bluuebunny/crossref_metadata_2025 huggingface dataset:
Amplitude and phase relations in a two-circuit parametric circuit of ferroresonance nature
Authors: Bedritsky Ivan , Jurayeva Kamila , Nazirova Zamira , Bazarov Laziz
Published: June 2021

The article presented a mathematical analysis of a double-circuit parametric circuit of ferroresonance nature at the fundamental frequency, performed by the harmonic balance method. The adjustment, current-voltage, and load characteristics of the circuit are given. The possibility of using this circuit in voltage regulators with direct current output is proved. Parametric sources of secondary power supply, in particular voltage stabilizers of ferromagnetic and ferroresonance nature, are used in autonomous vehicles (for example, in spacecraft, some types of intelligent transport systems) and in renewable energy sources due to their ability to operate in heavy environments (high and low temperatures, radiation, strong magnetic or electric fields).
Study of the electrical resistance, electrical strength and angle of separation of rice seeds from the drum surface
Authors: Aslanova Gulnoz , Charieva Makhbuba , Shoyimova Solikha , Sirojov Anvar , Pirnazarov Shokhruh
Published: June 2021

The article provides information on the “Dielectric” device for sorting seeds of agricultural crops and the results of theoretical research on seed sorting. The results of theoretical experiments showed that the diameter and number of turns of the working body of the device for sorting rice seeds in the “Dielectric” device, the expected result can be achieved by applying high voltage to the electrodes with opposite signals.
The usage of a combined machine in the process of preparing the land for planting
Authors: Juraev F. , KHamroyev G. , KHaydarova Z. , KHamroyev I. , Ibodov I.
Published: June 2021

The existing traditional technologies of land preparation, such as leveling, chiseling, harrowing, mulching, and many other agro-technical measures performed by separate units, are labor-intensive, which costly and overspending on material costs, where fuel consumption is 78-86 liters per hectare. In the unit that prepares the lands, we are proposing planting in one pass, five agrotechnical tillage operations were carried out at one time, and 35-45 l of fuel consumption was observed while each hectare of land was being tilled. Based on the research results on the efficiency of presowing tillage and the results of scientific research to increase the efficiency of this type of aggregates, an optimal variant of a combined aggregate is prepared and used for the direct preparation of lands for planting.
Synthesis of diamonds in the C – Mn - Ni - (H) system and the diamond-shaped mechanism
Authors: Negmatova Kamola , Daminov Abdusattor , Umarov Abdusalam , Аbed Nodira
Published: June 2021

Studying the dependence of the degree (α) and rate (ϑ) of the phase transformation of graphite into diamond on the synthesis time at different temperatures of the developed synthetic diamonds using the technology of high-pressure high-temperature synthesis in a metal melt (HPHT), we determined the critical mass of diamonds, which indicates the entry of the system into the stability region of graphite, where the graphitization of diamonds occurs. The role of implanted metals and hydrogen in the formation of synthetic diamonds and on its properties was also investigated.
Modeling the steering wheel influence by the driver on the vehicle's motion stability
Authors: Аkhmedov Doniyor , Alimukhamedov Shavkat , Tursunov Ibragim , Narziev Soyib , Riskaliev Davron
Published: June 2021

In this article, a mathematical model was developed to influence the intensity of the steering wheel turn by the driver on the vehicle's stability. Comparison of the developed mathematical model with the experiment results made it possible to establish their adequacy. The effect of the three conditional drivers on the intensity of the steering wheel was examined. When performing the 'J-turn' maneuver, comparing the indices of the 1st, 2nd and 3rd conditional drivers, their proximity to the requirements of the standard was established. It was found that the indices of the second conditional driver are closest to the standard requirements. When performing the 'Single Lane Change' maneuver by the first conventional driver, the standard deviation value from the specified trajectory was 0.102, and the correlation index was 0.88.
Substantiation of the selector drum parameters of the universal seeding device of the innovative seeder
Authors: Farmonov Erkin , Khudayarov B , Abdillaev T , Farmonova F
Published: June 2021

A review of technologies for sowing non-loose seeds of forage plants shows that seeders and devices that fully meet the requirements of agricultural technology have not yet been created. The available tools do not provide a stable sowing of seeds and their uniform placement in the field, so the distances between the nests are not the same in a row. The authors recommend designing the sampling drum for an innovative universal seeding machine with measuring grooves that ensure the same distance between the seed nests in a row, corresponding to the agrotechnical requirements for seeds. The main requirement when creating a seeder was the need to determine the number of grooves that determine the distance between the nests at different speeds of the unit. In addition, it is also required to ensure that the measuring grooves are filled with the required amount of seeds, which depends on the speed of rotation of the sampling drum. Based on preliminary laboratory experiments and theoretical studies, the optimal parameters of the sampling drum were determined: the diameter of the sampling drum is 100 mm; the speed of rotation of the sampling drum is 8-15 rpm; the number of measuring grooves – 10-12 pieces. These parameters at a speed of MTA -1.44 m/s provide the distance between the seed nests in a row and are 0.5-0.7 m.
Technology of obtaining a binder for the base of asphalt roads and roofing
Authors: Shukrullaev Botir , Bekturdiev Gulom , Isaev Nurbek , Omonov Saidbek
Published: June 2021

Processing of the local Mubarek oil sludge with subsequent production of a binder for the foundation of highways and roofing. Methods of the utilization of oil sludge were used to obtain a binder. Innovative technology for the production of asphalt pavement by the oxidation method has been developed. Investigations of the chemical composition of the binder for asphalt roads and elemental analysis of dehydration of oil sludge and its homogeneous state are presented.
Generalized dynamic model of hydrodynamic vibration dampener subject to viscous damping
Authors: Khromova Galina , Makhamadalieva Malika , Khromov Sergey
Published: June 2021

Use as an elastic body of the working fluid improves the efficiency of the hydraulic damper, reliability, and durability, in this case, the issues of improving the reliability of existing locomotives hydraulic dampers by upgrading separate the components for major repairs with the extension of the useful life are relevant. To increase the efficiency of damping dynamic vibrations and reduce the load on the support units and running gear elements, a modernized design of a hydro friction damper with improved damping properties was developed, for which an application was filed for the Patent of the Republic of Uzbekistan for Invention No. IAP 2021 0002.
Les phénomènes climatiques extrêmes en France
Authors:   La rédaction
Published: June 2021

De quelle nature sont les phénomènes climatiques extrêmes en France ? Comment évoluent-ils et comment les étudie-t-on ? Décryptage avec Jean-Michel Soubeyroux, directeur scientifique adjoint de la climatologie et des services climatiques à Météo France
Development and Psychometric Assessment of a Manufacturer Independent Knowledge Questionnaire on Real Time Continuous Glucose Monitoring for insulin-treated People with Diabetes
Authors: Schlueter Sandra , Freckmann Guido , Wernsing Marita , Roelver Klaus-Martin , Joerdening Mia , Holder Martin , Heinemann Lutz , Lange Karin
Published: June 2021

Background To benefit from real-time continuous glucose monitoring (rtCGM), users need practical skills and in-depth knowledge to analyze the glucose data appropriately and adapt insulin therapy accordingly. To assess the user’s knowledge about rtCGM, a psychometric knowledge test was developed and evaluated.

Method Experts on the use of rtCGM systems defined central knowledge contents in a Delphi process and developed a knowledge test comprising 40 multiple-choice items. For test-statistical review, people with insulin-treated diabetes and members of diabetes teams answered the knowledge test.

Results The 122 diabetes team members (age 46 (11) years; mean (SD)) and the 111 people with insulin-treated diabetes (age 42 (14) years, diabetes duration 20 (14) years, users of insulin pumps 64 %, previous usage of rtCGM 38 %, HbA1c 8.0 % [95 % CI 7.7–8.3] (64 mmol/mol [60–67]) had different levels of experiences using rtCGM systems. The internal consistency (Cronbach’s alpha) of the knowledge test was 0.92 for the whole sample, for people with diabetes 0.94, and for diabetes team members 0.84. Item difficulty ranged between 0.12 and 0.88 in people with diabetes and between 0.27 and 0.97 among diabetes team members. On average, people with diabetes answered 24.1 (9.9) items correctly, diabetes team members 29.2 (5.2) (p < 0.001); people with diabetes and previous rtCGM-experience had a higher knowledge compared to people without previous experience (29.2 (6.2) vs. 21.0 (10.4) (p = 0.001)). The quality of glucose control (measured by HbA1c) of the people with diabetes was significantly associated with the sum-score of the questionnaire (rho = –0.48, p < 0.001).

Conclusion The “rtCGM-Profi-Check” knowledge test provides high internal consistency, high selectivity, and content validity. It is suitable for objective, reliable, and valid assessment of the indispensable knowledge of people with diabetes to use different rtCGM systems successfully. The questionnaire is manufacturer-independent and is suitable to evaluate the needs and success of rtCGM education among persons with diabetes.
Auditory Hallucinations: An Audiological Horizon?
Authors: Musiek Frank E. , Morris Sarah , Ichiba Kayla , Clark Liza , Davidson Alyssa J.
Published: June 2021

Abstract Background Interesting data and theories have emerged regarding auditory hallucinations (AHs) in patients with schizophrenia. The possibility that these patients may have changes in the anatomy of the auditory cortex and/or subcortical structures of
the central auditory nervous system and present with deficits on audiological tests is important information to the audiology community. However, it seems clear that, in general, audiologists are not sufficiently aware of these findings. Purpose There are two main purposes
of this article: (1) to educate audiologists about AHs related to schizophrenia and related issues, and (2) to encourage audiologists and hearing scientists to become involved in the evaluation and research of AHs. This fascinating disorder is one in which audiologists/hearing scientists are
well suited to make a significant contribution. Research Design A review and synthesis of the literature was conducted. Relevant literature was identified through PubMed, Google Scholar, as well as independent book chapters and article searches. Keywords driving the searches
were AHs, auditory illusions, verbal and musical hallucinations, schizophrenia, and central auditory disorders. Given the currency of the topic, the information collected was primarily between 1990 and 2020. Study Sample The review is organized around categorization, prevalence,
models, mechanisms, anatomy, pathophysiology, and audiological correlates related to AHs. Data Collection and Analysis Searches were conducted using well-known search engines and manual searches by each author. This information on AHs was then analyzed collectively by the authors
for useful background and relevance, as well as important for the field of audiology. Results Several anatomical, physiological, and functional imaging studies have shown compromise of the auditory cortex in those with schizophrenia and AHs. Potentially related to this, are
studies that demonstrated sub-par performance on behavioral audiologic measures for this unique clinical population. These findings align well with the kind of hearing disorder for which audiologists are well-trained to make significant contributions. Conclusion Neurobiological
and audiological evidence is accumulating on patients with schizophrenia and AH potentially rendering it as both an auditory and psychiatric disorder. Audiologists should consider expanding their horizon and playing a role in the clinical investigation of this disorder.
Atrial Fibrillation, Oral Anticoagulants, and Concomitant Active Cancer: Benefits and Risks
Authors: Atterman Adriano , Friberg Leif , Asplund Kjell , Engdahl Johan
Published: June 2021

Aim To determine to what extent active cancer influences the benefit–risk relationship among patients with atrial fibrillation receiving oral anticoagulants for stroke prevention.

Methods In this cohort study of all patients with atrial fibrillation in the Swedish Patient register during 2006 to 2017, 8,228 patients with active cancer and 323,394 without cancer were followed up to 1 year after initiation of oral anticoagulants. Cox regression models, adjusting for confounders and the competing risk of death, were used to assess risk of cerebrovascular and bleeding events.

Results Among patients treated with oral anticoagulants, the risk for cerebrovascular events did not differ between cancer patients and noncancer patients (subhazard ratio [sHR]: 1.12, 95% confidence interval [CI]: 0.98–1.29). Cancer patients had a higher risk for bleedings (sHR: 1.69, CI: 1.56–1.82), but not for fatal bleedings (sHR: 1.17, CI: 0.80–1.70). Use of nonvitamin K oral anticoagulants was associated with lower risk of both cerebrovascular events and bleedings compared with warfarin.

Conclusion Patients with atrial fibrillation and active cancer appear to have similar net cerebrovascular benefit of oral anticoagulant treatment to patients without cancer, despite an increased risk of nonfatal bleedings. Use of nonvitamin K oral anticoagulants was associated with lower risk of all studied outcomes.
Tone Burst Masseter Vestibular Evoked Myogenic Potentials: Normative Values and Test‐Retest Reliability
Authors: Vignesh Sangu Srinivasan , Singh Niraj Kumar , Rajalakshmi Krishna
Published: June 2021

Abstract Background Masseter vestibular evoked myogenic potential (mVEMP) is a recent tool for the assessment of vestibular and trigeminal pathways. Though a few studies have recorded mVEMP using click stimuli, there are no reports of these potentials using the
more conventional VEMP eliciting stimuli, the tone bursts. Purpose The aim of the study is to establish normative values and determine the test‐retest reliability of tone burst evoked mVEMP. Research Design The research design type is normative study
design. Study Sample Forty-four healthy participants without hearing and vestibular deficits in the age range of 18 to 50 years participated in the study. Data Collection and Analysis All participants underwent mVEMP testing using 500 Hz tone-burst stimuli
at 125 dB peSPL. Ten participants underwent second mVEMP testing within 1 month of the initial testing to estimate the test‐retest reliability. Results Tone burst mVEMP showed robust responses in all participants. There were no significant ear and sex differences
on any mVEMP parameter (p > 0.05); however, males had significantly higher EMG normalized peak-to-peak amplitude than females. Intraclass correlation coefficient (ICC) values of tone burst mVEMP showed excellent test‐retest reliability (ICC >0.75) for ipsilateral
and contralateral p11 latency, ipsilateral EMG normalized p11-n21 peak to peak amplitude, and amplitude asymmetry ratio. Fair and good test‐retest reliability (0.4 < ICC > 0.75) was observed for ipsilateral and contralateral n21 latency, contralateral
EMG normalized peak-to-peak amplitude, and amplitude asymmetry ratio. Conclusion Tone burst mVEMP is a robust and reliable test for evaluating the functional integrity of the vestibulomasseteric reflex pathway.
Emerging lab-on-a-chip techniques provided longer view of effects of mechanical stress on cells
Authors: Liebendorfer Adam
Published: June 2021

Driven in part by applications of microfluidics, understanding how cells respond to physical forces, compress, and how cancer cells metastasize into the bloodstream are expanded.
Backscattering in nonlinear microring resonators via a Gaussian treatment of coupled cavity modes
Authors: McCutcheon Will
Published: June 2021

Systems of coupled cavity modes have the potential to provide bright quantum optical states of light in a highly versatile manner. Microring resonators, for instance, are highly scalable candidates for photon sources. Thanks to CMOS fabrication techniques for their small footprint and the relative ease of coupling many such microrings together. However, surface roughness of the waveguides and defects in the coupler geometry routinely induce splitting of the cavity modes due to backscattering and backcoupling. The parasitic back-propagating mode in a microring leads to hybridization of the modes, altering the linear and nonlinear properties of a system of coupled cavity modes and ultimately constraining the fidelity of quantum light sources that can be produced. In this paper, we derive a comprehensive general model for Gaussian nonlinear processes in systems of coupled cavity modes based on an effective field Hamiltonian and a dispersive input–output model. The resulting dynamics of the equations of motion are evaluated in a Gaussian process formalism via symplectic transformations on the optical modes. We then use this framework to numerically model and explore the problem of backscattering in microring resonators in physically relevant parameter regimes, involving the splitting of various resonances, and we calculate the consequent impurity and heralding efficiency of various heralded photon schemes. We provide a perturbative explanation of the observations and assess the correspondence between spontaneous and stimulated processes in these systems.
Performance, digestibility, nitrogen balance and ingestive behaviour of goat kids fed diets supplemented with condensed tannins from
Authors: Silveira Pimentel Paulo Roberto , Barcellos de Pellegrini Caius , Meira Galvão Jocasta , Santos Brant Lara Maria , Vaz Di Mambro Ribeiro Claudio , Mariniello Silva Thadeu , Barbosa Analivia Martins , Miguel da Silva Jarbas , Rocha Bezerra Leilson , Lopes Oliveira Ronaldo
Published: June 2021

Context Tannins are phenolic compounds derived from secondary plant metabolism that at moderate levels can limit the excessive degradation of the protein in the rumen and provide greater amino acids availability in the small intestine. Aims Two experiments were performed to determine the best level of inclusion of condensed tannins (CT) from Acacia mearnsii extract in the diet of goat kids. An experiment was performed with 32 castrated crossbreed Boer goat kids, with a mean age of 4 months and mean bodyweight (BW) of 19.7 ± 2.05 kg, to measure nutrient intake and performance, and another experiment was developed with 20 Boer goat kids, at 5 months of age and 29.0 ± 2.45 kg BW, in which the digestibility, nitrogen (N) balance, microbial protein synthesis, ingestive behaviour and blood urea N were determined. In both experiments, a completely randomised design was used, including CT levels at 0, 16, 32 and 48 g/kg DM. Results DM; crude protein; ether extract; neutral detergent fibre (NDF); non-fibrous carbohydrates and total digestible nutrients intakes, ether extract digestibility; time spent on ruminating, idling or chewing; number of chews per bolus; eating and ruminating rate of DM and NDF; N intake and retained, blood urea N and loin eye area were not affected (P > 0.05) by the addition of CT from A. mearnsii extract in the goat kid diets. However, the NDF g/kg BW and BW0.75 intakes and N faecal excretion showed a linear increase (P < 0.05). There was a linear increase trend (P < 0.1) in time spent eating, and a linear decrease on N urinary excretion by CT from A. mearnsii extract inclusion. The digestibility of DM, crude protein, NDF, non-fibrous carbohydrates and total digestible nutrients exhibited a linear decrease (P < 0.05) by CT from A. mearnsii extract inclusion. There was a quadratic increase (P < 0.05) in synthesis and microbial efficiency, final BW, average daily gain, total gain, gain:feed ratio, and hot and cold carcass weights and yields. Conclusion The inclusion of CT from A. mearnsii extract up to 17.7 g/kg DM is recommended, as it improves the synthesis and efficiency of microbial production, increasing the gain:feed ratio and performance of goat kids. Implications The use of condensed tannins from A. mearnsii does not affect the nutrient intakes on goat kids’ diet and also improves performance and carcass trait of these animals.
Meat and sensory eating quality of loin steaks from cattle slaughtered at different ages as a result of short, medium or long finishing systems
Authors: Hyslop J. , Duthie C.-A. , Rooke J. A. , Richardson R. I.
Published: June 2021

Context In the belief that feed costs and use of cereal grains are reduced, production systems based on grazed and conserved forage in which cattle are slaughtered at 30 to 36 months of age are increasingly advocated. Aims As there is a scarcity of information concerning meat quality traits of beef from such extended rearing systems, three finishing systems of different lengths (Short, 14–16 months; Medium, 20–24 months; Long, 31–34 months) were compared in which cattle were slaughtered at similar conformation and fat classification scores. Methods The experiment comprised a three (system) × two (gender) design with 24 Limousin cross-bred cattle (12 steers and 12 heifers) assigned to each system. Characteristics of the rib section (between and inclusive of the 5th and 10th ribs) and sensory properties of M. longissimus thoracis samples were then assessed. Key results Older (Long system) cattle had greater rib section and L. thoracis weights. L. thoracis was tougher in older (Long system) cattle when assessed by a trained sensory panel. Heifers had lower rib section weights than steers but neither rib section composition or meat toughness differed between genders. Gristle (visible connective tissue) in the rib section increased with system length and was associated with an increased perception of gristle on eating. Conclusions Overall meat quality was considered commercially acceptable regardless of system. Implications The likely increased greenhouse gas emissions but reduced utilisation of food resources from the Long system need to be considered in conjunction with the meat quality characteristics of the system.
Elite rhetoric can undermine democratic norms
Authors: Clayton Katherine , Davis Nicholas T. , Nyhan Brendan , Porter Ethan , Ryan Timothy J. , Wood Thomas J.
Published: June 2021

Significance

Democracies depend on candidates and parties affirming the legitimacy of election results even when they lose. These statements help maintain confidence that elections are free and fair and thereby facilitate the peaceful transfer of power. However, this norm has recently been challenged in the United States, where former president Donald Trump has repeatedly attacked the integrity of the 2020 US election. We evaluate the effect of this rhetoric in a multiwave survey experiment, which finds that exposure to Trump tweets questioning the integrity of US elections reduces trust and confidence in elections and increases beliefs that elections are rigged, although only among his supporters. These results show how norm violations by political leaders can undermine confidence in the democratic process.
Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA
Authors: Dai Liqiang , Xu Yongping , Du Zhenwei , Su Xiao-dong , Yu Jin
Published: June 2021

Significance

In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve the individual diffusional steps of protein on DNA. Here, we report mainly all-atom equilibrium simulations of a WRKY domain protein in association with and diffusion along DNA. We demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic motions. Processive protein diffusions on DNA have been further sampled in a coarse-grained model. We have also found preferential DNA-strand association of the domain protein, which becomes most prominent at specific DNA binding, and it can be common for small-domain proteins to balance movements on the DNA with the sequence recognition.
Xanthomonas vasicola pv. vasculorum (bacterial leaf streak of corn).
Authors: Triplett Lindsay , Patel Ravikumar
Published: June 2021

Xanthomonas vasicola pv. vasculorum (Xvv) is a bacterial pathogen that causes both bacterial leaf streak of maize and sugarcane gumming disease. After decades limited to South Africa, bacterial leaf streak of maize spread rapidly through maize-growing areas of Argentina, Brazil and the USA since 2014. The origin, method and biological underpinnings of this sudden spread are not well understood but are the subject of active research. Effective control methods remain elusive, but sanitation and crop debris management may limit the disease. Yield impact data are not yet available, but lesions may become severe enough to limit plant productivity in some varieties. The pathogen is not currently considered a quarantine threat by the USDA, EPPO or IPPC.
New and novel genetic tools for improving crops
Authors: Suprasanna Penna , Saddhe Ankush , Ghuge Sandip A. , Ingle Krishnanda P.
Published: June 2021

The basic tenet of crop improvement is the novel genetic variability that is achieved through selection, hybridization, mutation and recombination. The new technological innovations of plant breeding offer scope for transforming crop improvement with more precision and resolution. Advances in genomic-based tools and high-throughput phenotyping have enabled the analysis of genetic variation and identification of molecular signatures of agronomic traits. Molecular markers and molecular-marker-assisted breeding have facilitated the speedy selection of new, novel genetic combinations in breeding for high-yielding, stress-tolerant and nutritionally enriched crops. Transgenic methods have revolutionized modification for stress tolerance and higher productivity, and several genetically modified crops are under cultivation. Availability of genome sequencing platforms and genomic resources has significantly contributed to accessing novel genes and validating their functions. Genome-editing tools and recent advances of prime editing are now accessible for precise genetic alteration of plant traits. The new plant breeding tools will certainly foster development of highly productive, improved crop varieties for achieving food security and climate resilience.
Steady state temperature rise in multilayered tissue due to arbitrary periodic SAR using finite difference FFT and transfer function method
Authors: Gajda Gregory B , Paradis Jonathan , Lemay Eric
Published: June 2021

Steady state (SS) and transient temperature-rise in tissue from radiofrequency exposure forms the underlying basis for limits in international exposure guidelines. Periodically pulsed or intermittent exposures form a special case of having both peak and average levels, producing temperature-rise oscillations in the SS. Presented here is a method for determining tissue temperature-rise for periodic specific absorption rate (SAR) modulation having arbitrary waveform. It involves the finite difference solution of a form of the Pennes Bioheat Transfer equation (BHTE) and uses the concept of the transfer function and the Fast Fourier Transform (FFT). The time-dependent BHTE is converted to a SS harmonic version by assuming that the time-dependent SAR waveform and tissue temperature can both be represented by Fourier series. The transfer function is obtained from solutions of the harmonic BHTE for an assumed SAR waveform consisting of periodic impulses. The temperature versus time response for an arbitrary periodic SAR waveform is obtained from the inverse FFT of the product of the transfer function and the FFT of the actual SAR waveform. This method takes advantage of existing FFT algorithms on most computational platforms and the ability to store the transfer function for later re-use. The transfer function varies slowly with harmonic number, allowing interpolation and extrapolation to reduce the computational effort. The method is highly efficient for the case where repeated temperature-rise calculations for parameter variations in the SAR waveform are sought. Examples are given for a narrow, circularly symmetric beam incident on a planar skin/fat/muscle model with rectangular, triangular and cosine-pulsed SAR modulation waveforms. Calculations of temperature-rise crest factor as a function of rectangular pulse duty factor and pulse repetition frequency for the same exposure/tissue model are also presented as an example of the versatility of the method.
Case Report and Genomic Analysis of Cefiderocol-Resistant Escherichia coli Clinical Isolates
Authors: Price Travis K , Davar Kusha , Contreras Deisy , Ward Kevin W , Garner Omai B , Simner Patricia J , Yang Shangxin , Chandrasekaran Sukantha
Published: June 2021

Objectives

Cefiderocol is a novel siderophore cephalosporin with in vitro activity against multidrug-resistant (MDR), gram-negative bacteria and intrinsic structural stability to all classes of carbapenemases. We sought to identify gene variants that could affect the mechanism of action (MOA) of cefiderocol.

Methods

We report a case of bacteremia in a liver transplant candidate with a strain of carbapenem-resistant Escherichia coli that was found to be resistant to cefiderocol despite no prior treatment with this antimicrobial agent. Using whole-genome sequencing, we characterized the genomic content of this E coli isolate and assessed for genetic variants between related strains that were found to be cefiderocol susceptible.

Results

We identified several variants in genes with the potential to affect the mechanism of action of cefiderocol.

Conclusions

The cefiderocol resistance in the E coli isolate identified in this study is likely due to mutations in the cirA gene, an iron transporter gene.
Practical utility of mixed methods research in pharmacy practice
Authors: Dalpoas Stacy Elder , Shermock Kenneth M
Published: June 2021

Purpose

Our aim was to review key methodological concepts and provide a practical guide to employing mixed methods research to enhance pharmacy practice research.

Mixed methods research provides multiple organized analytic perspectives to thoroughly investigate complex social and scientific problems in a methodologically rigorous manner. This research design incorporates collection and analysis of both qualitative and quantitative data components to create a thorough understanding of a complex question. The 5 most commonly identified reasons for conducting mixed methods research include triangulation, complementarity, development, initiation, and expansion of results. For research questions that benefit from mixed methods research, we review how to structure the study, including timing, sequencing, and prioritization of methods. Illustrative examples from the literature highlight the utility of this methodology for clinical and operational pharmacy research questions.

Conclusion

Mixed methods designs can enhance pharmacy research inquiry, provide a means to understand complicated issues, and uncover optimal interventions.
Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins
Authors: Yamaguchi Hideki , Saito Yutaka
Published: June 2021

Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However, it is unclear how to effectively learn evolutionary properties of an engineering target protein from homologous sequences, taking into account the protein’s sequence-level structure called domain architecture (DA). Additionally, no optimal protocols are established for incorporating such properties into Transformer, the neural network well-known to perform the best in natural language processing research. This article proposes DA-aware evolutionary fine-tuning, or ‘evotuning’, protocols for Transformer-based variant effect prediction, considering various combinations of homology search, fine-tuning and sequence vectorization strategies. We exhaustively evaluated our protocols on diverse proteins with different functions and DAs. The results indicated that our protocols achieved significantly better performances than previous DA-unaware ones. The visualizations of attention maps suggested that the structural information was incorporated by evotuning without direct supervision, possibly leading to better prediction accuracy.
CLARINET: efficient learning of dynamic network models from literature
Authors: Ahmed Yasmine , Telmer Cheryl A , Miskov-Zivanov Natasa
Published: June 2021

Motivation

Creating or extending computational models of complex systems, such as intra- and intercellular biological networks, is a time and labor-intensive task, often limited by the knowledge and experience of modelers. Automating this process would enable rapid, consistent, comprehensive and robust analysis and understanding of complex systems.

Results

In this work, we present CLARINET (CLARIfying NETworks), a novel methodology and a tool for automatically expanding models using the information extracted from the literature by machine reading. CLARINET creates collaboration graphs from the extracted events and uses several novel metrics for evaluating these events individually, in pairs, and in groups. These metrics are based on the frequency of occurrence and co-occurrence of events in literature, and their connectivity to the baseline model. We tested how well CLARINET can reproduce manually built and curated models, when provided with varying amount of information in the baseline model and in the machine reading output. Our results show that CLARINET can recover all relevant interactions that are present in the reading output and it automatically reconstructs manually built models with average recall of 80% and average precision of 70%. CLARINET is highly scalable, its average runtime is at the order of ten seconds when processing several thousand interactions, outperforming other similar methods.

Availability and implementation

The data underlying this article are available in Bitbucket at https://bitbucket.org/biodesignlab/clarinet/src/master/

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Are small populations larger than they seem? Genetic insights into patchily distributed populations ofDrakaea glyptodon(Orchidaceae)
Authors: Trapnell Dorset W , Smallwood Patrick A , Dixon Kingsley W , Phillips Ryan D
Published: June 2021

Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. Ten populations of the common terrestrial orchid Drakaea glyptodon from south-western Australia were genotyped with ten nuclear and five plastid simple sequence repeat (SSR) markers. Levels and partitioning of genetic variation and effective population sizes (Ne) were estimated. Spatial genetic structure of nuclear diversity, together with plastid data, were used to infer the effective number of seed parents per population. We found high genetic diversity, Ne values that generally exceed predictions based on the number of flowering individuals and moderate levels of gene flow. Two populations were founded by less than five colonists suggesting some populations are colonized by few seeds, with growth largely resulting from in situ recruitment. A value of 3.65 for mp /ms indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that D. glyptodon is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes.
Transition to adulthood and transfer to adult care of adolescents with congenital heart disease: a global consensus statement of the ESC Association of Cardiovascular Nursing and Allied Professions (ACNAP), the ESC Working Group on Adult Congenital Heart Disease (WG ACHD), the Association for European Paediatric and Congenital Cardiology (AEPC), the Pan-African Society of Cardiology (PASCAR), the Asia-Pacific Pediatric Cardiac Society (APPCS), the Inter-American Society of Cardiology (IASC), the Cardiac Society of Australia and New Zealand (CSANZ), the International Society for Adult Congenital Heart Disease (ISACHD), the World Heart Federation (WHF), the European Congenital Heart Disease Organisation (ECHDO), and the Global Alliance for Rheumatic and Congenital Hearts (Global ARCH)
Authors: Moons Philip , Bratt Ewa-Lena , De Backer Julie , Goossens Eva , Hornung Tim , Tutarel Oktay , Zühlke Liesl , Araujo John Jairo , Callus Edward , Gabriel Harald , Shahid Nauman , Sliwa Karen , Verstappen Amy , Yang Hsiao-Ling , Thomet Corina
Published: June 2021

The vast majority of children with congenital heart disease (CHD) in high-income countries survive into adulthood. Further, paediatric cardiac services have expanded in middle-income countries. Both evolutions have resulted in an increasing number of CHD survivors. Expert care across the life span is necessitated. In adolescence, patients transition from being a dependent child to an independent adult. They are also advised to transfer from paediatrics to adult care. There is no universal consensus regarding how transitional care should be provided and how the transfer should be organized. This is even more challenging in countries with low resources. This consensus document describes issues and practices of transition and transfer of adolescents with CHD, accounting for different possibilities in high-, middle-, and low-income countries. Transitional care ought to be provided to all adolescents with CHD, taking into consideration the available resources. When reaching adulthood, patients ought to be transferred to adult care facilities/providers capable of managing their needs, and systems have to be in place to make sure that continuity of high-quality care is ensured after leaving paediatric cardiology.
Stress–strain characterization of seismic source fields using moment measures of mechanism complexity
Authors: Jordan Thomas H , Juarez Alan
Published: June 2021

Earthquake ruptures and seismic sequences can be very complex, involving slip in various directions on surfaces of variable orientation. How is this geometrical complexity in seismic energy release, here called mechanism complexity, governed by tectonic stress? We address this question using a probabilistic model for the distribution of double couples that is consistent with three assumptions commonly used in regional stress inversions: the tectonic stress is constant, slip vectors are aligned with the maximum shear traction in the plane of slip, and higher shear traction promotes more seismic energy release. We characterize the moment-tensor field of a stress-aligned source process in terms of an ordered set of principal-stress directions, a stress shape factor R, and a strain-sensitivity parameter $\kappa $. The latter governs the dependence of the seismic moment density on the shear-traction magnitude and therefore parametrizes the seismic strain response to the driving stress. These stress–strain characterization (SSC) parameters can be determined from moment measures of mechanism complexity observed in large earthquakes and seismic sequences. The moment measures considered here are the ratio of the Aki moment to the total seismic moment and the five fractions of the total-moment defined by linear mappings of the moment-tensor field onto an orthonormal basis of five deviatoric mechanisms. We construct this basis to be stress-oriented by choosing its leading member to be the centroid moment tensor (CMT) mechanism and three others representing orthogonal rotations of the CMT mechanism. From the projections of the stress-aligned field onto this stress-oriented basis, we derive explicit expressions for the expected values of the moment-fraction integrals as functions of R and $\kappa $. We apply the SSC methodology to a 39-yr focal mechanism catalogue of the San Jacinto Fault (SJF) zone and to realizations from the Graves–Pitarka stochastic rupture model. The SJF data are consistent with the SSC model, and the recovered parameters, $R = {\rm{ }}0.45 \pm 0.050$ and $\kappa = {\rm{ }}5.7 \pm 1.75$, indicate moderate mechanism complexity. The parameters from the Graves–Pitarka realizations, $R = {\rm{\ }}0.49 \pm 0.005,{\rm{\ \ }}\kappa = {\rm{\ }}9.5 \pm 0.375,$ imply lower mechanism complexity than the SJF catalogue, and their moment measures show inconsistencies with the SSC model that can be explained by differences in the modelling assumptions.
Green’s function representations for Marchenko imaging without up/down decomposition
Authors: Wapenaar Kees , Snieder Roel , de Ridder Sjoerd , Slob Evert
Published: June 2021

Marchenko methods are based on integral representations which express Green’s functions for virtual sources and/or receivers in the subsurface in terms of the reflection response at the surface. An underlying assumption is that inside the medium the wave field can be decomposed into downgoing and upgoing waves and that evanescent waves can be neglected. We present a new derivation of Green’s function representations which circumvents these assumptions, both for the acoustic and the elastodynamic situation. These representations form the basis for research into new Marchenko methods which have the potential to handle refracted and evanescent waves and to more accurately image steeply dipping reflectors.
Identification of the GlialCAM interactome: the G protein-coupled receptors GPRC5B and GPR37L1 modulate megalencephalic leukoencephalopathy proteins
Authors: Alonso-Gardón Marta , Elorza-Vidal Xabier , Castellanos Aida , La Sala Gina , Armand-Ugon Mercedes , Gilbert Alice , Di Pietro Chiara , Pla-Casillanis Adrià , Ciruela Francisco , Gasull Xavier , Nunes Virginia , Martínez Albert , Schulte Uwe , Cohen-Salmon Martine , Marazziti Daniela , Estévez Raúl
Published: June 2021

Megalencephalic Leukoencephalopathy with subcortical Cysts (MLC) is a type of vacuolating leukodystrophy, which is mainly caused by mutations in MLC1 or GLIALCAM. The two MLC-causing genes encode for membrane proteins of yet unknown function that have been linked to the regulation of different chloride channels such as the ClC-2 and VRAC. To gain insight into the role of MLC proteins, we have determined the brain GlialCAM interacting proteome. The proteome includes different transporters and ion channels known to be involved in the regulation of brain homeostasis, proteins related to adhesion or signaling as several G protein-coupled receptors (GPCRs), including the orphan GPRC5B and the proposed prosaposin receptor GPR37L1. Focusing on these two GPCRs, we could validate that they interact directly with MLC proteins. The inactivation of Gpr37l1 in mice upregulated MLC proteins without altering their localization. Conversely, a reduction of GPRC5B levels in primary astrocytes downregulated MLC proteins, leading to an impaired activation of ClC-2 and VRAC. The interaction between the GPCRs and MLC1 was dynamically regulated upon changes in the osmolarity or potassium concentration. We propose that GlialCAM and MLC1 associate with different integral membrane proteins modulating their functions and acting as a recruitment site for various signaling components as the GPCRs identified here. We hypothesized that the GlialCAM/MLC1 complex is working as an adhesion molecule coupled to a tetraspanin-like molecule performing regulatory effects through direct binding or influencing signal transduction events.
Is Intestinal Diversion an Effective Treatment for Distal Crohn’s Disease?
Authors: Lightner Amy L , Buhulaigah Hassan , Zaghiyan Karen , Holubar Stefan D , Steele Scott R , Jia Xue , McMichael John , Vaidya Prashansha , Fleshner Phillip R
Published: June 2021

Background

Fecal diversion with an ileostomy is selectively used in cases of medically refractory Crohn’s proctocolitis or advanced perianal disease. The aim of this study was to evaluate clinical improvement after fecal diversion in Crohn’s disease (CD) and factors associated with clinical improvement.

Methods

A retrospective chart review of adult CD patients undergoing ileostomy formation for distal disease between 2000 and 2019 at 2 CD referral centers was conducted. The primary outcome was the rate of clinical improvement with diversion that allowed for successful restoration of intestinal continuity. Secondary outcomes included the rate of clinical and endoscopic improvement after fecal diversion, ileostomy morbidity, need for subsequent total proctocolectomy and end ileostomy, and factors associated with a clinical response to fecal diversion.

Results

A total of 132 patients with a median age of 36 years (interquartile range, 25–49) were included. Mean duration of disease was 16.2 years (10.4) years. Indication for surgery was medically refractory proctocolitis with perianal disease (n = 59; 45%), perianal disease alone (n = 24; 18%), colitis (n = 37; 28%), proctitis (n = 4; 3%), proctocolitis alone (n = 4; 3%), and ileitis with perianal disease (n = 4; 3%). Medications used before surgery included corticosteroids (n = 59; 45%), immunomodulators (n = 55; 42%) and biologics (n = 82; 62%). The clinical and endoscopic response to diversion was 43.2% (n = 57) and 23.9% (n = 16). At a median follow-up of 35.3 months (interquartile range, 10.6–74.5), 25 patients (19%) had improved and had ileostomy reversal, but 86 (65%) did not improve, with 50 (38%) undergoing total proctocolectomy for persistent symptoms. There were no significant predictors of clinical improvement.

Conclusions

The use of a “temporary” ileostomy is largely ineffective in achieving clinical response.
Dual Phase-Shifted Ipsilateral Metachrony inAmericamysis bahia
Authors: Ruszczyk Melissa , Webster Donald R , Yen Jeannette
Published: June 2021

Synopsi

Previously documented metachrony in euphausiids focused on one, five-paddle metachronal stroke, where contralateral pleopod pairs on the same abdominal segment beat in tandem with each other, propelling the animal forward. In contrast, the mysid shrimp Americamysis bahia’s pleopods on the same abdominal segment beat independently of each other, resulting in two, five-paddle metachronal cycles running ipsilaterally along the length of the body, 180° out of phase. The morphology, kinematics, and nondimensional measurements of efficiency are compared primarily with the one-cycle Euphausia superba to determine how the two-cycle approach alters the design and kinematics of metachrony. Pleopodal swimming in A. bahia results in only fast-forward swimming, with speeds greater than 2 BL/s (body lengths per second), and can reach speeds up to 12 BL/s, through a combination of increasing stroke amplitude, increasing beat frequency, and changing their inter-limb phase lag. Trends with Strouhal number and advance ratio suggest that the kinematics of metachrony in A. bahia are favored to achieve large normalized swimming speeds.