bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the utility of CASP14 models for molecular replacement
Authors: Millán Claudia , Keegan Ronan M. , Pereira Joana , Sammito Massimo D. , Simpkin Adam J. , McCoy Airlie J. , Lupas Andrei N. , Hartmann Marcus D. , Rigden Daniel J. , Read Randy J. 
Published: June 2021

AbstractThe assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real-world application. In CASP7, the metric for molecular replacement assessment involved full likelihood-based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood-based rigid-body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined likelihood (LLG) score. This enabled multi-copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative-expected-LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X-ray, NMR or cryo-EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.
Changes in dynamic transitions between integrated and segregated states underlie visual hallucinations in Parkinson’s disease
Authors: Zarkali Angeliki , Luppi Andrea I. , Stamatakis Emmanuel A. , Reeves Suzanne , McColgan Peter , Leyland Louise-Ann , Lees Andrew J. , Weil Rimona S. 
Published: June 2021

AbstractBackgroundVisual hallucinations in Parkinsons disease (PD) are transient, suggesting a change in dynamic brain states. However, the causes underlying these dynamic brain changes are not known.MethodsFocusing on fundamental network properties of integration and segregation, we used rsfMRI to examine alterations in temporal dynamics in PD patients with hallucinations (n=16) compared to those without hallucinations (n=75) and a group of normal controls (n=32). We used network control theory to examine how structural connectivity guides transitions between functional states. We then studied the brain regions most involved in these state transitions, and examined corresponding neurotransmitter density profiles and receptor gene expression in health.ResultsThere were significantly altered temporal dynamics in PD with hallucinations, with an increased proportion of time spent in the Segregated state compared to non-hallucinators and controls; less between-state transitions; and increased dwell time in the Segregated state. The energy cost needed to transition from integrated-to-segregated state was lower in PD-hallucinators compared to non-hallucinators. This was primarily driven by subcortical and transmodal cortical brain regions, including the thalamus and default mode network regions. The regional energy needed to transition from integrated-to-segregated state was significantly correlated with regional neurotransmitter density and gene expression profiles for serotoninergic (including 5HT2A), GABAergic, noradrenergic and cholinergic but not dopaminergic density profiles.ConclusionsWe describe the patterns of temporal functional dynamics in PD-hallucinations, and link these with neurotransmitter systems involved in early sensory and complex visual processing. Our findings provide mechanistic insights into visual hallucinations in PD and highlighting potential therapeutic targets.
Negative online reviews, brand equity and emotional contagion
Authors: Ahmad Fayez , Guzmán Francisco 
Published: June 2021

PurposeDespite the growing consensus that consumers extensively use online reviews and that negative reviews can significantly damage brand equity, it remains uncertain whether negative online reviews that focus on different aspects of a service have a similar or differential effect on brand equity. This study aims to fill this gap and explores the mediating role of emotional contagion and what kind of response helps better deter their negative effect.Design/methodology/approachThis research is conducted through a one-panel study and three experimental studies. SAS enterprise miner is used for text mining analysis and Analysis of variance (ANOVA) and Process macro models are used to analyze the experimental data.FindingsNegative reviews related to the tangibility, responsiveness and empathy dimensions have a more detrimental effect on brand equity than negative reviews related to the assurance and reliability dimensions. The results also provide evidence that emotional contagion is more prevalent when consumers read reviews that are specific to the empathy and responsiveness dimensions. Finally, accommodative responses from the service provider are more effective in deterring the effect of a negative online review on brand equity.Research limitations/implicationsThe generalizability of this study is limited to the restaurant and hotel industry.Practical implicationsThe findings will also help the brand manager in understanding the comparative effect of service quality-specific negative reviews on brand equity and also the type of responses that brand managers should give to negative reviews.Originality/valueDespite online reviews receiving increased attention in academic research, Service quality (SERVQUAL) dimension-specific reviews have not been studied until now. This study contributes to the service quality-related literature by providing evidence that not all negative online reviews related to different Service quality (SERVQUAL) dimensions equally affect brand equity.
Financial support services for beekeepers: a case study of development interventions in Fiji's Northern Division
Authors: Hinton Jordanna , Schouten Cooper , Stimpson Kerrie , Lloyd David 
Published: June 2021

PurposeThis paper analyses financial support services (loans and grants) from the perspective of beekeepers in Fiji's Northern Division.Design/methodology/approachA mixed-method, case study approach was used with key informant interviews, focus groups, semi-structured interviews and questionnaires.FindingsFinancial support was found to be an appropriate intervention. While beekeepers have access to loans, matching grants or small business grants to assist the establishment and growth of their activities, the appropriateness of these services varies based on the experience and skill of beekeepers. Capacity building was an important shortcoming in all financial services. It is recommended beekeeping clients undertake outcome-based, practical and/or mentorship-styled training to ensure beekeepers have the appropriate skills to maintain a viable enterprise.Research limitations/implicationsThis study was limited by a small sample size. Further research is needed to understand long-term impacts of financial support services and the availability and appropriateness of these within and between regions.Social implicationsRecommendations are provided to encourage effective financial support for beekeepers to improve the productivity, profitability and sustainability of their activities. This can impact beekeepers' livelihoods by increasing household income and income security.Originality/valueThere is a paucity of literature on the effectiveness of financial interventions to support beekeeping enterprises. This is the first study to compare financial support services from the perspective of beekeepers in the Pacific region.
A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics
Authors: Kessler Camille , Brambilla Alice , Waldvogel Dominique , Camenisch Glauco , Biebach Iris , Leigh Deborah M. , Grossen Christine , Croll Daniel 
Published: June 2021

AbstractPolymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
Application of 3D Static Modelling in Reservoir Characterization: A Case Study from the Qishn Formation in Sharyoof Oil Field, Masila Basin, Yemen
Authors: ABDULLAH Emad A. , ABDELMAKSOUD Ahmed , HASSAN Musab A. 
Published: June 2021

AbstractThree‐dimensional (3D) static modelling techniques are applied to the characterization of the Qishn Formation (Fm.) in the Sharyoof oil field locating within the Masila basin, southeastern Yemen. The present study was initiated by the seismic structural interpretation, followed by building a 3D structural framework, in addition to analysing well log data and from these, 3D facies and petrophysical models are constructed. In the Sharyoof oil field, the Qishn Fm. exhibits depth values within the range of 400–780 m below sea level, with a general increase towards the SSE. A set of high dip angle normal faults with a general ENE–WSW trend dissect the rocks. The strata are also folded as a main anticline with an axis that is parallel to the fault trend, formed as a result of basement uplift. According to the facies models, the Qishn Fm. comprises 43.83% limestone, 21.53% shale, 21.26% sandstone, 13.21% siltstone and 0.17% dolomite. The Qishn Carbonates Member has low porosity values making it a potential seal for the underlying reservoirs whereas the Upper Qishn Clastics S1A and C have good reservoir quality and S1B has fair reservoir quality. The Upper Qishn Clastics S2 and S3 also have fair reservoir quality, while the Lower Qishn Clastics zone has good reservoir quality. The water saturation decreases towards the west and east and increases towards north and south. The total original oil in‐place (OOIP) of the Upper Qishn clastics is 106 million STB within the S1A, S1C and S2 zones. Drilling of development wells is recommended in the eastern study area, where good trapping configuration is exhibited in addition to the presence of a potential seal (Upper Qishn Carbonates Member) and reservoir (Qishn Clastics Member) with high porosity and low water saturation.
Prediction of Shale Gas Pressure based on Multi‐channel Seismic Inversion in Fuling
Authors: XING Lei , LI Yu , LI Qianqian , LIU Yaowen , WAN Yunqiang , YANG Huiliang 
Published: June 2021

AbstractThe accurate prediction of formation pressure is important in oil/gas exploration and development. However, the achievement of this goal remains challenging, due to insufficient logging data and the low predictive data accuracy from seismic data. In this work, a case study was carried out in the Baima area of Wulong, in order to develop a workflow for accurately predicting shale gas formation pressure. The multi‐channel stack method was first used, as well as the inversion of single‐channel seismic data, to construct velocity and density models of the formation. Combined with the existing well‐logging data, the velocity and density models of the whole well section were established. The shale gas formation pressure was then estimated using the Eaton method. The results show that the multi‐channel seismic stacking method has a higher accuracy than the inversion of the formation velocity obtained by the single‐channel seismic method. The discrepancies between our predicted formation pressure and the actual formation pressure measurement are within an acceptable range, indicating that our workflow is effective.
First Record ofPetalodusOwen, 1840 (Chondrichthyes, Petalodontidae) in the Lower Permian (Cisuralian) of China
Authors: GAI Zhikun , BAI Zhijun , LIN Xianghong , MENG Xinyuan , ZHANG Junwen 
Published: June 2021

AbstractThe Petalodontiformes are a small intriguing group of Permo–Carboniferous chondrichthyans.Petalodusis the longest known petalodont genus generally considered representative of the order. The first definite fossil record of seven well‐preservedPetalodusteeth has been found in the Qianshi limestone in the Lower Permian (Cisuralian) middle–upper Taiyuan Formation in Yangquan City, Shanxi Province, North China. The specimens are characterized by petal‐shaped teeth with a spade‐like crown, and a long, tongue‐shaped root; the crown is circled with a band or cingulum composed of imbricated ridges at the base. All seven teeth are assigned to the speciesP. ohioenesisbecause of their vertically narrow cingulum and much longer root.Petalodusis a worldwide genus, with fossil localities mainly concentrated in the Laurussia supercontinent. The occurrence ofPetalodusteeth in Yangquan not only is the first fossil record in China, but also only the second record in Asia. The Yangquan fossil site was part of the paleoequatorial North China Craton during the Early Permian, and was isolated from Laurusia and East Gondwana by the Paleo‐Tethys Ocean. The successful dispersal ofPetalodusfrom Laurusia to the North China Block along Paleo‐Tethys may support the possibility thatPetalodustaxa were active free‐swimmers rather than bottom dwellers. The new finding increases the petalodont diversity in eastern Asia, and also sheds new light on the distribution and stratigraphic range.
Making Unequal Democracy Work? The Effects of Income on Voter Turnout in Northern Italy
Authors: Schafer Jerome , Cantoni Enrico , Bellettini Giorgio , Berti Ceroni Carlotta 
Published: June 2021

AbstractIn many democracies, voter turnout is higher among the rich than the poor. But do changes in income lead to changes in electoral participation? We address this question with unique administrative data matching a decade of individual tax records with voter rolls in a large municipality in northern Italy. We document several important findings. First, levels of income and turnout both dropped disproportionately among relatively poor citizens following the Great Recession. Second, we show that within‐individual changes in income have an effect on participation, which is modest on average due to diminishing returns, but can be consequential among the poor. Third, we find that declining turnout of voters facing economic insecurity has exacerbated the income skew in participation, suggesting that income inequality and turnout inequality may reinforce each other. We discuss the theoretical implications of these results, set in a context with strong civic traditions and low barriers to voting.
Change We Can Believe In: Structural and Content Dynamics within Belief Networks
Authors: Fishman Nic , Davis Nicholas T. 
Published: June 2021

AbstractScholars have used network analysis to explore the structural properties of mass ideology. This article incorporates two important, though ignored features in past research by investigating howtimeshapes the properties of belief networksfor different populations of people—those who exhibit high and low levels of political knowledge. We find that (1) belief network density increases asymmetrically among people with high relative to low knowledge; (2) symbolic preferences are more central to belief networks irrespective of survey timing or population; in contrast, policy beliefs exhibit some increase in centrality over time among the politically knowledgeable; and (3) a belief's centrality is unrelated to the amount of change it explains in other beliefs. Troublingly, this latter finding presents problems for describing belief networks using the vernacular of Conversian belief systems—a disconnect that seems grounded in the mismatch between Converse's individual‐level theory and network analysis' population‐based properties.
The anatomical distribution of non‐melanoma skin cancer: a retrospective cohort study of 22 303 Australian cases
Authors: Khalid Aafreen , van Essen Phillipa , Crittenden Tamara A. , Dean Nicola R. 
Published: June 2021

AbstractBackgroundNon‐melanoma skin cancers (NMSC) are the most common skin cancers worldwide with research establishing that ultraviolet (UV) radiation influences occurrence. However, recent studies about NMSC tumour frequencies suggested high NMSC predilections in low UV‐exposed skin regions.MethodsThe ‘Human Surface Anatomy Labeling System’ was used to define 100 skin regions to map NMSC locations excised at Flinders Medical Centre (FMC) between 1 January 2012 and 31 December 2017. Data were retrieved from the FMC histopathology database. A customised phrase algorithm was used to run a systematic word search on the dataset to quantify NMSC locations.ResultsA total of 22 303 NMSC excisions were identified; 80% were head and neck excisions. Scalp, periocular and nasal regions showed a significantly greater predilection for basal cell carcinomas (BCC). Squamous cell carcinomas (SCC) had significantly more excisions in lip, neck and scalp regions. Regarding gender‐related variations, more males had BCC excisions in ear regions and more females had nasal, lip, and ankle excisions. In SCC excisions, more males had scalp excisions and more females had leg and lip excisions. Considering age‐related variation, significantly higher proportions of BCC were found with forehead excisions compared to scalp, neck and lower limb regions for SCC, all being highest for 60–79‐year age groups.ConclusionThe relationship between NMSC type and anatomical distribution may be partially explained by gender and age affecting NMSC predilections particularly in the head and neck. However, other skin regions could not be explained solely by these factors.
Using a validated tool to assess whole‐body cadaveric simulation course on open general and emergency surgery
Authors: Killoran Callie B. , Roeder Luisa , James‐McAlpine Janelle , de Costa Alan 
Published: June 2021

AbstractBackgroundThe Anatomy of Surgical Exposure (ASE) is a cadaver‐based operative surgery simulation course that aims to teach techniques and exposures commonly used in open surgical operations. In this study, we used a validated tool to determine efficacy of assessing skills acquisition in the simulated environment. Our aims were to investigate if the ASE course improves the candidates' surgical performance, and to assess if the validated Objective Structured Assessment of Technical Skill (OSATS) template could be a useful tool for assessing technical skills.MethodsParticipants (n = 33) undertook supervised assessment of specific procedures at 10 cadaveric stations over a 2‐year period; performance was marked using the OSATS template. This template utilizes a seven‐item score to assess general and specific surgical techniques and knowledge using a 5‐point Likert scale. Experienced tutors assessed each surgery for each participant; individual and comparative data over the 3‐day course was used to provide each participant specific feedback at course completion.ResultsAverage OSATS scores did not improve significantly over the 3‐day OSATS course. There was a significant positive correlation observed between surgical trainees and OSATS total scores (P = 0.001, r = 0.747), number of years of post‐graduation, and total OSATS scores (P = 0.001, r = 0.527).ConclusionsOur findings indicate that those on the surgical training pathway and those who had graduated earlier, had an overall higher score than those not yet on surgical training. The template was able to provide on‐site specific candidate feedback by the end of the course, identifying areas of improvement of technical surgical skills.
The effect of perioperative hemadsorption in patients operated for acute infective endocarditis—A randomized controlled study
Authors: Asch Silke , Kaufmann Tobias Peter , Walter Michaela , Leistner Marcus , Danner Bernd C. , Perl Thorsten , Kutschka Ingo , Niehaus Heidi 
Published: June 2021

AbstractPatients operated for infective endocarditis (IE) are at high risk of developing an excessive systemic hyperinflammatory state, resulting in systemic inflammatory response syndrome and septic shock. Hemoadsorption (HA) by cytokine adsorbers has been successfully applied to remove inflammatory mediators. This randomized controlled trial investigates the effect of perioperative HA therapy on inflammatory parameters and hemodynamic status in patients operated for IE. A total of 20 patients were randomly assigned to either HA therapy or the control group. HA therapy was initiated intraoperatively and continued for 24 hours postoperatively. Cytokine levels (IL‐6, IL‐1b, TNF‐α), leukocytes, C‐reactive protein (CRP), and Procalcitonin (PCT) as well as catecholamine support, and volume requirement were compared between both groups. Operative procedures included aortic (n = 7), mitral (n = 6), and multiple valve surgery (n = 7). All patients survived to discharge. No significant differences concerning median cytokine levels (IL‐6 and TNF‐α) were observed between both groups. CRP and PCT baseline levels were significantly higher in the HA group (59.5 vs. 26.3 mg/dL, P = .029 and 0.17 vs. 0.05 µg/L, P = .015) equalizing after surgery. Patients in the HA group required significantly higher doses of vasopressors (0.093 vs. 0.025 µg/kg/min norepinephrine, P = .029) at 12 hours postoperatively as well as significantly more overall volume replacement (7217 vs. 4185 mL at 12 hours, P = .015; 12 021 vs. 4850 mL at 48 hours, P = .015). HA therapy did neither result in a reduction of inflammatory parameters nor result in an improvement of hemodynamic parameters in patients operated for IE. For a more targeted use of HA therapy, appropriate selection criteria are required.