bluuebunny/crossref_metadata_2025_split huggingface dataset:
The R‐factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures
Authors: Holton James M. , Classen Scott , Frankel Kenneth A. , Tainer John A. 
Published: July 2014

In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R‐factor gap. There is no such gap in small‐molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R‐factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein‐solvent interface may be improved by synergies between small‐angle X‐ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill.DatabaseCoordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws.
Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer
Authors: Avrahamov N. , Antler G. , Yechieli Y. , Gavrieli I. , Joye S. B. , Saxton M. , Turchyn A. V. , Sivan O. 
Published: July 2014

AbstractGeochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ13CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed (34ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate‐driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment.
The cumulative impact of annual coral bleaching can turn some coral species winners into losers
Authors: Grottoli Andréa G. , Warner Mark E. , Levas Stephen J. , Aschaffenburg Matthew D. , Schoepf Verena , McGinley Michael , Baumann Justin , Matsui Yohei 
Published: July 2014

AbstractMass coral bleaching events caused by elevated seawater temperatures result in extensive coral loss throughout the tropics, and are projected to increase in frequency and severity. If bleaching becomes an annual event later in this century, more than 90% of coral reefs worldwide may be at risk of long‐term degradation. While corals can recover from single isolated bleaching and can acclimate to recurring bleaching events that are separated by multiple years, it is currently unknown if and how they will survive and possibly acclimatize to annual coral bleaching. Here, we demonstrate for the first time that annual coral bleaching can dramatically alter thermal tolerance in Caribbean corals. We found that high coral energy reserves and changes in the dominant algal endosymbiont type (Symbiodinium spp.) facilitated rapid acclimation in Porites divaricata, whereas low energy reserves and a lack of algal phenotypic plasticity significantly increased susceptibility in Porites astreoides to bleaching the following year. Phenotypic plasticity in the dominant endosymbiont type of Orbicella faveolata did not prevent repeat bleaching, but may have facilitated rapid recovery. Thus, coral holobiont response to an isolated single bleaching event is not an accurate predictor of its response to bleaching the following year. Rather, the cumulative impact of annual coral bleaching can turn some coral species ‘winners’ into ‘losers’, and can also facilitate acclimation and turn some coral species ‘losers’ into ‘winners’. Overall, these findings indicate that cumulative impact of annual coral bleaching could result in some species becoming increasingly susceptible to bleaching and face a long‐term decline, while phenotypically plastic coral species will acclimatize and persist. Thus, annual coral bleaching and recovery could contribute to the selective loss of coral diversity as well as the overall decline of coral reefs in the Caribbean.
Scaling up experimental ocean acidification and warming research: from individuals to the ecosystem
Authors: Queirós Ana M. , Fernandes José A. , Faulwetter Sarah , Nunes Joana , Rastrick Samuel P. S. , Mieszkowska Nova , Artioli Yuri , Yool Andrew , Calosi Piero , Arvanitidis Christos , Findlay Helen S. , Barange Manuel , Cheung William W. L. , Widdicombe Stephen 
Published: July 2014

AbstractUnderstanding long‐term, ecosystem‐level impacts of climate change is challenging because experimental research frequently focuses on short‐term, individual‐level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14‐month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual‐level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual‐level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large‐scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local‐environmental conditions and resource availability. Such changes in macro‐scale distributions cannot be predicted by investigating individual‐level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long‐term, multiscale responses to multiple stressors, in an ecosystem context.
The British Nursing Index and CINAHL: a comparison of journal title coverage and the implications for information professionals
Authors: Briscoe Simon , Cooper Chris 
Published: July 2014

AbstractObjectivesThis paper compares the journal coverage of the British Nursing Index (BNI) and the Cumulative Index to Nursing and Allied Health Literature (CINAHL). The main objectives are to assess whether BNI is a useful source of UK publications and to consider the implications for information professionals.MethodsLists of the journals indexed in BNI and CINAHL, CINAHL Plus and CINAHL Complete were compared. The date coverage and article entry date of a selection of UK nursing journals were also compared.ResultsOne hundred and fifty‐nine journals are uniquely indexed in BNI compared with the basic version of CINAHL. Eighty‐one journals are uniquely indexed in BNI compared with all versions of CINAHL. Fifty‐one of these journals are UK publications. Most of the selected UK nursing journals have earlier start and entry dates in CINAHL than BNI.ConclusionBNI is smaller than CINAHL, and BNI indexes a relatively small number of unique journals. An information professional with access to CINAHL Plus or CINAHL Complete could reasonably not search BNI for a nursing topic, particularly if the topic is not UK specific. UK nursing research is more likely to benefit from using BNI, although the acquisition of BNI by ProQuest could impact this finding.
First report of the spectrum of δ‐globin gene mutations in Omani subjects – identification of novel mutations
Authors: Alkindi S. , AlZadjali S. , Daar S. , Ambusaidi R. , Gravell D. , Al Haddabi H. , Krishnamoorthy R. , Pathare A. 
Published: July 2014

SummaryIntroductionBoth coinheritance of thalassemic δ‐globin mutation and coexistence of iron deficiency anemia (IDA) tend to decrease HbA2 (α2δ2) level and thereby poses a diagnostic conundrum in β‐thalassemia trait.MethodsWe retrospectively studied 78 Omani subjects, presenting with low HbA2 level by high‐performance liquid chromatography (HPLC), and their DNA was sequenced for the presence of mutations in the δ‐globin gene (HBD). In these subjects, their serum ferritin levels allowed evaluation of the degree of iron deficiency.ResultsOverall, six different δ‐globin gene mutations were observed in 40 study subjects (51.3%) and IDA in 33 subjects, with the remaining five subjects showing normal HBD sequence and serum ferritin level. Among the subjects with δ‐globin gene mutations, seven had an associated IDA confirmed by significantly low serum ferritin levels. Heterozygosity for the delta (+) cd27G‐‐>T mutation (HbA2‐Yialousa; HBD: c.82G>T) was the most common abnormality observed (n = 26, 66.6%) followed by heterozygosity for HBD c.‐118C‐>T (d ‐68 C‐>T) (n = 6, 15.4%), for cd16G‐‐>C (n = 4, 10.3%), for cd98G‐‐>A (n = 2, 5.1%), for cd142G‐‐>C (n = 1, 2.6%), and for cd147G‐‐>T (n = 1, 2.6%).ConclusionsThese delta mutations exhibit low HbA2 either due to a shift in the HPLC position or due to their bona fide thalassemic feature. Two mutations, namely cd142 G‐‐>C (GCC to CCC, Ala to Pro) and stop codon cd147 G‐‐>T (stop to Leu with elongation of 15 amino acids), herein first reported are novel. Coexistence of IDA could lead to erroneous diagnostic interpretation unless it is specifically looked for.
Social Trinitarianism: A Discussion of Some Recent Theological Criticisms
Authors: van den Brink Gijsbert 
Published: July 2014

AbstractIn this article I briefly summarize the development of social trinitarianism in order to arrive at a description of its most important defining coordinates. Next, leaving aside the philosophical debate, I discuss some of the theological criticisms that have recently been leveled against it. It will turn out that social trinitarianism can be redefined in such a way that these objections are taken into account insofar as they are justified, but without losing the momentum social trinitarianism gave to the recent renewal of trinitarian thinking. Finally, having proceeded thus far in a defensive way, I will briefly explore two more constructive arguments in favour of social (or relational) trinitarianism.
Beyond Existentialism: Kierkegaard on the Human Relationship with the God Who is Wholly Other
Authors: Torrance Andrew B. 
Published: July 2014

AbstractRecent scholarship argues that, for Kierkegaard, God's absolute alterity is a consequence of sin that is overcome by the redemptive activity of Jesus Christ. On such a reading, the work of Christ delivers individuals to lives of faith that are not infinitely qualitatively different from God. This fails to recognize that the absolute otherness of God is overcome not simply by the redemptive work of Christ but in and through the person of Christ. The failure to grasp this has tied Kierkegaard to an anthropocentric theology that prioritizes Christ's contribution to existential human development. This article challenges this perception by establishing Kierkegaard's emphasis that God would remain infinitely removed from humanity were it not for the continuing mediation of Jesus Christ.
Merit and the Finnish Luther
Authors: Wahlberg Mats 
Published: July 2014

AbstractThe concept of merit, according to a Catholic understanding, is dictated by the nature of the divine grace that moves Christians to good works without violating their freedom. The Lutheran tradition, however, rejects the meritorious character of good works, at least in the context of salvation. In this article, it is argued that the new, Finnish Luther interpretation undermines the basis for Lutheranism's traditional resistance to the notion of merit. A tentative conclusion is that a Lutheranism that appropriates the Finnish interpretation has reason to embrace the applicability of merit‐language in soteriological contexts.
The dental development in patients with Aperts syndrome
Authors: Woods Eva , Parekh Susan , Evans Robert , Moles David R. , Gill Daljit 
Published: July 2014

ObjectivesThe aim of this retrospective study was to quantify the level of dental developmental delay in a group of patients with Aperts syndrome when compared to matched controls.MethodsTwenty‐six Dental Panoramic Tomographic (DPT) radiographs of patients with Apert syndrome attending Great Ormond Street Hospital were compared to controls (n = 29) from the Eastman Dental Hospital, UK. Dental development was assessed using the staging systems of Demirjian and Haavikko, and dental age (DA) was estimated using the weighted averages method.ResultsDental age, as estimated using the 12 stages of Haavikko and eight stages of Demirjian, suggested no statistical evidence of developmental delay between the Aperts and control group.ConclusionsThe hypothesis ‘that there is no difference in the dental development of subjects with Apert syndrome, when compared to a group of matched controls’, was accepted.
Lead Isotopic Composition in Biogenic Certified Reference Materials Determined by Different ICP‐based Mass Spectrometric Techniques
Authors: Ďurišová Jana , Ackerman Lukáš , Strnad Ladislav , Chrastný Vladislav , Borovička Jan 
Published: July 2014

This work presents data for the radiogenic Pb isotopic ratios (206Pb/207Pb and 208Pb/206Pb) in nine biogenic certified reference materials (NIST SRM 1515, 1566b, 1570a, 1573a, 1575a; BCR 100, BCR 101, BCR 670 and IAEA 359), which are suitable for analytical quality control in environmental research. The results were obtained using three different types of ICP‐based mass spectrometer (quadrupole‐based/magnetic sector field single‐collector ICP‐MS instruments and a multi‐collector ICP‐MS) and applying different mass bias correction procedures (calibrator‐sample bracketing and external Tl normalisation) with and without Pb separation from the matrix using ion exchange chromatography. In the majority of the samples, the measurements from all three of the ICP‐MS instruments were in agreement within ± 0.1%, despite the lower analytical precision of the single‐collector ICP‐MS instruments. We demonstrate that the presence of the sample matrix did not significantly influence the Pb isotopic ratios measured by magnetic sector field ICP‐MS, whereas the use of the two different mass bias corrections resulted in a systematic difference of 0.09% for the 208Pb/206Pb ratio.
Home nurses and patient depression. Attitudes, competences and the effects of a minimal intervention
Authors: Van Daele Tom , Vansteenwegen Debora , Hermans Dirk , Van den Bergh Omer , Van Audenhove Chantal 
Published: July 2014

AbstractAimTo explore attitudes and confidence in professional competence of home nurses concerning depression and to evaluate the capacity of a minimal intervention in helping home nurses to detect depression in patients and their family caregivers.BackgroundLong‐term ill patients have an elevated risk to develop comorbid depression, as do their family caregivers. However, most primary care providers have little training to detect patients at risk. A minimal intervention to help home nurses detect symptoms of depression was therefore evaluated.DesignQuasi‐experimental field study with pre‐measures, postmeasures and follow‐up measures.MethodsFrom the Fall of 2012–Spring of 2013, home nurses (N = 92) in three regions in Antwerp (Belgium) were assigned to a 1‐hour intervention (consisting of information, skill training and discussion; N = 63) or to a control condition (N = 29). The Depression Attitude Questionnaire and the Morris Confidence Scale were completed before the intervention and 3 and 7 months afterwards. For 3 months, the number of detections of depression in patients in each region was monitored.FindingsNo significant changes were found in attitude or confidence in professional competences, except for a decline in the role attitude for home nurses in the intervention group. Home nurses who followed the intervention did detect significantly more depressed patients compared with controls.ConclusionThese findings suggest that a minimal intervention can allow home nurses to be more responsive to symptoms of depression in patients and their family caregivers. The implications of these findings are discussed and suggestions for future research are made.
Effects of doxycycline on clinical, microbiological and immunological parameters in well‐controlled diabetes type‐2 patients with periodontal disease: a randomized, controlled clinical trial
Authors: Tsalikis Lazaros , Sakellari Dimitra , Dagalis Panagiotis , Boura Panagiota , Konstantinidis Antonios 
Published: July 2014

AbstractAimTo evaluate the clinical, microbiological and immunological effects of systemic doxycycline as an adjunct to scaling and root planing (SRP) in chronic periodontitis patients with well‐controlled type 2 diabetes.Materials and MethodsSixty‐six patients compliant to oral hygiene (Hygiene Index <20%) allocated to either a test (systemic doxycycline for 21 days) or a control (placebo) group participated in the present randomized controlled trial (RCT). Clinical assessments were recorded at baseline, 3 and 6 months after therapy and included clinical attachment level (CAL), set as the primary outcome of the study, probing pocket depth (PPD), recession (RE) and bleeding on probing (BOP). At the same time points, counts of 15 subgingival species were evaluated by “checkerboard” DNA‐DNA hybridization, gingival crevicular fluid samples were analysed for matrix metalloproteinase‐8 (MMP‐8) by ELISA and HbA1c levels were determined. Comparisons between and within groups were performed by non‐parametric tests (Mann–Whitney, Wilcoxon signed‐ranks and z‐test for proportions with Bonferroni corrections) at the 0.05 level.ResultsNo major differences were noticed in clinical and microbiological parameters of periodontal disease or levels of MMP‐8 between the two groups.ConclusionsAdjunctive systemic doxycycline does not seem to significantly enhance the effects of SRP in well‐controlled diabetes type 2 patients.
Subgingival air‐polishing with erythritol during periodontal maintenance
Authors: Müller Nada , Moëne Raphaël , Cancela José A. , Mombelli Andrea 
Published: July 2014

AbstractObjectivesTo evaluate repeated subgingival air‐polishing in residual pockets with a new erythritol powder containing 0.3% chlorhexidine.Material and MethodsSingle‐centre, examiner masked, randomized clinical trial of 12 months with a two‐arm, within‐subject parallel design. Fifty patients in periodontal maintenance were monitored in 3‐month intervals. At months 0, 3, 6 and 9, all sites presenting with a probing depth (PD) >4 mm were subject to subgingival air‐polishing (test side) or ultrasonic debridement (control side). The primary endpoint was presence/absence of PD >4 mm after 12 months.ResultsTotally 6918 sites were monitored at baseline, 457 of them had a PD >4 mm (range 5–9 mm). The number of pockets >4 mm per subject, PD and bleeding on probing were significantly lower at month 12. Differences between test and control were not significant. There was a significant difference in favour of air‐polishing for the perception of pain/discomfort. Differences of frequencies at >1000 and >100,000 cells/ml of six microorganisms between baseline and month 12 were not significant. At month 12, test sites were less frequently positive for Aggregatibacter actinomycetemcomitans at >1000 cells/ml than controls, and counts never exceeded 100,000 cells/ml.ConclusionsRepeated subgingival air‐polishing reduced the number of pockets >4 mm similar to ultrasonic debridement. It was safe and induced less pain.
Social networks of people with mild intellectual disabilities: characteristics, satisfaction, wishes and quality of life
Authors: van Asselt‐Goverts A. E. , Embregts P. J. C. M. , Hendriks A. H. C. 
Published: July 2014

AbstractBackgroundA supportive social network is crucial for facilitating social inclusion, which can, in turn, contribute to the quality of life (QOL) for people with intellectual disabilities (ID). In this study, we investigate how people with mild ID perceive their social networks and which network characteristics relate to satisfaction with the network and perceived QOL.MethodData were gathered from 33 young adults with a mild to borderline ID using structured questionnaires: the MSNA to map the social network, the IDQOL‐16 to assess QOL, and a questionnaire to determine satisfaction and wishes with regard to the social network.ResultsThe majority of the participants (73.1%) were satisfied with their social networks. Improvement in the area of strengthening existing ties (e.g. more frequent contact, better contact) was desired as opposed to expansion of the network. Affection – especially towards family and professionals – was most strongly related to perceived QOL. It appears to be essential that relatives live in the same town, can frequently meet up and provide both emotional and practical support.ConclusionsThe significance of family and the importance of high‐quality interpersonal relationships between professional and client in the lives of young adults with ID cannot be overestimated. Although measures of satisfaction and wishes can have limitations, in actual practice it is considered useful to assess the opinions of clients with respect to their social networks. Interventions can then be tailored to the needs and wishes of the persons themselves.