bluuebunny/crossref_metadata_2025_split huggingface dataset:
From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook‐associated protein FlgK
Authors: Gourlay Louise J. , Thomas Rachael J. , Peri Claudio , Conchillo‐Solé Oscar , Ferrer‐Navarro Mario , Nithichanon Arnone , Vila Jordi , Daura Xavier , Lertmemongkolchai Ganjana , Titball Richard , Colombo Giorgio , Bolognesi Martino 
Published: February 2015

Melioidosis, caused by the Gram‐negative bacterium Burkholderia pseudomallei, is a potentially fatal infection that is endemic in Southeast Asia and Northern Australia that is poorly controlled by antibiotics. Research efforts to identify antigenic components for a melioidosis vaccine have led to the identification of several proteins, including subunits forming the flagella that mediate bacterial motility, host colonization, and virulence. This study focuses on the B. pseudomallei flagellar hook‐associated protein (FlgKBp), and provides the first insights into the 3D structure of FlgK proteins as targets for structure‐based antigen engineering. The FlgKBp crystal structure (presented here at 1.8‐Å resolution) reveals a multidomain fold, comprising two small β‐domains protruding from a large elongated α‐helical bundle core. The evident structural similarity to flagellin, the flagellar filament subunit protein, suggests that, depending on the bacterial species, flagellar hook‐associated proteins are likely to show a conserved, elongated α‐helical bundle scaffold coupled to a variable number of smaller domains. Furthermore, we present immune serum recognition data confirming, in agreement with previous findings, that recovered melioidosis patients produce elevated levels of antibodies against FlgKBp, in comparison with seronegative and seropositive healthy subjects. Moreover, we show that FlgKBp has cytotoxic effects on cultured murine macrophages, suggesting an important role in bacterial pathogenesis. Finally, computational epitope prediction methods applied to the FlgKBp crystal structure, coupled with in vitro mapping, allowed us to predict three antigenic regions that locate to discrete protein domains. Taken together, our results point to FlgKBp as a candidate for the design and production of epitope‐containing subunits/domains as potential vaccine components.
Is the island biogeography model a poor predictor of biodiversity patterns in shallow lakes?
Authors: Nolby Luke E. , Zimmer Kyle D. , Hanson Mark A. , Herwig Brian R. 
Published: February 2015

Summary

The classic island biogeography model (IBM) predicts highest species richness in large, connected habitats due to colonisation and reduced risk of extinction. Promoting large, connected habitats has subsequently become a common theme in conservation biology.

However, the IBM does not account for direct and indirect interactions among species. For example, planktivorous and benthivorous fish may reduce biodiversity in shallow lakes by inducing shifts to a turbid‐water lake state with low habitat complexity.

We assessed relationships between species richness, landscape features, fish biomass and lake state in 104 shallow lakes in Minnesota, U.S.A. First, we tested whether lake size and connectivity influenced species richness of fish and biomass of planktivores and benthivores (fish biomass). We subsequently tested whether fish biomass affected the probability that lakes were in turbid versus clear‐water states. Finally, we tested whether species richness of macrophytes and taxon richness of aquatic invertebrates showed stronger relationships with lake size and connectivity or with fish biomass and lake state.

Fish richness and biomass both increased with lake size and were higher in connected basins. Fish biomass, in turn, increased the probability that lakes would be turbid. In contrast, macrophyte and invertebrate richness were unrelated to lake size or connectivity. Instead, macrophyte richness was best predicted by lake state, while invertebrate richness was predicted by lake state and fish biomass. Richness of both macrophytes and invertebrates was higher in clear lakes, and invertebrate richness was inversely related to fish biomass.

Our results indicate the IBM poorly explains the diversity of macrophytes and invertebrates in shallow lakes, with diversity more strongly driven by biotic interactions and influences associated with fish. We suggest that ecological implications of increased connectivity and lake size should be considered in future conservation strategies for shallow lakes.
Reef‐coral refugia in a rapidly changing ocean
Authors: Cacciapaglia Chris , van Woesik Robert 
Published: February 2015

AbstractThis study sought to identify climate‐change thermal‐stress refugia for reef corals in the Indian and Pacific Oceans. A species distribution modeling approach was used to identify refugia for 12 coral species that differed considerably in their local response to thermal stress. We hypothesized that the local response of coral species to thermal stress might be similarly reflected as a regional response to climate change. We assessed the contemporary geographic range of each species and determined their temperature and irradiance preferences using ak‐fold algorithm to randomly select training and evaluation sites. That information was applied to downscaled outputs of global climate models to predict where each species is likely to exist by the year 2100. Our model was run with and without a 1 °C capacity to adapt to the rising ocean temperature. The results show a positive exponential relationship between the current area of habitat that coral species occupy and the predicted area of habitat that they will occupy by 2100. There was considerable decoupling between scales of response, however, and with further ocean warming some ‘winners’ at local scales will likely become ‘losers’ at regional scales. We predicted that nine of the 12 species examined will lose 24–50% of their current habitat. Most reductions are predicted to occur between the latitudes 5–15°, in both hemispheres. Yet when we modeled a 1 °C capacity to adapt, two ubiquitous species,Acropora hyacinthusandAcropora digitifera, were predicted to retain much of their current habitat. By contrast, the thermally tolerantPorites lobatais expected to increase its current distribution by 14%, particularly southward along the east and west coasts of Australia. Five areas were identified as Indian Ocean refugia, and seven areas were identified as Pacific Ocean refugia for reef corals under climate change. All 12 of these reef‐coral refugia deserve high‐conservation status.
Polytolerance to abiotic stresses: how universal is the shade–drought tolerance trade‐off in woody species?
Authors: Laanisto Lauri , Niinemets Ülo 
Published: February 2015

AbstractAimsAccording to traditional ecophysiological theories stress tolerance of plants is predominately determined by universal physiochemical constraints. Plant acclimation to environmental stress therefore compromises plant performance under a different stress, hindering successful toleration of several abiotic stress factors simultaneously. Yet recent studies have shown that these trade‐offs are less exclusive than postulated so far, leaving more wiggle room for gaining polytolerance through adaptations. We tested whether polytolerance to shade and drought depends on cold and waterlogging tolerances – hypothesizing that polytolerance patterns in different species groups (angiosperms versus gymnosperms; deciduous versus evergreen; species originating from North America, Europe and East Asia) depend on the length of the vegetation period and species dormancy through limiting the duration of favourable growing season.LocationNorthern Hemisphere.MethodsOur study analysed four main abiotic stress factors – shade, drought, cold and waterlogging stress – for 806 Northern Hemisphere woody species using cross‐calibrated tolerance rankings. The importance of trade‐offs among species ecological potentials was evaluated using species‐specific estimates of polytolerance to chosen factors.ResultsWe found that both cold and waterlogging tolerance are negatively related to species capabilities of simultaneously tolerating low‐light and low‐water conditions. While this pattern was different in angiosperms and gymnosperms, species region of origin and leaf type had no effect on this relationship.Main conclusionsOur results demonstrate that adaptation to different abiotic stress factors in woody plants is highly complex. The length of the vegetation period and dormancy are the key factors explaining why woody plants are less capable of tolerating both shade and drought in habitats where vegetation period is relatively short and the water table high. While dormancy enables angiosperms to more successfully face additional stress factors besides shade and drought, gymnosperms have lower polytolerance, but can better tolerate of shade and drought when other environmental factors are favourable.
Hospital admissions of older people for oral health‐related conditions: implications for the future
Authors: Kruger Estie , Tennant Marc 
Published: February 2015

ObjectiveThis study analysed all hospitalisations of persons over the age of 65 years for oral health‐related conditions, over a decade, and projected future hospitalisation rates.BackgroundThe proportion of older Australians is increasing, and their oral health is improving. At the same time, there is concern about the increasing burden that hospitalisations place on government health budgets.MethodsHospitalisation data of all patients older than 65 years, admitted to hospital for an oral health‐related condition in Western Australia over a decade, were analysed.ResultsOver a ten‐year period, a total of 11608 people over the age of 65 were admitted to hospital, with 10% 85 years and older, 52% were men, and 0.1% were Aboriginal patients. The highest rates of hospitalisation were for those from the most disadvantaged areas. Over ten years, there was a significant annual increase in rates of hospitalisation (4.4%). Overall, most admissions were for ‘Malignant neoplasms’ (16.6%), ‘Dental caries’ (15.4%) and ‘Other disorders of the teeth and supporting structures’ (14.3%). These three conditions accounted for almost half of all admissions (46.4%). Projections indicate high future burdens of hospitalisation.ConclusionsIt is of concern that hospitalisations for oral health‐related reasons among the oldest patients include high numbers with potentially preventable conditions such as dental caries. Projections indicate that if current trends are set to continue, hospitalisations for oral health‐related conditions among Western Australians older than 65 years will place a considerable burden on the health system.
Generation of 3D Spatially Variable Anisotropy for Groundwater Flow Simulations
Authors: Borghi Andrea , Renard Philippe , Courrioux Gabriel 
Published: February 2015

AbstractSedimentary units generally present anisotropy in their hydraulic properties, with higher hydraulic conductivity along bedding planes, rather than perpendicular to them. This common property leads to a modeling challenge if the sedimentary structure is folded. In this paper, we show that the gradient of the geological potential used by implicit geological modeling techniques can be used to compute full hydraulic conductivity tensors varying in space according to the geological orientation. For that purpose, the gradient of the potential, a vector normal to the bedding, is used to construct a rotation matrix that allows the estimation of the 3D hydraulic conductivity tensor in a single matrix operation. A synthetic 2D cross section example is used to illustrate the method and show that flow simulations performed in such a folded environment are highly influenced by this rotating anisotropy. When using the proposed method, the streamlines follow very closely the folded formation. This is not the case with an isotropic model.
Hemodialysis decreases carotid‐brachial and carotid‐femoral pulse wave velocities: A 5‐year follow‐up study
Authors: Cabrera Fischer Edmundo I. , Bia Daniel , Galli Cintia , Valtuille Rodolfo , Zócalo Yanina , Wray Sandra , Armentano Ricardo L. 
Published: February 2015

AbstractAortic stiffness is a prognostic parameter associated with patient mortality. Vascular access creation has been shown to have effects on arterial stiffness both in the aorta and in the upper limb arteries in chronically hemodialyzed patients (CHPs). However, no longitudinal studies have been conducted in order to characterize the evolution of arterial stiffness in CHPs. The aims of this work were (a) to measure baseline pulse wave velocity (PWV) in the carotid‐femoral and in right and left carotid‐brachial pathways in a cohort of CHP and (b) to conduct a 5‐year prospective study on the same cohort to determine possible time‐related differences. Pulse wave velocity was measured both in the carotid‐femoral and in the carotid‐brachial pathways, and clinical and biochemical parameters were collected in 25 CHPs, which were followed up after a 5‐year lapse. Right and left carotid‐brachial pathway PWV values showed significant decreases after the 5‐year follow‐up, independently of the presence of the vascular access (P < 0.001). Additionally, baseline carotid‐brachial PWV was significantly higher (P < 0.001) than values measured 5 years later for upper limbs with vascular access (11.97 ± 2.97 m/sec vs. 6.76 ± 1.48 m/sec, respectively) and without vascular access (12.25 ± 2.38 m/sec vs. 7.18 ± 1.88 m/sec, respectively). Similarly, PWV values in the carotid‐femoral pathway decreased significantly (P < 0.001) over the same period (13.27 ± 2.96 m/sec vs. 9.75 ± 2.99 m/sec, respectively). The 5‐year follow‐up of PWV showed significant decreases in both carotid‐brachial and carotid‐femoral pathways. The general changes in arterial stiffness could be related to the vascular access creation, hemodialysis therapy, and to the improvement of arterial pressure management.
Serum sulfatide abnormality is associated with increased oxidative stress in hemodialysis patients
Authors: Yuzhe Huang , Kamijo Yuji , Hashimoto Koji , Harada Makoto , Kanno Taro , Sugiyama Eiko , Kyogashima Mamoru , Oguchi Tomomasa , Nakajima Takero , Kanno Yutaka , Aoyama Toshifumi 
Published: February 2015

AbstractSulfatides are major glycosphingolipids of lipoproteins that influence atherosclerosis and blood coagulation. Our previous cross‐sectional study of hemodialysis patients showed that serum sulfatide levels decreased markedly with increasing duration of hemodialysis treatment, which may contribute to the development of cardiovascular disease. However, this past study could not demonstrate the time‐dependent change in serum sulfatide levels in each patient, and the underlying mechanism is unknown. To confirm the time‐dependent aggravation of serum sulfatide abnormality, 95 stable hemodialysis outpatients were followed up for 3 years. To show the underlying mechanisms, we statistically analyzed correlations between serum sulfatide levels and clinical factors, including an oxidative stress marker, malondialdehyde. Serum sulfatides were quantified by mass spectrometry after conversion to lysosulfatides. Malondialdehyde was measured using a colorimetric assay. The results showed a time‐dependent decrease in serum sulfatide levels associated with increased malondialdehyde levels, although the absolute level of serum malondialdehyde does not determine the baseline level of serum sulfatides. Multiple linear regression analysis showed a significant correlation only between the time‐dependent change in serum sulfatide levels and the time‐dependent change in serum malondialdehyde levels. This study demonstrated, for the first time, a time‐dependent aggravation of serum sulfatide abnormality in hemodialysis patients, as well as the potential relationship between serum sulfatide abnormality and increasing oxidative stress. These findings suggest that oxidative stress might be an aggravating factor in serum sulfatide abnormality. As continuation of hemodialysis treatment hardly improves abnormal serum sulfatide levels or increased oxidative stress, development of novel therapeutic strategies may be important.
Onabotulinum ToxinAfor the Treatment of Headache in Service Members With a History of Mild Traumatic Brain Injury: A Cohort Study
Authors: Yerry Juanita A. , Kuehn Devon , Finkel Alan G. 
Published: February 2015

ObjectivePost‐traumatic headache (PTH) of the migraine type is a common complication of mild traumatic brain injury (including blast injuries) in active duty service members. Persistent and near‐daily headache occur. Usual preventive medications may have unacceptable side effects. Anecdotal reports suggest that onabotulinum toxinA(OBA) might be an effective treatment in these patients.MethodsThis study is a real‐time retrospective consecutive case series of all patients treated withOBAat the Concussion Care Clinic of Womack Army Medical Center, Ft. Bragg,NC, betweenAugust 2008 andAugust 2012. Clinical treatment and pharmacy records were corroborated with the electronic medical records in the Armed Forces Health Longitudinal Technology Application to determine demographics, current headache and treatment characteristics, and clinical and occupational outcomes.ResultsSixty‐four subjects (63 male) with mean age of 31.3 + 7.5 (range 20‐59) years were evaluated and treated. Blast injuries were most common (n = 36; 56.3%) and 7 patients (11%) reported a prior history of headache. Most patients (36; 56.3%) described more than 1 headache type and 48 (75%) patients had continuous pain. The most prevalent treating diagnosis was mixed continuous headache with migraine features on more than 15 days per month (n = 26; 40.6%). The mean time from injury to the first injections was 10.8 + 21.9 (1‐96) months. Forty (62.5%) patients received theFood andDrugAdministration‐approved chronic migraine injection protocol. Forty‐one (64%) patients reported being better. Two patients discontinued for side effects. Twenty‐seven (41%) remained on active duty.ConclusionsWe demonstrate that active duty military patients with headaches related to concussions may benefit from treatment withOBA. Further studies are indicated.
No Microstructural White Matter Alterations in Chronic and Episodic Migraineurs: A Case–Control Diffusion Tensor Magnetic Resonance Imaging Study
Authors: Neeb Lars , Bastian Kaili , Villringer Kersten , Gits Hunter C. , Israel Heike , Reuter Uwe , Fiebach Jochen B. 
Published: February 2015

BackgroundIn patients with episodic migraine (EM), diffusion tensor imaging (DTI) revealed microstructural white matter alterations in various brain regions related to pain processing. Some of these changes were correlated with migraine duration and attack frequency, suggesting that migraine is a progressive disease with proceeding structural alterations of the brain. This study aimed to identify possible microstructural white matter alterations in patients with chronic migraine (CM) using DTI. We hypothesized that alterations in DTI are more pronounced in patients with CM compared with EM.MethodsIndividually, age‐ and sex‐matched subjects with CM without aura, EM without aura, and healthy controls (n = 21 per group) underwent conventional head magnetic resonance imaging and DTI imaging in a 3T MRI scanner and were included in analysis. DTI data were analyzed using a tract‐based spatial statistics approach. Fractional anisotropy (FA), mean diffusivity, radial diffusivity, and axial diffusivity were compared between subjects with CM and EM, CM and controls, EM and controls, as well as between all subjects with migraine (EM + CM) and controls.ResultsIn chronic migraineurs (mean age 49 ± 7.5 years), we did not find any statistically significant difference (P < .05, threshold‐free cluster enhancement corrected for multiple comparison) in DTI‐derived parameters in comparison with episodic migraineurs (FA: P > .245) and healthy controls (FA: P > .099). In contrast to previous DTI studies, we did not find alterations in DTI‐derived indices in subjects with EM compared with healthy controls (FA: P > .486).ConclusionsNo microstructural white matter changes could be observed in middle‐aged chronic and episodic migraineurs using DTI. CM does not seem to be a risk factor for progressive microstructural changes in DTI.
Trust, temporality and systems: how do patients understand patient safety in primary care? A qualitative study
Authors: Rhodes Penny , Campbell Stephen , Sanders Caroline 
Published: February 2015

AbstractIntroductionPatient safety research has tended to focus on hospital settings, although most clinical encounters occur in primary care, and to emphasize practitioner errors, rather than patients' own understandings of safety.ObjectiveTo explore patients' understandings of safety in primary care.MethodsQualitative interviews were conducted with patients recruited from general practices in northwest England. Participants were asked basic socio‐demographic information; thereafter, topics were largely introduced by interviewees themselves. Transcripts were coded and analysed using NVivo10 (qualitative data software), following a process of constant comparison.ResultsThirty‐eight people (14 men, 24 women) from 19 general practices in rural, small town and city locations were interviewed. Many of their concerns (about access, length of consultation, relationship continuity) have been discussed in terms of quality, but, in the interviews, were raised as matters of safety. Three broad themes were identified: (i) trust and psycho‐social aspects of professional–patient relationships; (ii) choice, continuity, access, and the temporal underpinnings of safety; and (iii) organizational and systems‐level tensions constraining safety.DiscussionConceptualizations of safety included common reliance on a bureaucratic framework of accreditation, accountability, procedural rules and regulation, but were also individual and context‐dependent. For patients, safety is not just a property of systems, but personal and contingent and is realized in the interaction between doctor and patient. However, it is the systems approach that has dominated safety thinking, and patients' individualistic and relational conceptualizations are poorly accommodated within current service organization.
In vivo evaluation of the inflammatory response and IL‐6 immunoexpression promoted by Biodentine and MTA Angelus
Authors: da Fonseca T. S. , da Silva G. F. , Tanomaru‐Filho M. , Sasso‐Cerri E. , Guerreiro‐Tanomaru J. M. , Cerri P. S. 
Published: February 2015

AbstractAimTo evaluate the inflammatory process induced by Biodentine and mineral trioxide aggregate (MTA) in rat subcutaneous tissues.MethodologyA polyethylene tube filled with Biodentine (n = 20) or MTA (n = 20) was placed into the dorsal subcutaneous of forty male rats; in the control group (CG; n = 20), empty tubes were implanted. After 7, 15, 30 and 60 days, the polyethylene tubes surrounded by connective tissue were fixed and embedded in paraffin. The number of inflammatory cells was estimated in HE‐stained sections; numerical density of interleukin‐6 (IL‐6)‐immunolabelled cells was also performed. The differences amongst the groups were analysed statistically by Tukey's test (P ≤ 0.05).ResultsA high number of inflammatory cells and IL‐6‐positive cells were observed at 7 days, in all groups; however, in the Biodentine group, the number of inflammatory cells and IL‐6‐immunolabelled cells was significantly higher (P ≤ 0.05) in comparison with the other groups at 7 and 15 days. In the capsules of animals from all groups, a gradual and significant reduction (P ≤ 0.05) of these parameters was seen over time. At 60 days, the capsules exhibited numerous fibroblasts and bundles of collagen fibres; in addition, the number of IL‐6‐positive cells was not significantly different amongst Biodentine, MTA and control groups.ConclusionsThere was a significant regression in the inflammatory reaction in the capsules indicating, therefore, that Biodentine is a biocompatible material.