bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving accuracy of direct and maternal genetic effects in genomic evaluations using pooled boar semen: a simulation study1
Authors: Maiorano Amanda M , Assen Alula , Bijma Piter , Chen Ching-Yi , Silva Josineudson Augusto II Vasconcelos , Herring William O , Tsuruta Shogo , Misztal Ignacy , Lourenco Daniela A L
Published: June 2019

Pooling semen of multiple boars is commonly used in swine production systems. Compared with single boar systems, this technique changes family structure creating maternal half-sib families. The aim of this simulation study was to investigate how pooling semen affects the accuracy of estimating direct and maternal effects for individual piglet birth weight, in purebred pigs. Different scenarios of pooling semen were simulated by allowing the same female to mate from 1 to 6 boars, per insemination, whereas litter size was kept constant (N = 12). In each pooled boar scenario, genomic information was used to construct either the genomic relationship matrix (G) or to reconstruct pedigree in addition to G. Genotypes were generated for 60,000 SNPs evenly distributed across 18 autosomes. From the 5 simulated generations, only animals from generations 3 to 5 were genotyped (N = 36,000). Direct and maternal true breeding values (TBV) were computed as the sum of the effects of the 1,080 QTLs. Phenotypes were constructed as the sum of direct TBV, maternal TBV, an overall mean of 1.25 kg, and a residual effect. The simulated heritabilities for direct and maternal effects were 0.056 and 0.19, respectively, and the genetic correlation between both effects was −0.25. All simulations were replicated 5 times. Variance components and direct and maternal heritability were estimated using average information REML. Predictions were computed via pedigree-based BLUP and single-step genomic BLUP (ssGBLUP). Genotyped littermates in the last generation were used for validation. Prediction accuracies were calculated as correlations between EBV and TBV for direct (accdirect) and maternal (accmat) effects. When boars were known, accdirect were 0.21 (1 boar) and 0.26 (6 boars) for BLUP, whereas for ssGBLUP, they were 0.38 (1 boar) and 0.43 (6 boars). When boars were unknown, accdirect was lower in BLUP but similar in ssGBLUP. For the scenario with known boars, accmat was 0.58 and 0.63 for 1 and 6 boars, respectively, under ssGBLUP. For unknown boars, accmat was 0.63 for 2 boars and 0.62 for 6 boars in ssGBLUP. In general, accdirect and accmat were lower in the single-boar scenario compared with pooled semen scenarios, indicating that a half-sib structure is more adequate to estimate direct and maternal effects. Using pooled semen from multiple boars can help us to improve accuracy of predicting maternal and direct effects when maternal half-sib families are larger than 2.
The Effect of Question Characteristics on Question Reading Behaviors in Telephone Surveys
Authors: Olson Kristen , Smyth Jolene D , Kirchner Antje
Published: June 2019

Asking questions fluently, exactly as worded, and at a reasonable pace is a fundamental part of a survey interviewer’s role. Doing so allows the question to be asked as intended by the researcher and may decrease the risk of measurement error and contribute to rapport. Despite the central importance placed on reading questions exactly as worded, interviewers commonly misread questions, and it is not always clear why. Thus, understanding the risk of measurement error requires understanding how different interviewers, respondents, and question features may trigger question reading problems. In this article, we evaluate the effects of question features on question asking behaviors, controlling for interviewer and respondent characteristics. We also examine how question asking behaviors are related to question-asking time. Using two nationally representative telephone surveys in the United States, we find that longer questions and questions with transition statements are less likely to be read exactly and fluently, that questions with higher reading levels and parentheticals are less likely to be read exactly across both surveys and that disfluent readings decrease as interviewers gain experience across the field period. Other question characteristics vary in their associations with the outcomes across the two surveys. We also find that inexact and disfluent question readings are longer, but read at a faster pace, than exact and fluent question reading. We conclude with implications for interviewer training and questionnaire design.
AGN in dwarf galaxies: frequency, triggering processes and the plausibility of AGN feedback
Authors: Kaviraj Sugata , Martin Garreth , Silk Joseph
Published: June 2019

While active galactic nuclei (AGN) are considered to be key drivers of the evolution of massive galaxies, their potentially significant role in the dwarf-galaxy regime (M* < 109 M⊙) remains largely unexplored. We combine optical and infrared data, from the Hyper Suprime-Cam (HSC) and the Wide-field Infrared Explorer, respectively, to explore the properties of ∼800 AGN in dwarfs at low redshift (z < 0.3). Infrared-selected AGN fractions are ∼10–30 per cent in dwarfs, which, for reasonable duty cycles, indicates a high black hole (BH)-occupation fraction. Visual inspection of the deep HSC images indicates that the merger fraction in dwarf AGN (∼6 per cent) shows no excess compared to a control sample of non-AGN, suggesting that the AGN-triggering processes are secular in nature. Energetic arguments indicate that, in both dwarfs and massive galaxies, bolometric AGN luminosities (LAGN) are significantly greater than supernova luminosities (LSN). LAGN/LSN is, in fact, higher in dwarfs, with predictions from simulations suggesting that this ratio only increases with redshift. Together with the potentially high BH-occupation fraction, this suggests that if AGN feedback is an important driver of massive-galaxy evolution, the same is likely to be true in the dwarf regime, contrary to our classical thinking.
Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Authors: Platt Roy N , McDew-White Marina , Le Clec’h Winka , Chevalier Frédéric D , Allan Fiona , Emery Aidan M , Garba Amadou , Hamidou Amina A , Ame Shaali M , Webster Joanne P , Rollinson David , Webster Bonnie L , Anderson Timothy J C
Published: June 2019

Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3–8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108–613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.
Symbolic Interactionism in Communication
Authors: Fernback Jan
Published: June 2019

Symbolic interactionism has nearly a hundred-year history as an approach to understanding human communication. With its roots in pragmatism (Dewey), social theory (Mead, Blumer), and later social psychology (Goffman), symbolic interactionism contends that humans interpret and assign meaning to events via an elaborate set of symbols. The meanings of these symbols originate and evolve through human social interaction. These interactions form the foundation for people’s notions of self and society. Thus, the material world, as well as concepts of self, is constructed through an interactive, communicative process. Observing neither idealist nor materialist suppositions about ontological precedence, symbolic interactionism is a micro-level theory addressing how the social world is created and sustained through continual and varied interactions among people. It is useful in the study of communication because it explains meaning creation among interlocutors; symbolic interactionism is a theory of language, communication, and socialization. Symbolic interactionism centers on the subjective interpretation of meaning by individual actors. Symbolic interactionists do not deny that institutional structures possess social importance; rather, they attend to the act of meaning construction—how repeated, significant interactions among people, within themselves, and with environments construct the social order. With the interpretive turn in social theory—in which subjective epistemologies gained scholarly value—during the 1980s and beyond, symbolic interactionism became more prominent and influential in other theoretical strains, including identity theory, feminist and queer theories, post-structuralism, critical race theory, and theories of performativity. Increasingly, symbolic interactionism is being applied to the study of social institutions in a meso or macro sense. Methodologically, symbolic interactionism’s emphasis on symbolic meaning, human agency, and interpretive epistemology compels it toward discourse and textual analysis, ethnography, observation, and performance studies. However, a form of symbolic interactionism promoted chiefly by Manford Kuhn introduced a quantitative vein to the scientific study of human interactive behavior. With its broad perspectives (including Karl Weick’s work in organizational culture), symbolic interactionism has gained status in the study of communication.
HIV Care for Patients With Complex Needs: A Controlled Evaluation of a Walk-In, Incentivized Care Model
Authors: Dombrowski Julia C , Galagan Sean R , Ramchandani Meena , Dhanireddy Shireesha , Harrington Robert D , Moore Allison , Hara Katie , Eastment Mckenna , Golden Matthew R
Published: June 2019

Background

New approaches are needed to provide care to persons with HIV who do not engage in conventionally organized HIV clinics. The Max Clinic in Seattle, Washington, is a walk-in, incentivized HIV care model located in a public health STD clinic that provides care in collaboration with a comprehensive HIV primary care clinic (the Madison Clinic).

Methods

We compared outcomes in the first 50 patients enrolled in Max Clinic and 100 randomly selected matched Madison Clinic control patients; patients in both groups were virally unsuppressed (viral load [VL] >200 copies/mL) at baseline. The primary outcome was any VL indicating viral suppression (≥1 VL <200 copies/mL) during the 12 months postbaseline. Secondary outcomes were continuous viral suppression (≥2 consecutive suppressed VLs ≥60 days apart) and engagement in care (≥2 medical visits ≥60 days apart). We compared outcomes in the 12 months pre- and postbaseline and used generalized estimating equations to compare changes in Max vs control patients, adjusting for unstable housing, substance use, and psychiatric disorders.

Results

Viral suppression improved in both groups pre-to-post (20% to 82% Max patients; P < .001; and 51% to 65% controls; P = .04), with a larger improvement in Max patients (adjusted relative risk ratio [aRRR], 3.2; 95% confidence interval [CI], 1.8–5.9). Continuous viral suppression and engagement in care increased in both groups but did not differ significantly (continuous viral suppression: aRRR, 1.5; 95% CI, 0.5–5.2; engagement: aRRR, 1.3; 95% CI, 0.9–1.9).

Conclusions

The Max Clinic improved viral suppression among patients with complex medical and social needs.
Long-Lasting Transcriptional Changes in Circulating Monocytes of Acute Q Fever Patients
Authors: Raijmakers Ruud Ph , Stenos John , Keijmel Stephan P , Ter Horst Rob , Novakovic Boris , Nguyen Chelsea , Van Der Meer Jos Wm , Netea Mihai G , Bleeker-Rovers Chantal P , Joosten Leo Ab , Graves Stephen R
Published: June 2019

Objective

Although most patients recover from acute Q fever, around 20% develop Q fever fatigue syndrome (QFS), a debilitating fatigue syndrome that lasts at least 6 months. This study investigated transcriptional profiles of circulating monocytes and circulating cytokines as a subsequent mirror of myeloid cell function, 1 and 6 months after an acute Q fever infection.

Methods

Total RNA of circulating monocytes was collected from 11 acute Q fever patients and 15 healthy controls, matched for age (±5 years) and sex. Samples were collected at a median of 27 days (baseline, interquartile range, 15–35 days) after the infection and again 6 months thereafter. Transcriptome analysis was performed using RNA sequencing. Additionally, concentrations of circulating interleukin (IL)-10, IL-1β, IL-1Ra, and IL-6 were measured in serum.

Results

At baseline, acute Q fever patients clearly show a differential transcriptional program compared with healthy controls. This is still the case at follow-up, albeit to a lesser extent. At baseline, a significant difference in levels of circulating IL-10 (P = .0019), IL-1β (P = .0067), IL-1Ra (P = .0008), and IL-6 (P = .0003) was seen. At follow-up, this difference had decreased for IL-10 (P = .0136) and IL-1Ra (P = .0017) and had become nonsignificant for IL-1β (P = .1139) and IL-6 (P = .2792).

Conclusions

We show that an acute Q fever infection has a long-term effect on the transcriptional program of circulating monocytes and, therefore, likely their myeloid progenitor cells, as well as concentrations of circulating IL-10, IL-1β, IL-1Ra, and IL-6.
Variation in Susceptibility of Tanoak to the NA1 and EU1 Lineages of Phytophthora ramorum, the Cause of Sudden Oak Death
Authors: Søndreli Kelsey L. , Kanaskie Alan , Keriö Susanna , LeBoldus Jared M.
Published: June 2019

Phytophthora ramorum, the cause of sudden oak death (SOD), kills tanoak (Notholithocarpus densiflorus) trees in southwestern Oregon and California. Two lineages of P. ramorum are now found in wildland forests of Oregon (NA1 and EU1). In addition to the management of SOD in forest ecosystems, disease resistance could be used as a way to mitigate the impact of P. ramorum. The objectives of this study were to (i) characterize the variability in resistance of N. densiflorus among families using lesion length; (ii) determine whether lineage, isolate, family, or their interactions significantly affect variation in lesion length; and (iii) determine whether there are differences among isolates and among families in terms of lesion length. The parameters isolate nested within lineage (isolate[lineage]) and family × isolate(lineage) interaction explained the majority of the variation in lesion length. There was no significant difference between the NA1 and EU1 lineages in terms of mean lesion length; however, there were differences among the six isolates. Lesions on seedlings collected from surviving trees at infested sites were smaller, on average, than lesions of seedlings collected from trees at noninfested sites (P = 0.0064). The results indicate that there is potential to establish a breeding program for tanoak resistance to SOD and that several isolates of P. ramorum should be used in an artificial inoculation assay.
Relationship between sorptivity and capillary coefficient for water absorption of cement-based materials: theory analysis and experiment
Authors: Yang Lin , Gao Danying , Zhang Yunsheng , Tang Jiyu , Li Ying
Published: June 2019

The durability of cement-based materials depends on the property of water absorption. In this work, a technique of X-ray CT combined with CsCl enhancing was used to continuously monitor the dynamic process of water uptake in cement-based materials and the gravimetric method was used to measure the amount of water absorption. The relationship between the capillary coefficient (
k
) and sorptivity (
S
) was firstly established based on theory analysis and well verified by the experiment results. In accordance with theory analysis and experiment results, it is found that the ratio of sorptivity to capillary coefficient equals the porosity (
φ
) of materials, i.e.
S
/
k
=
φ
. This model provides a simple method for obtaining the capillary coefficient of porous materials from the measurement of sorptivity and porosity.
Harbour porpoise responses to pile-driving diminish over time
Authors: Graham Isla M. , Merchant Nathan D. , Farcas Adrian , Barton Tim R. , Cheney Barbara , Bono Saliza , Thompson Paul M.
Published: June 2019

Estimating impacts of offshore windfarm construction on marine mammals requires data on displacement in relation to different noise levels and sources. Using echolocation detectors and noise recorders, we investigated harbour porpoise behavioural responses to piling noise during the 10-month foundation installation of a North Sea windfarm. Current UK guidance assumes total displacement within 26 km of pile driving. By contrast, we recorded a 50% probability of response within 7.4 km (95% CI = 5.7–9.4) at the first location piled, decreasing to 1.3 km (95% CI = 0.2–2.8) by the final location; representing 28% (95% CI = 21–35) and 18% (95% CI = 13–23) displacement of individuals within 26 km. Distance proved as good a predictor of responses as audiogram-weighted received levels, presenting a more practicable variable for environmental assessments. Critically, acoustic deterrent device (ADD) use and vessel activity increased response levels. Policy and management to minimize impacts of renewables on cetaceans have concentrated on pile-driving noise. Our results highlight the need to consider trade-offs between efforts to reduce far-field behavioural disturbance and near-field injury through ADD use.
Facile synthesis of porous Mo
2
C/C composites by using luffa sponge-derived carbon template in molten salt media
Authors: Huang Minzhong , Zeng Wanyi , Zhu Ziwen
Published: June 2019

Herein, we report the synthesis of a new type of porous Mo
2
C/C composite by using luffa sponge-derived carbon template and ammonium molybdate ((NH
4
)
6
Mo
7
O
24
•4H
2
O) in molten NaCl–KCl salt media. The product exhibits a higher specific surface area and three-dimensional porous structure, including macrochannels, micropores and mesopores. The desirable porous structure results from the carbon template structure and Mo
2
C coating formed.
Optimising the use of molecular tools for the diagnosis of yaws
Authors: Munson Morgan , Creswell Benjamin , Kondobala Kofi , Ganiwu Bawa , Lomotey Rita Dede , Oppong Paul , Agyeman Frederick Opoku , Kotye Nana , Diwura Mukaila , Ako Ebenezer Padi , Simpson Shirley Victoria , Addo Kennedy Kwasi , Pickering Harry , Handley Rebecca , Houghton Joanna , Kwakye Cynthia , Marks Michael
Published: June 2019

Introduction

Yaws is a neglected tropical disease and results in lesions of skin, soft tissues and bones. PCR plays an important part in surveillance.

Methods

Children suspected to have yaws were enrolled. From the largest lesion paired swabs were collected; one into transport medium and one as a dry swab. In children with multiple lesions we collected additional swabs from up to four subsequent lesions. Swabs in transport medium were maintained in a cold-chain whilst dry swabs were stored at ambient temperature. Swabs were tested by PCR for Treponema pallidum and Haemophilus ducreyi.

Results

Of 55 individuals, 10 (18%) had at least 1 positive PCR for T. pallidum and 12 (22%) had at least 1 positive result for H. ducreyi. Concordance was 100% between swabs in transport medium and dry swabs. One patient had PCR-confirmed yaws on the swab of a third lesion when both the first and second lesions were PCR-negative.

Discussion

Storing swabs in transport medium and transporting in a cold chain did not improve yield, however detection of T. pallidum is increased by swabbing additional lesions. As the target for yaws is eradication approaches to sample collection need revisiting to ensure cases are not missed.
Perception of whole-body motion during balance perturbations is impaired in Parkinson’s disease and is associated with balance impairment
Authors: Bong Sistania M. , McKay J. Lucas , Factor Stewart A. , Ting Lena H.
Published: June 2019

Background

In addition to motor deficits, Parkinson’s disease (PD) may cause perceptual impairments. The role of perceptual impairments in sensorimotor function is unclear, and has typically been studied in single-joint motions. Research Question: We hypothesized that perception of whole-body motion is impaired in PD and contributes to balance impairments. We tested 1) whether directional acuity to whole body perturbations during standing was worse in people with PD compared to neurotypical older adults (NOA), and 2) whether balance ability, as assessed by the MiniBESTest, was associated with poor directional acuity in either group.

Methods

Participants were exposed to pairs of support-surface translation perturbations in a two-alternative forced choice testing paradigm developed previously in a young healthy population. The first perturbation of each pair was directly backward and the second deviated to the left or right (1°–44°). Participants judged and reported whether the perturbations in each pair were in the “same” or “different” direction. This information was used to calculate directional acuity thresholds corresponding to “just-noticeable differences” in perturbation direction. Linear mixed models determined associations between directional thresholds and clinical variables including MDS UPDRS-III score, age, and MiniBESTest score. Results: 20 PD (64±7 y, 12 male, ⩾12 hours since last intake of antiparkinsonian medications) and 12 NOA (64±8, 6 male) were assessed. Directional thresholds were higher (worse) among PD participants (17.6±5.9° vs. 12.8±3.3°, P<0.01). Linear mixed models further showed that higher thresholds were associated with MDS UPDRS-III score (P<0.01), and were associated with poorer balance ability among PD participants (P<0.01), but not among NOA participants (P=0.40). Significance: Perception of whole-body motion is impaired in PD and may contribute to impaired balance and falls.
Trends and variation in unsafe prescribing of methotrexate: a cohort study in English NHS primary care
Authors: MacKenna Brian , Curtis Helen J , Walker Alex J , Croker Richard , Bacon Seb , Goldacre Ben
Published: June 2019

Objective

To describe trends and geographical variation in methotrexate prescribing that breaches national safety recommendations; deaths from methotrexate poisoning; and associated litigation.

Methods

A retrospective cohort study of English NHS primary care prescribing data, complemented by information obtained through Freedom of Information (FOI) requests. The main outcome measures were: (1) variation in ratio of breaching / adherent prescribing, geographically and over time, between General Practices and Clinical Commissioning Groups; (2) description of responses to FOI requests.

Results

Out of 7349 NHS General Practices in England, 1689 practices prescribed both 2.5mg and 10mg tablets to individual patients in 2017, breaching national guidance. In April 2018, 697 practices (at the 90th centile and above) prescribed at least 14.3% of all methotrexate as 10mg tablets, breaching national guidance. The 66 practices at the 99th percentile and above gave at least 52.4% of all prescribed methotrexate in the form of 10 mg tablets. The prescribing of 10mg tablets has fallen over 7 years, with 10mg tablets as a proportion of all methotrexate tablets falling from 9.1% to 3.4%. 21 deaths caused by methotrexate poisoning have been reported from 1993-2017.

Conclusions

The prevalence of unsafe methotrexate prescribing has reduced but it remains common, with substantial variation between organisations. We recommend the NHS invests in better strategies around implementation of safety recommendations. 21 deaths have been attributed to methotrexate poisoning but with no further details easily available: the full coroners reports for these deaths should be reviewed to identify recurring themes.
Brain state stability during working memory is explained by network control theory, modulated by dopamine D1/D2 receptor function, and diminished in schizophrenia
Authors: Braun Urs , Harneit Anais , Pergola Giulio , Menara Tommaso , Schaefer Axel , Betzel Richard F. , Zang Zhenxiang , Schweiger Janina I. , Schwarz Kristina , Chen Junfang , Blasi Giuseppe , Bertolino Alessandro , Durstewitz Daniel , Pasqualetti Fabio , Schwarz Emanuel , Meyer-Lindenberg Andreas , Bassett Danielle S. , Tost Heike
Published: June 2019

Dynamical brain state transitions are critical for flexible working memory but the network mechanisms are incompletely understood. Here, we show that working memory entails brain-wide switching between activity states. The stability of states relates to dopamine D1 receptor gene expression while state transitions are influenced by D2 receptor expression and pharmacological modulation. Schizophrenia patients show altered network control properties, including a more diverse energy landscape and decreased stability of working memory representations.
Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide
Authors: Trumbo DR , Salerno PE , Logan KA , Alldredge M , Gagne RB , Kozakiewicz CP , Kraberger S , Fountain-Jones N , Craft ME , Carver S , Ernest HB , Crooks K , VandeWoude S , Funk WC
Published: June 2019

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 134 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more overall population substructure in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.
Differential Treatment Benefit Prediction For Treatment Selection in Depression: A Deep Learning Analysis of STAR*D and CO-MED Data
Authors: Mehltretter Joseph , Fratila Robert , Benrimoh David , Kapelner Adam , Perlman Kelly , Snook Emily , Israel Sonia , Miresco Marc , Turecki Gustavo
Published: June 2019

Background

Depression affects one in nine people, but treatment response rates remain low. There is significant potential in the use of computational modelling techniques to predict individual patient responses and thus provide more personalized treatment. Deep learning is a promising computational technique that can be used for differential treatment selection based on predicted remission probability.

Methods

Using STAR*D and CO-MED trial data, we employed deep neural networks to predict remission after feature selection. Differential treatment benefit was estimated in terms of improvement of population remission rates after application of the model for treatment selection using both naive and conservative approaches. The naïve approach assessed population remission rate in five sets of 200 patients held apart from the training set; the conservative approach used bootstrapping for sample generation and focused on population remission rate for patients who actually received the drug predicted by the model compared to the general population.

Results

Our deep learning model predicted remission in a pooled CO-MED/STAR*D dataset (including four treatments) with an AUC of 0.69 using 17 input features. Our naive analysis showed an improvement of remission of over 30% (from a 34.33% population remission rate to 46.12%). Our conservative analysis showed a 7.2% improvement in population remission rate (p= 0.01, C.I. 2.48% ± .5%).

Conclusion

Our model serves as proof-of-concept that deep learning has utility in differential prediction of antidepressant response when selecting from a number of treatment options. These models may have significant real-world clinical implications.
Protein:Protein Interactions in the Cytoplasmic Membrane Influencing Sugar Transport and Phosphorylation Activities of theE. coliPhosphotransferase System
Authors: Aboulwafa Mohammad , Zhang Zhongge , Saier Milton H.
Published: June 2019

The multicomponent phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system (PTS) inEscherichia colitakes up sugar substrates and concomitantly phosphorylates them. We have recently provided evidence that many of the integral membrane PTS permeases interact with the fructose PTS (FruA/FruB) [1]. However, the biochemical and physiological significance of this finding was not known. We have carried out molecular genetic/biochemical/physiological studies that show that interactions of the fructose PTS often enhance, but sometimes inhibit the activities of other PTS transporters many fold, depending on the target PTS system under study. Thus, the glucose, mannose, mannitol and N- acetylglucosamine permeases exhibit enhancedin vivosugar transport and sometimesin vitroPEP-dependent sugar phosphorylation activities while the galactitol and trehalose systems show inhibited activities. This is observed when the fructose system is induced to high levels and prevented when thefruA/fruBgenes are deleted. Overexpression of thefruAand/orfruBgenes in the absence of fructose induction during growth also enhances the rates of uptake of other hexoses. The β-galactosidase activities ofman, mtl,andgat-lacZtranscriptional fusions and the sugar-specific transphosphorylation activities of these enzyme transporters were not affected either by frustose induction orfruABoverexpression, showing that the rates of synthesis and protein levels in the membrane of the target PTS permeases were not altered. We thus suggest that specific protein-protein interactions within the cytoplasmic membrane regulate transportin vivo(and sometimes the PEP-dependent phosphorylation activitiesin vitroof PTS permeases) in a physiologically meaningful way that may help to provide a hierarchy of preferred PTS sugars. These observations appear to be applicable in principle to other types of transport systems as well.
The Ca2+ Permeation Mechanism of the Ryanodine Receptor Revealed by a Multi-Site Ion Model
Authors: Zhang Aihua , Yu Hua , Liu Chunhong , Song Chen
Published: June 2019

The ryanodine receptors (RyR) are ion channels responsible for the release of Ca2+ from the sarco/endoplasmic reticulum and play a crucial role in the precise control of Ca2+ concentration in the cytosol. The detailed permeation mechanism of Ca2+ through RyR is still elusive. By using molecular dynamics simulations with a specially designed Ca2+ model, here we show that multiple Ca2+ accumulate in the upper selectivity filter of RyR1, but only one Ca2+ can enter and translocate in the narrow pore at a time. The Ca2+ is nearly fully hydrated during the whole permeation process, with the first solvation shell intact even at the narrowest constrict sites of the selectivity filter and gate. These results present a one-at-a-time permeation pattern for the hydrated ions, which is distinct from the fully/partially dehydrated knock-on permeation in K+ and Na+ channels and uncovers the underlying reason for the high permeability and low selectivity of the RyR channels.
Construction of (3,8)-connected three-dimensional cobalt(II) and copper(II) coordination polymers with 1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene and benzene-1,3,5-tricarboxylate ligands
Authors: Zhang Ya-Qian , Blatov Vladislav A. , Lv Xiu-Xiu , Tang Ding-Yi , Qian Lin-Lu , Li Ke , Li Bao-Long
Published: June 2019

Coordination polymers (CPs) have been widely studied because of their diverse and adjustable topologies and wide-ranging applications in luminescence, chemical sensors, magnetism, photocatalysis, gas adsorption and separation. In the present work, two coordination polymers, namely poly[(μ5-benzene-1,3,5-tricarboxylato-κ6
O
1:O
1′:O
3:O
3:O
5,O
5′){μ3-1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene-κ3
N:N′:N′′}di-μ3-hydroxido-dicobalt(II)], [Co2(C9H3O6)(OH)(C12H12N6)]
n
or [Co2(btc)(OH)(mtrb)]
n
, (1), and poly[[diaquabis(μ3-benzene-1,3,5-tricarboxylato-κ3
O
1:O
3:O
5)bis{μ3-1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene-κ3
N:N′:N′′}tetra-μ3-hydroxido-tetracopper(II)] monohydrate], {[Cu4(C9H3O6)2(OH)2(C12H12N6)2(H2O)2]·H2O}
n
or {[Cu4(btc)2(OH)2(mtrb)2(H2O)2]·H2O}
n
, (2), were synthesized by the hydrothermal method using 1,3-bis[(1,2,4-triazol-4-yl)methyl]benzene (mtrb) and benzene-1,3,5-tricarboxylate (btc3−). CP (1) exhibits a (3,8)-coordinated three-dimensional (3D) network of the 3,8T38 topological type, with a point symbol of {4,5,6}2{42·56·616·72·82}, based on the tetranuclear hydroxide cobalt(II) cluster [Co4(μ3-OH)2]. CP (2) shows a (3,8)-coordinated tfz-d topology, with a point symbol of {43}2{46·618·84}, based on the tetranuclear hydroxide copper(II) cluster [Cu4(μ3-OH)2]. The different (3,8)-coordinated 3D networks based on tetranuclear hydroxide–metal clusters of (1) and (2) are controlled by the different central metal ions [CoII for (1) and CuII for (2)]. The thermal stabilities and solid-state optical diffuse-reflection spectra were measured. The energy band gaps (E
g) obtained for (1) and (2) were 2.72 and 2.29 eV, respectively. CPs (1) and (2) exhibit good photocatalytic degradation of the organic dyes methylene blue (MB) and rhodamine B (RhB) under visible-light irradiation.
Temperature-dependent atomic B factor: an ab initio calculation
Authors: Malica Cristiano , Dal Corso Andrea
Published: June 2019

The Debye–Waller factor explains the temperature dependence of the intensities of X-ray or neutron diffraction peaks. It is defined in terms of the B matrix whose elements B
αβ are mean-square atomic displacements in different directions. These quantities, introduced in several contexts, account for the effects of temperature and quantum fluctuations on the lattice dynamics. This paper presents an implementation of the B factor (8π2
B
αβ) in the thermo_pw software, a driver of Quantum ESPRESSO routines that provides several thermodynamic properties of materials. The B factor can be calculated from the ab initio phonon frequencies and displacements or can be estimated, although less accurately, from the elastic constants, using the Debye model. The B factors are computed for a few elemental crystals: silicon, ruthenium, magnesium and cadmium; the harmonic approximation at fixed geometry is compared with the quasi-harmonic approximation where the B factors are calculated accounting for thermal expansion. The results are compared with the available experimental data.
Crystal structures of the naturally fused CS and cytochrome b
5 reductase (b
5R) domains of Ncb5or reveal an expanded CS fold, extensive CS–b
5R interactions and productive binding of the NAD(P)+ nicotinamide ring
Authors: Benson David R. , Lovell Scott , Mehzabeen Nurjahan , Galeva Nadezhda , Cooper Anne , Gao Philip , Battaile Kevin P. , Zhu Hao
Published: June 2019

Ncb5or (NADH-cytochrome b
5 oxidoreductase), a cytosolic ferric reductase implicated in diabetes and neurological diseases, comprises three distinct domains, cytochrome b
5 (b
5) and cytochrome b
5 reductase (b
5R) domains separated by a CHORD–Sgt1 (CS) domain, and a novel 50-residue N-terminal region. Understanding how interdomain interactions in Ncb5or facilitate the shuttling of electrons from NAD(P)H to heme, and how the process compares with the microsomal b
5 (Cyb5A) and b
5R (Cyb5R3) system, is of interest. A high-resolution structure of the b
5 domain (PDB entry 3lf5) has previously been reported, which exhibits substantial differences in comparison to Cyb5A. The structural characterization of a construct comprising the naturally fused CS and b
5R domains with bound FAD and NAD+ (PDB entry 6mv1) or NADP+ (PDB entry 6mv2) is now reported. The structures reveal that the linker between the CS and b
5R cores is more ordered than predicted, with much of it extending the β-sandwich motif of the CS domain. This limits the flexibility between the two domains, which recognize one another via a short β-sheet motif and a network of conserved side-chain hydrogen bonds, salt bridges and cation–π interactions. Notable differences in FAD–protein interactions in Ncb5or and Cyb5R3 provide insight into the selectivity for docking of their respective b
5 redox partners. The structures also afford a structural explanation for the unusual ability of Ncb5or to utilize both NADH and NADPH, and represent the first examples of native, fully oxidized b
5R family members in which the nicotinamide ring of NAD(P)+ resides in the active site. Finally, the structures, together with sequence alignments, show that the b
5R domain is more closely related to single-domain Cyb5R proteins from plants, fungi and some protists than to Cyb5R3 from animals.
Exhaust toxicity evaluation in a gas turbine engine fueled by aviation fuel containing synthesized hydrocarbons
Authors: Gawron Bartosz , Białecki Tomasz , Janicka Anna , Zawiślak Maciej , Górniak Aleksander
Published: June 2019

Purpose

The purpose of this paper is to examine the toxicological impacts of exhaust generated during the combustion process of aviation fuel containing synthesized hydrocarbons.

Design/methodology/approach

Tests on aircraft turbine engines in full scale are complex and expensive. Therefore, a miniature turbojet engine was used in this paper as a source of exhaust gases. Toxicity was tested using innovative BAT–CELL Bio–Ambient Cell method, which consists of determination of real toxic impact of the exhaust gases on the human lung A549 and mouse L929 cells. The research was of a comparative nature. The engine was powered by a conventional jet fuel and a blend of conventional jet fuel with synthesized hydrocarbons.

Findings

The results show that the BAT–CELL method allows determination of the real exhaust toxicity during the combustion process in a turbine engine. The addition of a synthetic component to conventional jet fuel affected the reduction of toxicity of exhaust gases. It was confirmed for both tested cell lines.

Originality/value

In the literature related to the area of aviation, numerous publications in the field of testing the emission of exhaust gaseous components, particulates or volatile organic compounds can be found. However, there is a lack of research related to the evaluation of the real exhaust toxicity. In addition, it appears that the data given in aviation sector, mainly related to the emission levels of gaseous exhaust components (CO, Nox and HC) and particulate matters, might be insufficient. To fully describe the engine exhaust emissions, they should be supplemented with additional tests, i.e. in terms of toxicity.
The impact of incentive framing format and language congruency on readers’ post-reading responses to email advertisements
Authors: Leung Daniel , Tsou Megan
Published: June 2019

Purpose

This paper aims to examine how incentive framing format and language congruency interactively influence readers’ post-reading responses to hotel-related email advertisements.

Design/methodology/approach

A 2 (incentive framing format: amount-off versus percentage-off) × 2 (language congruency: use of readers’ native language versus use of readers’ foreign language) between-subject experiment was conducted with 233 bilingual speakers from China.

Findings

The findings unveil that readers are more likely to be enticed to search for more information about the promoted hotel restaurant, click the call-to-action button and share the promotional message with friends and families if an email advertisement presents the incentive of a price promotion in the form of amount-off (versus percentage-off). The indirect impact of language congruency is also verified. Specifically, the impact of incentive framing format on readers’ post-reading response is more salient when information is communicated using readers’ native (versus non-native) language.

Practical implications

The findings provide actionable clues for hoteliers to optimize their email marketing campaigns. If hotels want to publicize a price promotion for their high-priced service (e.g. hotel restaurant dining) via email advertisements, marketers should present the incentive in the form of amount-off. Hotels should also personalize the language used in the email advertisements according to readers’ native language.

Originality/value

This study enriches the literature on email marketing by explicating how hoteliers can improve the efficacy of email marketing via personalizing the incentive framing format and language used in the email advertisement according to the readers’ preferences.
An empirical analysis of rural farmers’ financing intention of inclusive finance in China
Authors: Aisaiti Gulizhaer , Liu Luhao , Xie Jiaping , Yang Jun
Published: June 2019

Purpose

The purpose of this paper is to investigate and understand China’s rural farmers’ financing intention of inclusive finance, and it examines related drivers like knowledge of inclusive finance, perceived benefits and perceived risks of ordering finance. Besides, the social enterprise embeddedness and digital finance are integrated into the conceptual model to further investigate their moderating impact.

Design/methodology/approach

The authors designed an inclusive finance intention model to examine the relations between dependent variable knowledge of inclusive finance, intermediary variables perceived benefits and perceived risks of ordering finance and the independent variable financing intention of inclusive finance. The embeddedness of social enterprise and digital finance were identified as modifying factors. Both exploratory and conclusive research strategies were applied. A structured questionnaire was developed to collect empirical data from the rural areas of China.

Findings

It suggests that knowledge of inclusive finance can strengthen both perceived benefits and perceived risk of ordering finance. Interestingly, the embeddness of social enterprise can significantly reduce risk perceptions and improve perceived benefits of ordering finance. Furthermore, perceived benefits of ordering finance can positively enhance rural farmers’ financing intention of inclusive finance, whereas perceived risks can negatively influence the financing intention. Moreover, digital finance as a modifying factor can significantly strengthen the positive correlation between perceived benefits of ordering finance and financing intention of inclusive finance.

Practical implications

The research indicates that a systematic inclusive finance educational project is needed to enhance rural farmers’ understanding of inclusive finance and its components. Moreover, the study reveals that it is crucial to promote social enterprise participation and digital finance to develop inclusive finance in rural China, as the service attributes of social enterprise and efficiency of digital finance can greatly reduce the existing transaction cost of farmers.

Originality/value

The conceptual model would potentially contribute to researchers interested in investigating the financing intention of inclusive financial services relating to rural population. The integration of social enterprise embeddedness and digital finance is the uniqueness of this research conceptual model.
Pitfall benchmarking of cleaning costs in hospitals
Authors: Koch David , Eitzinger Sabrina
Published: June 2019

Purpose

It is typical of public real estate benchmarking reports to show only highly aggregated benchmarks based on buildings’ floor areas. They hardly provide disaggregated benchmarks for usage clusters. The aim of this study is to show the caveats from highly aggregated benchmarking without consideration of cluster-specific characteristics.

Design/methodology/approach

Based on the parameters of the German facility management association 812 standards, cleaning costs and costs for the surfaces of seven hospitals have been collected and allocated to specific room clusters. Using these basic data, a calculation and simulation conducted with the aim of simulating facilities that are comparable in the sum of costs yet feature varying sub-clusters as cost drivers. In particular, during this simulation, area ratios were varied randomly and the average cleaning costs per cluster were held constant for all hospitals. Therefore, the costs per square meter in the clusters of all simulated hospitals are identical and the full costs only depend on the area ratios.

Findings

The simulation shows that highly aggregated cleaning costs lead to large spans, and thus, to misinterpretations in the field of action. In the case, the aggregate benchmark ranges from 40.6 to 66.5 EUR/m², although, for all hospitals the same costs per square meter had been used. Thus, the bias results only from varying the share of area across the clusters. This finding is caused by a well-known statistical problem: the Simpson’s paradoxon, which currently receives little attention in real estate benchmarking.

Practical implications

The results show, that the regular benchmarking with high aggregated data, often used in practice, cannot be recommended. The author consider using a detailed benchmarking as meaningful and purposeful. To be able to make a detailed benchmarking, it is essential to identify and collect the influencing factors. Only if all important factors, in this case, the clusters will be regarded in the benchmarking, a reasonable benchmarking and useful interpretation can be given. Using a simple benchmarking to get a rough overview is refused steadfastly.

Originality/value

The study highlights that a comparison with public benchmarking reports (operation costs) must be taken with great caution. The author has quantified the bias from the aggregated benchmarking and have shown, that the Simpson’s paradox fully explains the consequences.