackground  The contractile deceleration point (CDP) is an important landmark for interpreting esophageal pressure topography (EPT) plots. Previous analysis in normal subjects confirmed that the CDP could be localized using an algorithm that found the time during peristalsis at which a maximal length of the distal esophagus was contracting concurrently (tML method). This study aimed to test the tML method for localizing CDP in patients with abnormal motility.Methods  High‐resolution manometry studies of 75 patients with normal and disordered peristalsis were analyzed. Two experts, JEP and YX, used the original tangent‐intersection method to score CDP coordinates for the first two swallows of each study. Alternative computerized algorithms tested against the expert were: (i) the tML method, (ii & iii) the intercept between the leading edge of the 30‐mmHg isobaric contour and a line 2.0 cm (or 10% of esophageal length) proximal to the esophagogastric junction (EGJ) at rest, or (iv) the ‘tML‐3 cm’ method, which added the stipulation that the CDP be within 3 cm of the EGJ.Key Results  All tested algorithms were highly correlated with the expert. However, the tMl‐3 cm method was better in the sense that it eliminated outliers (>1 s discrepancy with the expert) that occurred with the other methods usually attributable to weak distal peristalsis.Conclusions & Inferences  Optimal automated CDP localization was achieved in both normal and a spectrum of abnormal motility using the tML method with the added stipulation that the CDP be restricted to within the distal 3 cm of the EGJ at rest.
Changes in genome content generated via segregation of non‐allelic homologs
Authors: Liu Sanzhen , Ying Kai , Yeh Cheng‐Ting , Yang Jinliang , Swanson‐Wagner Ruth , Wu Wei , Richmond Todd , Gerhardt Daniel J. , Lai Jinsheng , Springer Nathan , Nettleton Dan , Jeddeloh Jeffrey A. , Schnable Patrick S. 
Published: June 2012

SummaryA careful analysis of two maize recombinant inbred lines (RILs) relative to their inbred parents revealed the presence of several hundred apparently de novo copy number variants (CNVs). These changes in genome content were validated via both PCR and whole exome‐array capture‐and‐sequencing experiments. One hundred and eighty‐five genomic regions, which overlap with 38 high‐confidence genes, exhibited apparently de novo copy number variation (CNV) in these two RILs and in many instances the same apparently de novo CNV events were observed in multiple RILs. Further analyses revealed that these recurrent apparently de novo CNVs were caused by segregation of single‐copy homologous sequences that are located in non‐allelic positions in the two parental inbred lines. F1 individuals derived from these inbred lines will be hemizygous for each of these non‐allelic homologs but RIL genotypes will contain these sequences at zero, one or two genomic loci. Hence, the segregation of non‐allelic homologs may contribute to transgressive segregation. Indeed, statistical associations between phenotypic quantitative trait loci and genomic losses were observed for two of 14 tested pairs of non‐allelic homologs.