bluuebunny/crossref_metadata_2025_split huggingface dataset:
Achievements and challenges in structural bioinformatics and computational biophysics
Authors: Samish Ilan , Bourne Philip E. , Najmanovich Rafael J. 
Published: December 2014

Abstract
Motivation: The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects.
Results: An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results.
Conclusion: The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field.
Contact: Rafael.Najmanovich@USherbrooke.ca
Comparison of Serum Hemagglutinin and Neuraminidase Inhibition Antibodies After 2010–2011 Trivalent Inactivated Influenza Vaccination in Healthcare Personnel
Authors: Laguio-Vila Maryrose R. , Thompson Mark G. , Reynolds Sue , Spencer Sarah M. , Gaglani Manjusha , Naleway Allison , Ball Sarah , Bozeman Sam , Baker Steven , Martínez-Sobrido Luis , Levine Min , Katz Jackie , Fry Alicia M. , Treanor John J. 
Published: December 2014

Abstract
Background.  Most inactivated influenza vaccines contain purified and standardized hemagglutinin (HA) and residual neuraminidase (NA) antigens. Vaccine-associated HA antibody responses (hemagglutination inhibition [HAI]) are well described, but less is known about the immune response to the NA.
Methods.  Serum of 1349 healthcare personnel (HCP) electing or declining the 2010–2011 trivalent-inactivated influenza vaccine ([IIV3], containing A/California/7/2009 p(H1N1), A/Perth/16/2009 [H3N2], B/Brisbane/60/2008 strains) were tested for NA-inhibiting (NAI) antibody by a modified lectin-based assay using pseudotyped N1 and N2 influenza A viruses with an irrelevant (H5) HA. Neuraminidase-inhibiting and HAI antibody titers were evaluated approximately 30 days after vaccination and end-of-season for those with polymerase chain reaction (PCR)-confirmed influenza infection.
Results.  In 916 HCP (68%) receiving IIV3, a 2-fold increase in N1 and N2 NAI antibody occurred in 63.7% and 47.3%, respectively. Smaller responses occurred in HCP age &gt;50 years and those without prior 2009–2010 IIV3 nor monovalent A(H1N1)pdm09 influenza vaccinations. Forty-four PCR-confirmed influenza infections were observed, primarily affecting those with lower pre-exposure HAI and NAI antibodies. Higher pre-NAI titers correlated with shorter duration of illness for A(H1N1)pdm09 virus infections.
Conclusions.  Trivalent-inactivated influenza vaccine is modestly immunogenic for N1 and N2 antigens in HCP. Vaccines eliciting robust NA immune responses may improve efficacy and reduce influenza-associated morbidity.
Coeliac Disease Screening Among a Large Cohort of Overweight/Obese Children
Authors: Nenna Raffaella , Mosca Antonella , Mennini Maurizio , Papa Raffaele E. , Petrarca Laura , Mercurio Roberta , Montuori Monica , Piedimonte Alessandra , Bavastrelli Maria , De Lucia Ilaria C. , Bonamico Margherita , Vania Andrea 
Published: December 2014

ABSTRACTCoeliac disease (CD) is a chronic, gluten‐dependent enteropathy with a prevalence of approximately 1% in Western countries. Up to now, CD has been described only in sporadic cases of obesity. Our study aimed to evaluate retrospectively CD prevalence in a large series of overweight/obese children and adolescents. Among the 1527 overweight/obese children and adolescents consecutively evaluated, 17 (7 boys, 1.11%) were positive for serology and showed villous atrophy. In all of the patients with CD a well‐balanced gluten‐free diet was started, and a loss of weight rapidly obtained. Our study demonstrates that CD prevalence in overweight/obese children is similar to the general paediatric population in Italy.
Online Self-Report Data for Duchenne Muscular Dystrophy confirms natural history and can be used to assess for therapeutic benefits
Authors: Wang Richard T. , Silverstein Cheri , Ulm J. Wes , Jankovic Ivana , Eskin Ascia , Lu Ake , Rangel Miller Vanessa , Cantor Rita M. , Li Ning , Elashoff Robert , Martin Ann S. , Peay Holly , Nelson Stanley F. 
Published: December 2014

ABSTRACTTo assess the utility of online patient self-report outcomes in a rare disease, we attempted to observe the effects of corticosteroids in delaying age at fulltime wheelchair use in Duchenne muscular dystrophy (DMD) using data from 1,057 males from DuchenneConnect, an online registry. Data collected were compared to prior natural history data in regard to age at diagnosis, mutation spectrum, and age at loss of ambulation. Because registrants reported differences in steroid and other medication usage, as well as age and ambulation status, we could explore these data for correlations with age at loss of ambulation. Using multivariate analysis, current steroid usage was the most significant and largest independent predictor of improved wheelchair-free survival. Thus, these online self-report data were sufficient to retrospectively observe that current steroid use by patients with DMD is associated with a delay in loss of ambulation. Comparing commonly used steroid drugs, deflazacort prolonged ambulation longer than prednisone (median 14 years and 13 years, respectively). Further, use of Vitamin D and Coenzyme Q10, insurance status, and age at diagnosis after 4 years were also significant, but smaller, independent predictors of longer wheelchair-free survival. Nine other common supplements were also individually tested but had lower study power. This study demonstrates the utility of DuchenneConnect data to observe therapeutic differences, and highlights needs for improvement in quality and quantity of patient-report data, which may allow exploration of drug/therapeutic practice combinations impractical to study in clinical trial settings. Further, with the low barrier to participation, we anticipate substantial growth in the dataset in the coming years.
An experimental test of the relationship between melanism and desiccation survival in insects
Authors: Rajpurohit Subhash , Peterson Lisa Marie , Orr Andrew , Marlon Anthony J. , Gibbs Allen G 
Published: December 2014

AbstractWe used experimental evolution to test the ‘melanism-desiccation’ hypothesis, which proposes that dark cuticle in severalDrosophilaspecies is an adaptation for increased desiccation tolerance. We selected for dark and light body pigmentation in replicated populations ofD. melanogasterand assayed traits related to water balance. We also scored pigmentation and desiccation tolerance in populations selected for desiccation survival. Populations in both selection regimes showed large differences in the traits directly under selection. However, after over 40 generations of pigmentation selection, dark-selected populations were not more desiccation-tolerant than light-selected and control populations, nor did we find significant changes in carbohydrate amounts that could affect desiccation resistance. Body pigmentation of desiccation-selected populations did not differ from control populations after over 140 generations of selection. Our results do not support an important role for melanization inDrosophilawater balance.
Increasing the effectiveness of electrical resistivity tomography using γ11n configurations
Authors: Szalai S. , Lemperger I. , Metwaly M. , Kis Á. , Wesztergom V. , Szokoli K. , Novák A. 
Published: December 2014

ABSTRACTA new array type, i.e., the γ11n arrays, is introduced in this paper, in which the sequence of the current (C) and potential (P) electrodes is CPCP, and the distance between the last two electrodes is n times the distance between the first two ones and that of the second one and the third one. These arrays are called quasinull arrays because they are—according to their array and behaviour—between the traditional and null arrays. It is shown by numerical modelling that, in detecting small‐effect inhomogeneity, these configurations may be more effective than the traditional ones, including the optimized Stummer configuration. Certain γ11n configurations—especially the γ112, γ113, and γ114—produced better results both in horizontal and vertical resolution investigations. Based on the numerical studies, the γ11n configurations seem to be very promising in problems where the anomalies are similar to the numerically investigated ones, i.e., they can detect and characterize, e.g., tunnels, caves, cables, tubes, abandoned riverbeds, or discontinuity, in a clay layer with greater efficacy than those of the traditional configurations. γ11n measurements need less data than traditional configurations; therefore, the time demand of electrical resistivity tomography measurements can be shortened by their use.
Microhabitat associations of vascular epiphytes in a wet tropical forest canopy
Authors: Woods Carrie L. , Cardelús Catherine L. , DeWalt Saara J. 
Published: December 2014

Summary

In tropical forests, vascular epiphyte diversity increases with tree size, which could result from an increase in area, time for colonization or an increase in microhabitat heterogeneity within‐tree crowns if vascular epiphyte species are specialized to particular microhabitats within the crown. The importance of microhabitats in structuring epiphyte communities has been hypothesized for more than 120 years but not yet confirmed.

We tested the importance of microhabitats in structuring epiphyte communities by examining microhabitat heterogeneity and epiphyte communities within the crowns of different‐sized Virola koschnyi (Myristicaceae) emergent trees in a Costa Rican tropical wet forest. We tested the degree to which epiphyte species composition was associated with environmental conditions and resources (i.e. microhabitats) using multivariate analyses and a null model that compared the observed epiphyte assemblages amongst different‐sized trees and crown zones with assemblages generated randomly. This study is the first to rigorously examine the degree of microhabitat specialization in epiphyte communities.

Microhabitat heterogeneity, epiphyte species richness and abundance increased with tree size. The largest trees had the highest microhabitat and epiphyte diversity and a unique inner crown microhabitat with canopy humus. The few epiphytes found on small trees were mostly bark ferns. Large trees had different epiphyte communities in different parts of the crown; the inner crown contained species not abundant in any other microhabitat (i.e. aroids, cyclanths and humus ferns), and the outer crown contained bark ferns and atmospheric bromeliads.

Variation in species composition amongst tree size classes was significantly related to the mean daily maximum vapour pressure deficit and tree diameter, while variation within large tree crowns was significantly related to canopy humus cover.

Microhabitat specialization of epiphyte species increased with tree size with 6% of species significantly associated with small trees and 57% significantly associated with large trees. Of the species present in large tree crowns, 23% were specialized to the unique inner crown microhabitat.

Synthesis. The increase in microhabitat heterogeneity within tree crowns as trees grow contributes to changes in epiphyte community structure, which supports decades‐old hypotheses of the importance of microhabitat diversity and specialization in structuring tropical epiphyte communities.
Flow‐mediated dilatation, using time course data, shows maturation of the brachial artery from young children to mid‐adolescents
Authors: Kontos Anna , Pamula Yvonne , Martin James , Gent Roger , Lushington Kurt , Baumert Mathias , Willoughby Scott , Richardson Malcolm , Couper Jennifer , Kennedy Declan 
Published: December 2014

SummaryFlow‐mediated dilatation (FMD) is a tool widely used to measure arterial responsiveness to sheer stress. However, there is scant literature to show how the peripheral arterial response changes as the vascular system matures. One reason for this is that the feasibility of measuring FMD in younger children has not been established. The aim of the present study was to assess brachial artery function at rest and during the FMD response after 4 min ischaemia of the forearm in children aged 6–15 years. Time to reach maximum FMD (FMDmax) was found to be correlated with age (r = 0.4, P < 0.05), resting brachial artery diameter (r = 0.4, P < 0.05), height (r = 0.4, P < 0.05), body mass index (BMI; r = 0.45, P < 0.05), body surface area (r = 0.44, P < 0.05) and resting blood flow (r = 0.37, P < 0.05). However, there was no correlation between the traditional FMD response at 60 s or FMD maximal dilation and age, resting brachial artery diameter, height, weight, BMI, body surface area and resting blood flow. In conclusion, the time taken to reach the maximal dilation response is related to age, brachial artery luminal diameter and body habitus, but not the traditional measure of FMD response at 60 s or the maximal dilatation percentage.
The Impact of Medicaid Reform on Children's Dental Care Utilization in Connecticut, Maryland, and Texas
Authors: Nasseh Kamyar , Vujicic Marko 
Published: December 2014

ObjectiveTo measure the impact of Medicaid reforms, in particular increases in Medicaid dental fees in Connecticut, Maryland, and Texas, on access to dental care among Medicaid‐eligible children.Data2007 and 2011–2012 National Survey of Children's Health.Study DesignDifference‐in‐differences and triple differences models were used to measure the impact of reforms.Principal FindingsRelative to Medicaid‐ineligible children and all children from a group of control states, preventive dental care utilization increased among Medicaid‐eligible children in Connecticut and Texas. Unmet dental need declined among Medicaid‐eligible children in Texas.ConclusionsIncreasing Medicaid dental fees closer to private insurance fee levels has a significant impact on dental care utilization and unmet dental need among Medicaid‐eligible children.
Recovery of Spray Paint Traces from Clothing by Beating
Authors: Olderiks Maurice , Baiker Martin , van Velzen Jill , van der Weerd Jaap 
Published: December 2014

AbstractManual recovery of spray paints from textiles using a microscope, the routine method in many laboratories, is often laborious. Beating the clothing with a plastic rod, the routine method used for recovery of glass traces within the authors’ laboratory, is proposed as an alternative. The efficiency of the method was evaluated by spray tests with fluorescent paint. In these tests, paint particles in the acquired debris samples, as well as those remaining on the textiles, were investigated. The results show that beating is an efficient way to recover and concentrate paint particles. A good efficiency for jeans fabric and rough knitwear is reported. The results appeared to be less satisfactory for smooth woven fabric. Application of the method in casework was effective for graffiti paints as well as for flaked car paint.
On the Possibility of Nonfat Frying using Molten Glucose
Authors: Al‐Khusaibi Mohammed , Ahmad Tarmizi Azmil Haizam , Niranjan Keshavan 
Published: December 2014

AbstractFried products impose a health concerns due to considerable amount of oil they contain. Production of snack foods with minimal oil content and good management of oil during frying to minimize the production of toxic compounds continue to be challenging aims. This paper aims to investigate the possibility of producing a fat‐free food snack by replacing frying oil with a nonfat medium. Glucose was melted and its temperature was then brought to 185 °C and used to fry potato strips, to obtain a product referred here as glucose fries. The resulting product was compared with French fries prepared conventionally under conditions that resulted in similar final moisture content. The resulting products were also examined for crust formation, texture parameters, color development and glucose content. Stereo microscope images showed that similar crusts were formed in the glucose fries and French fries. Texture parameters were found to be similar for both products at 5 and 2 mm penetration depth. The maximum hardness at 2 mm penetration depth was also similar for both products, but different from cooked potato. The color development that characterized French fries was also observed in glucose fries. The glucose content in glucose fries was found to be twice the content of French fries, which is to be expected because glucose absorbed or adhered to the surface. In conclusion, glucose fries, with similar texture and color characteristics to that of French fries, can be prepared by using a nonfat frying medium.
Improvement of Flavor and Viscosity in Hot and Cold Break Tomato Juice and Sauce by Peel Removal
Authors: Mirondo Rita , Barringer Sheryl 
Published: December 2014

AbstractTomatoes are typically not peeled before being made into juice but the peels contain enzymes that affect the odor, flavor, and viscosity of the juice. The peels are removed in the finisher, but their presence during the break process may affect quality. Juice was processed from peeled and unpeeled tomatoes using hot or cold break. The juices were pasteurized by high temperature short time (HTST), low temperature long time (LTLT), or with a retort. The control samples were treated with 10% calcium chloride to stop enzymatic activity in the juice. Sauce was made from juice and the tomato products were analyzed for volatiles, color, viscosity, and by sensory. Cold break juice made with peel contained higher levels of some lipoxygenase‐, carotenoid‐, and amino acid–derived volatiles, than the juice made without peel. Because of the lack of enzyme activity, hot break juices had lower levels of these volatiles and there was no significant difference between hot break juices made with and without peel. CaCl2‐treated and HTST juice had higher levels of most of the volatiles than LTLT, including the lipoxygenase‐derived volatiles. The presence of peel produced a significant decrease in the viscosity of the cold break juice and sauce. There was no significant difference in the hue angle, total soluble solids, pH, titratable acidity, and vitamin C for most of the treatments. The texture, flavor, and overall liking of cold break juice made without peel were preferred over cold break juice made with peel whereas the color was less preferred. Between the sauces no significant differences in preference were obtained.
Clinical equipoise: Protons and the child with craniopharyngioma
Authors: Conroy Ruth , Gomes Lavier , Owen Catherine , Buchsbaum Jeffrey , Ahern Verity 
Published: December 2014

AbstractIntroductionChildhood craniopharyngioma is a complex condition to manage. Survival figures are high but the potential for long‐term morbidity is great. There is much debate regarding the best management for these tumours with increasing interest in the use of proton beam therapy. We have therefore reviewed our radiotherapy (RT) practice at Westmead Hospital and the literature regarding the use of protons for these children.MethodsThree children have received fractionated stereotactic RT for craniopharyngioma at Westmead Hospital since 2007. Each RT plan was reviewed and additional organs at risk were contoured to enable comparison with published proton data.ResultsPlanning target volume coverage was similar with all modalities: with the conformity index ranging from 0.70 to 0.78 in our patients compared with 0.50–0.84 in the published data. RT dose to temporal lobes, hippocampi and whole brain was also similar with protons and photons. Proton beam therapy may give lower dose to the Circle of Willis than stereotactic RT.ConclusionCurrently there is no clear evidence that proton beam therapy will improve survival or reduce morbidity for children with craniopharyngioma. However, proton therapy has the potential to reduce RT dose to the Circle of Willis, which may reduce the risk of future cerebrovascular complications. We propose that more resources should be allocated to ensuring these patients are managed by experienced multidisciplinary teams through the continuum from diagnosis to long‐term follow‐up.
Development and assessment of a new dermal attachment for short‐term tagging studies of baleen whales
Authors: Baumgartner Mark F. , Hammar Terry , Robbins Jooke 
Published: December 2014

Summary

Current studies of fine‐scale baleen whale diving and foraging behaviour rely on archival suction cup tags that remain attached over time scales of hours. However, skin irregularities can make suction cup attachment unreliable, and traditional pole deployment of suction cup tags is challenging in moderate sea conditions or when whales are evasive.

We developed a new tag attachment to overcome these limitations. The attachment features a short (6·5–7·5 cm) needle that anchors in the whale's dermis (epidermis and blubber) to which a free‐floating tag is attached via a severable tethered link. The needle, tag and a detachable ‘carrier rocket’ with fletching are fitted together to form a projectile that can be deployed at distances of up to 20 m using a compressed‐air launcher. A corrosive release mechanism allows the tag to separate from the needle after a specified period of time so that the tag can be recovered.

The dermal attachment was evaluated during a study of humpback whales (Megaptera novaeangliae) in the Gulf of Maine and then subsequently deployed on bowhead whales (Balaena mysticetus) near Barrow, Alaska. Monitoring of tagged humpback whales indicated that the needle was shed several days after deployment, the attachment site healed shortly thereafter, and there were no discernible behavioural or health effects over time scales of days to months after tagging. Bowhead whales showed little immediate reaction to tagging; the most common response was a prolonged dive right after tag deployment. On average, respiration rates of tagged bowhead whales were elevated after tag attachment, but returned to the same rate as undisturbed bowheads within 1–1·5 h.

When compared to suction cups, the dermal anchor provided a more reliable attachment and it can be applied from greater distances and in rougher sea conditions; it is therefore a useful alternative in circumstances where suction cup tags cannot be easily deployed.