bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body size as a magic trait in two plant-feeding insect species
Authors: Glover Ashleigh N. , Bendall Emily E. , Terbot John W. , Payne Nicole , Webb Avery , Filbeck Ashley , Norman Gavin , Linnen Catherine R. 
Published: October 2022

AbstractWhen gene flow accompanies speciation, recombination can decouple divergently selected loci and loci conferring reproductive isolation. This barrier to sympatric divergence disappears when assortative mating and disruptive selection involve the same “magic” trait. Although magic traits could be widespread, the relative importance of different types of magic traits to speciation remains unclear. Because body size frequently contributes to host adaptation and assortative mating in plant-feeding insects, we evaluated several magic trait predictions for this trait in a pair of sympatricNeodiprionsawfly species adapted to different pine hosts. A large morphological dataset revealed that sawfly adults from populations and species that use thicker-needled pines are consistently larger than those that use thinner needled-pines. Fitness data from recombinant backcross females revealed that egg size is under divergent selection between the preferred pines. Lastly, mating assays revealed strong size-assortative mating within and between species in three different crosses, with the strongest prezygotic isolation between populations that have the greatest interspecific size differences. Together, our data support body size as a magic trait in pine sawflies and possibly many other plant-feeding insects. Our work also demonstrates how intraspecific variation in morphology and ecology can cause geographic variation in the strength of prezygotic isolation.
Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy
Authors: Rodriguez Jonathan , Iniguez Abdon , Jena Nilamani , Tata Prasanthi , Liu Joan , Lander Arthur D. , Lowengrub John S. , Van Etten Richard A. 
Published: October 2022

AbstractChronic myeloid leukemia (CML) is a blood cancer characterized by dysregulated production of maturing myeloid cells driven by the product of the Philadelphia chromosome, the BCR-ABL1 tyrosine kinase. Tyrosine kinase inhibitors (TKI) have proved effective in treating CML but there is still a cohort of patients who do not respond to TKI therapy even in the absence of mutations in the BCR-ABL1 kinase domain that mediate drug resistance. To discover novel strategies to improve TKI therapy in CML, we developed a nonlinear mathematical model of CML hematopoiesis that incorporates feedback control and lineage branching. Cell-cell interactions were constrained using an automated model selection method together with previous observations and newin vivodata from a chimericBCR-ABL1transgenic mouse model of CML. The resulting quantitative model captures the dynamics of normal and CML cells at various stages of the disease and exhibits variable responses to TKI treatment, consistent with those of CML patients. The model predicts that an increase in the proportion of CML stem cells in the bone marrow would decrease the tendency of the disease to respond to TKI therapy, in concordance with clinical data and confirmed experimentally in mice. The model further suggests that a key predictor of refractory response to TKI treatment is an increased probability of self-renewal of normal hematopoietic stem cells. We use these insights to develop a clinical prognostic criterion to predict the efficacy of TKI treatment and to design strategies to improve treatment response. The model predicts that stimulating the differentiation of leukemic stem cells while applying TKI therapy can significantly improve treatment outcomes.
Development of a polymicrobial checkerboard assay as a tool for determining combinatorial antibiotic effectiveness in polymicrobial communities
Authors: Black Caroline , Al Mahmud Hafij , Wilson Sabrina , Smith Allie C. , Wakeman Catherine A. 
Published: October 2022

ABSTRACTAIMSTo establish a methodology for identifying the effects of combinatorial antibiotic treatment on individual members of a polymicrobial community.METHODS AND RESULTSBoth gentamicin and ceftazidime were diluted to concentrations ranging from 0.06 μg ml-1to 128 μg ml-1. An equal ratio polymicrobial community ofStaphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, andAcinetobacter baumanniiwas inoculated into the combined antibiotics in the checkerboard and incubated for 18 hours in static conditions. After incubation, visible turbidity of the overall community was recorded, and bacteria from the wells were diluted to 10-3and then spot plated on selective and differential media. After 24 hours, colony-forming unit (CFU) counts were obtained for each species.CONCLUSIONSVisible turbidity is not truly indicative of cell viability, and the polymicrobial community can decrease the antibiotic susceptibility ofP. aeruginosa, rendering the clinically-established beneficial combination of gentamicin and ceftazidime ineffective.SIGNIFICANCEPrevious checkerboard methodology which focuses on using visible turbidity to determine monomicrobial antibiotic susceptibility fails to account for polymicrobial cooperation that has been shown to reduce antibiotic efficacy. Our new methodology could be implemented in clinical microbiology laboratories with minimal impact on the overall time for diagnosis.
Upper Limit Efficiency Estimates for Electromicrobial Production of Drop-In Jet Fuels
Authors: Sheppard Timothy J. , Specht David , Barstow Buz 
Published: October 2022

AbstractMicrobes which participate in extracellular electron uptake or H2oxidation have an extraordinary ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be of particular value in the efficient production of hydrocarbon blends for use in aviation. Because of exacting standards for fuel energy density and the costs of new aviation infrastructure, liquid hydrocarbon fuels will be necessary for the foreseeable future, precluding direct electrification. Production of hydrocarbons using electrically-powered microbes employing fatty acid synthesis-based production of alkanes could be an efficient means to produce drop-in replacement jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-energy conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency iswhen using extracellular electron uptake for electron delivery andwhen using H2-oxidation. The efficiency of production of the jet fuel blend can be raised towhen using the Formolase formate-assimilation pathway and H2-oxidation, and towith the Wood-Ljungdahl pathway. The production efficiency can be further raised by swapping the well-known ADO pathway for alkane termination with for the recently discovered MCH pathway. If these systems were were supplied with electricity with a maximally-efficient silicon solar photovoltaic, even the least efficient would exceed the maximum efficiency of all known forms of photosynthesis.
Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic
Authors: Aranega-Bou Paz , Brown Natalie , Stigling Abigail , D’Costa Wilhemina , Verlander Neville Q , Pottage Thomas , Bennett Allan , Moore Ginny 
Published: October 2022

AbstractThe virucidal activity of a quaternary ammonium compound (QAC)-based antimicrobial coating used by the UK rail industry during the COVID-19 pandemic was evaluated using the bacteriophage ϕ6 as a surrogate for SARS-CoV-2. Immediately after application and in the absence of interfering substance, the product showed efficacy (>3 log10reduction) on some materials typically used in rail carriages (stainless steel, high pressure laminate and plastic), variable efficacy on glass and no efficacy (<3 log10reduction) on a train armrest made of Terluran 22. If, after application of the product, the surfaces remained undisturbed, the antimicrobial coating retained its efficacy for at least 28 days on all materials where it was effective immediately after application. However, regardless of the material coated or time since application, the presence of organic debris (fetal bovine serum) significantly reduced the viricidal activity of the coating. Wiping the surface with a wetted cloth after organic debris deposition was not sufficient to restore efficacy. We conclude that the product is likely to be of limited effectiveness in a busy multi-user environment such as public transport.ImportanceThis study evaluated the performance of a commercially available antimicrobial coating used by the transport industry in the UK during the COVID-19 pandemic. While the product initially showed efficacy against ϕ6 when applied to some materials, when organic debris was subsequently deposited, the efficacy was severely diminished and could not be recovered through wiping (cleaning) the surface. This highlights the importance of including relevant materials and conditions when evaluating antimicrobial coatings in the laboratory. Further efforts are required to identify suitable infection prevention and control practices for the transport industry.
Biometric linkage of longitudinally collected electronic case report forms and confirmation of subject identity: An open framework for ODK and related tools
Authors: Roberts Chrissy h , Stott Callum , Shawe-Taylor Marianne , Chaudhry Zain , Lal Sham , Marks Michael 
Published: October 2022

ABSTRACTThe availability of low-cost biometric hardware sensors and software makes it possible to rapidly, affordably and securely sample and store a unique and invariant biological signature (or biometric “template”) of participants in research and trials. This has applications in consent, linkage of case reporting forms collected at different times, and in confirmation of participant identity for purposes of safety monitoring and adherence to international data laws.The use of mobile electronic data collection software has recently become commonplace in clinical trials and research. A raft of tools based on the open-source ODK project now provide diverse options for data management that work consistently in resource-restricted settings, but none have built-in functionality for capturing biometric templates.In this study, we report the development and testing of a novel open-source app and associated method for capturing and matching biometric fingerprint templates during data collection with the popular data platforms ODK, KoBoToolbox, SurveyCTO, Ona and CommCare.Using data from more than 1000 fingers, we show that fingerprint templates can be used to link data forms with high accuracy and that this accuracy increases with the addition of multiple fingerprints on each data form. By focussing on publishing open-source code and documentation, and by using an affordable (<£50) and mass-produced model of fingerprint sensor, we are able to make this platform freely available to the large global user community that utilises ODK and related data collection systems.
Identifying Contextual and Spatial Risk Factors for Post-Acute Sequelae of SARS-CoV-2 Infection: An EHR-based Cohort Study from the RECOVER Program
Authors: Zhang Yongkang , Hu Hui , Fokaidis Vasilios , Lewis V Colby , Xu Jie , Zang Chengxi , Xu Zhenxing , Wang Fei , Koropsak Michael , Bian Jiang , Hall Jaclyn , Rothman Russell L. , Shenkman Elizabeth A. , Wei Wei-Qi , Weiner Mark G. , Carton Thomas W. , Kaushal Rainu 
Published: October 2022

AbstractPost-acute sequelae of SARS-CoV-2 infection (PASC) affects a wide range of organ systems among a large proportion of patients with SARS-CoV-2 infection. Although studies have identified a broad set of patient-level risk factors for PASC, little is known about the contextual and spatial risk factors for PASC. Using electronic health data of patients with COVID-19 from two large clinical research networks in New York City and Florida, we identified contextual and spatial risk factors from nearly 200 environmental characteristics for 23 PASC symptoms and conditions of eight organ systems. We conducted a two-phase environment-wide association study. In Phase 1, we ran a mixed effects logistic regression with 5-digit ZIP Code tabulation area (ZCTA5) random intercepts for each PASC outcome and each contextual and spatial factor, adjusting for a comprehensive set of patient-level confounders. In Phase 2, we ran a mixed effects logistic regression for each PASC outcome including all significant (false positive discovery adjusted p-value < 0.05) contextual and spatial characteristics identified from Phase I and adjusting for confounders. We identified air toxicants (e.g., methyl methacrylate), criteria air pollutants (e.g., sulfur dioxide), particulate matter (PM2.5) compositions (e.g., ammonium), neighborhood deprivation, and built environment (e.g., food access) that were associated with increased risk of PASC conditions related to nervous, respiratory, blood, circulatory, endocrine, and other organ systems. Specific contextual and spatial risk factors for each PASC condition and symptom were different across New York City area and Florida. Future research is warranted to extend the analyses to other regions and examine more granular contextual and spatial characteristics to inform public health efforts to help patients recover from SARS-CoV-2 infection.
Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation
Authors: Fujita Hideaki , Kaneshiro Junichi , Takeda Maki , Sasaki Kensuke , Yamamoto Rikako , Umetsu Daiki , Kuranaga Erina , Higo Shuichiro , Kondo Takumi , Asano Yasuhiro , Sakata Yasushi , Miyagawa Shigeru , Watanabe Tomonobu M 
Published: October 2022

AbstractEstimation of dynamic change of crossbridge formation in living cardiomyocytes is expected to provide crucial information for elucidating cardiomyopathy mechanisms, efficacy of an intervention, and other parameters. Here, we developed an assay system to dynamically measure second harmonic generation (SHG) polarization in pulsating cardiomyocyte and proved that the SHG anisotropy derived from myosin filaments in disease-model cardiomyocytes depended on their crossbridge status, providing an evaluation method for myosin force generation. Experiments utilizing an inheritable mutation that induces excessive myosin-actin interactions revealed that the correlation between sarcomere length and SHG anisotropy represents crossbridge formation ratio during pulsation. Furthermore, the present method found that ultraviolet irradiation induced an increased population of attached crossbridges that lost force-generating ability upon myocardial differentiation, causing acquired dysfunction. Taking an advantage of infrared two-photon excitation in SHG microscopy, myocardial dysfunction could be intravitally evaluated in aDrosophiladisease model. Thus, along with the establishment of the methodology, we successfully demonstrated the applicability and effectiveness of the present method to evaluate the actomyosin activity of a drug or genetic defect on living cardiomyocytes.
Obscurin Rho GEF domains are phosphorylated by MST-family kinases but do not exhibit nucleotide exchange factor activity towards Rho GTPasesin vitro
Authors: Koch Daniel , Kho Ay Lin , Fukuzawa Atsushi , Alexandrovich Alexander , Beavil Andrew , Pfuhl Mark , Rees Martin , Gautel Mathias 
Published: October 2022

AbstractObscurin is a giant muscle protein (>800 kDa) featuring multiple signalling domains, including an SH3-DH-PH domain triplet from the Trio-subfamily of guanosine nucleotide exchange factors (GEFs). While previous research suggests that these domains can activate the small GTPases RhoA and RhoQ in cells,in vitrocharacterization of these interactions using biophysical techniques has been hampered by the intrinsic instability of obscurin GEF domains. To study substrate specificity, mechanism and regulation of obscurin GEF function by individual domains, we successfully optimized recombinant production of obscurin GEF domains and found that MST-family kinases phosphorylate the obscurin DH domain at Thr5798. Despite extensive testing of multiple GEF domain fragments, we did not detect any nucleotide exchange activityin vitroagainst 9 representative small GTPases. Bioinformatic analyses show that obscurin differs from other Trio-subfamily GEFs in several important aspects. While further research is necessary to evaluate obscurin GEF activityin vivo, our results indicate that obscurin has atypical GEF domains that, if catalytically active at all, are subject to complex regulation.
Crystal structure of the capsular polysaccharide-synthesis enzyme CapG from Staphylococcus aureus
Authors: Tien Ni , Ho Chien-Yi , Lai Shu-Jung , Lin Yu-Chuan , Yang Chia-Shin , Wang Yu-Chuan , Huang Wei-Chien , Chen Yeh , Chang Jui-Jen 
Published: October 2022

Bacterial capsular polysaccharides provide protection against environmental stress and immune evasion from the host immune system, and are therefore considered to be attractive therapeutic targets for the development of anti-infectious reagents. Here, we focused on CapG, one of the key enzymes in the synthesis pathway of capsular polysaccharides type 5 (CP5) from the opportunistic pathogen Staphylococcus aureus. SaCapG catalyses the 2-epimerization of UDP-N-acetyl-D-talosamine (UDP-TalNAc) to UDP-N-acetyl-D-fucosamine (UDP-FucNAc), which is one of the nucleotide-activated precursors for the synthesis of the trisaccharide repeating units of CP5. Here, the cloning, expression and purification of recombinant SaCapG are reported. After extensive efforts, single crystals of SaCapG were successfully obtained which belonged to space group C2 and exhibited unit-cell parameters a = 302.91, b = 84.34, c = 145.09 Å, β = 110.65°. The structure was solved by molecular replacement and was refined to 3.2 Å resolution. The asymmetric unit revealed a homohexameric assembly of SaCapG, which was consistent with gel-filtration analysis. Structural comparison with UDP-N-acetyl-D-glucosamine 2-epimerase from Methanocaldococcus jannaschii identified α2, the α2–α3 loop and α10 as a gate-regulated switch controlling substrate entry and/or product release.
Perceived quality of life in patients with heart failure: a cross-sectional study among adults in Kingdom of Bahrain
Authors: Ghuloom Amina Mohamed , Sanad Hala Mohamed 
Published: October 2022

PurposeThe aim of this study is to assess the perceived quality of life of Bahraini patients with heart failure.Design/methodology/approachA sample of 250 patients aged 18 years and older was recruited using a cross-sectional design. Minnesota Living with Heart Failure Questionnaire version three was employed to obtain data from participants on their socio-demographic characteristics and their perceived quality of life.FindingsThe mean age of patients was 69.0 ± 8.1 years and 78% were males. Almost half of the patients with third/fourth degree heart failure had difficulties in earning a living (48.4%) since they had long periods of hospital stays (49.2%). The quality of life is inversely proportional to the age of the patients with third/fourth degree heart failure (p < 0.001). Most of the patients had a poor quality of life (74.8%); about 21.6% had a moderate quality of life, while only few patients (3.6%) had a good quality of life.Originality/valueThe quality of life among Bahraini patients diagnosed with third/fourth degree heart failure is generally poor. Further, advanced age, low level of education, not currently married and low income were shown to be associated with poor quality of life. A need exists to include a quality of life assessment tool as part of the management of these patients.
A unified general framework for small and finite strain two-invariants elastoplasticity
Authors: Spiezia Nicolò , Salomoni Valentina Anna Lia 
Published: October 2022

PurposeThis paper proposes a unified original general framework, designed to theoretically develop and to extremely easily implement elastoplastic constitutive laws defined in the so called two-invariants space, both in small and finite strain regime.Design/methodology/approachA general return mapping algorithm is proposed, and particularly a standard procedure is developed to compute the two algorithmic tangent operators, required to solve the Newton–Raphson scheme at the local and global level and thus cast the elastoplastic algorithm within a FEM code.FindingsThis work demonstrates that the proposed procedure is fully general and can be applied whatever is the elastic law, the yield surface, the plastic potential function and the hardening law. Several numerical examples are reported, not only to demonstrate the accuracy and robustness of the algorithm, but also explain how to use this general algorithm also in other applications.Originality/valueThe proposed algorithm and its numerical implementation into a FEM code is new and original. The usefulness and the value of the algorithm is twofold: (1) it can be implemented in a small and finite strain simulation FEM code, in order to handle different types of constitutive laws in the same modular way, thus fully leveraging on modern object-oriented coding approach; (2) it can be used as a framework to develop (and then to implement) new constitutive models, since the researcher can simply define the relevant functions (and its main derivatives) and automatically get the numerical algorithm.
Opposing brand activism: triggers and strategies of consumers’ antibrand actions
Authors: Pöyry Essi , Laaksonen Salla-Maaria 
Published: October 2022

Purpose
In brand activism, a brand promotes contested sociopolitical causes to highlight its values. Brand activism also alienates those consumers who disagree with the cause, who might, consequently, target the brand with critical, negative or even aggressive actions. This paper aims to study the triggers and strategies of consumers’ antibrand actions given in response to brand activism.

Design/methodology/approach
Qualitative content analysis and multiple correspondence analysis were used to study consumer responses directed at a chocolate brand’s campaign that advocated civilized online conversions and opposed hate speech, a politically heated topic. In total, 1,615 messages were collected from social media platforms.

Findings
Field infringement, political accusations and questioned impact of the campaign triggered consumers to turn against the campaign. Strategies to undermine it included boycotting, discrediting the brand and trapping. Trapping – creatively using technological affordances to create harm to the brand – was typically triggered by political associations.

Research limitations/implications
Findings relate to the critical responses regarding one campaign only.

Practical implications
By understanding the political discussion around the chosen cause, including the opponents’ typical triggers and strategies, brand activism can more credibly advocate for contested social causes and communicate brand values.

Originality/value
Political antibrand actions are distinct from the previously identified functional and ethical antibrand actions, and they are noninstrumental by nature. Practices that are native to social media are central to political antibrand actions, and social media platforms contribute to how such disappointment is articulated and acted upon.