bluuebunny/crossref_metadata_2025 huggingface dataset:
Study case: cost-benefit of a photovoltaic system to reduce the consumption of the irrigation pumps in a Honduran sugar cane farm
Authors: Stwolinsky García K , Reyes Duke A
Published: July 2021

This paper presents the results of the case study on the cost-benefit (B/C) of the implementation of a photovoltaic solar system on a sugar cane farm. “El Modelo’s” farm, electric pumping system represents an electricity consumption of 1,087.2 (MWh/year), which translates into an expense of the 19.7%. The study is based on three analyzes: market, technical, and financial. The market analysis represents the current demand profile, this profile shows that more than 70% of the energy is consumed during the insolation time. The technical analysis is based on the interpretation of meteorological data, such as the annual global radiation representing 1,800 (kWh/m2) and a daily insolation duration of approximately 8 hours; the design of a grid-connected photovoltaic system of 4,431 (m2), with an installed power of 474.2 (kW) and the comparison of its simulation of operation between Helioscope and PVsyst, which presents an annual power generation of 686.2 (MWh). The financial analysis has the purpose of calculating the B/C, for which a leveled cost of energy (LCOE) of 0.0425 ($/kWh) is calculated, thanks to this factor a projection of the current value of savings of $ 1,009,148.71 is established, which are compared with the current value of the initial investment costs of $ 555,603.44, these values are related to establish a B/C of 1.82, which assumed that this project is profitable.
THE USE OF DIGITAL INNOVATIONS IN THE DEVELOPMENT OF THE ARCTIC
Authors: Dyatlov S A , Didenko N I , Abakumova M V , Kulik S V
Published: July 2021

The paper describes the application of Industry 4.0 technologies, gives an overview of previous research on digital innovations, and defines goals and objectives of the research. The core concept of «Industry 4.0 technology» and features of the ways to exploit it in the Arctic institutions have been examined. There has been carried out an analysis of international practices to apply Industry 4.0 technologies in all spheres of life. The flexible automated production of goods or services based on new generation robotics and factories in the Arctic zone has been considered as being the highest stage of complex automated production. An example of automated use of products and services are «smart houses», or «smart things». Methods of collection of advanced production technologies have been discussed. A strategy has been developed to select the most advanced production technologies for spheres of life and the best possible strategic option has been defined. Financial and time resources were chosen as optimization criteria.
Southeast Asian technologies at enterprises in Arctic zone of Russian Federation
Authors: Chistalyova T. , Eidemiller K. Yu. , Zhuravel V P , Rubtsova A V , Bocharov A A
Published: July 2021

Within the domestic and foreign policy of Russia the Arctic is one of the most important regions, the development of this region ranks a significant place in the plans and strategies of Russian government. The brilliant potential of the region is of particular interest to a number of countries, including the countries of Southeast Asia. It is reasonable that concerned states choose Russia as their partner in the polar region since Russia possesses the largest territories in the Arctic and resolutely develops them. For the Russian Federation such attention to the Arctic is beneficial because of the prospects of technological and economic cooperation. However, are there any possibilities for the states, far from the polar territories, to become crucial partners for the Russian North? In the paper, the authors analyzed this issue and have made the conclusion that despite the mutual interest of both parties in the development of cooperation in the Arctic, the current circumstances and conditions result in the fact that the partnership consists only of the separate joint ventures, not systematic joint work.
Strategic management of industrial enterprise digital maturity in a global economic space of the ecosystem economy
Authors: Gileva T A , Galimova M P , Babkin A V , Gorshenina M E
Published: July 2021

Most traditional businesses are now in the early stages of a digital transformation process that is essential to stay competitive. One of the distinctive features of the digital environment is the development of ecosystems that change the established rules of competition and business conduct, and break down the boundaries between industries. Therefore, the purpose of this article is to explore the possibilities and formulate recommendations for the use of business ecosystems as a strategic factor in the development of traditional industrial enterprises. The analysis of research in the field of creation and functioning of business ecosystems was carried out, the features and strategic advantages were highlighted. It was shown that the business ecosystem is only one of the successful management models in the digital economy. The factors of choosing the preferred model are picked out: the stability of the industry, the features of the value proposition and the level of coordination of partner companies required for its creation. The necessity is noted and clarification of some provisions in the field of strategic management as a methodology for managing the development of industrial enterprises (in terms of the limited scheduling, modular and “two-speed” format of the digital transformation strategy) is formulated. The characteristics of models for assessing the digital maturity of an enterprise as a tool for managing its development are given. In the context of the growing role of business ecosystems in economic development, it is proposed to supplement such model with a block for assessing the readiness of an enterprise for partnership. A model of strategic management of enterprise development in a digital environment has been developed based on an assessment of the gap in terms of digital maturity.
Development of a resource-saving technology for industrial processing of hematite-containing raw materials based on computer modelling
Authors: Khokhulya M S , Fomin A V
Published: July 2021

The paper presents the results of the research aimed at recovery of hematite from current and stockpiled tailings produced at the mineral processing plant of Olkon JSC. The authors investigated material composition of tailing samples. Using methods of computational fluid dynamics and the ANSYS software, the models of spiral separation of the tailings have been developed. The use of computer modelling has shown that spiral separators can be recommended for tailings processing. The modelling results were confirmed with industrial spiral separation tests conducted at the processing plant. The authors developed a gravity separation technology for processing the magnetic separation tailings and stockpiled tailings. The proposed technology allows recovering hematite concentrate with a hematite iron content of 54.5% and recovery of 75.4% from current tailings containing 5.2% of hematite iron. It was also shown that hematite concentrate can be recovered from stockpiled tailings using the separation technology based on the use of spiral separation. The gravity separation technology provides for resources economy at the mineral processing plant. The use of stockpiled tailing as a raw material source can reduce negative environmental impact.
Asymptotic Counting in Conformal Dynamical Systems
Authors: Pollicott Mark , Urbanski Mariusz
Published: July 2021

In this monograph we consider the general setting of conformal graph directed Markov systems modeled by countable state symbolic subshifts of finite type. We deal with two classes of such systems: attracting and parabolic. The latter being treated by means of the former.

We prove fairly complete asymptotic counting results for multipliers and diameters associated with preimages or periodic orbits ordered by a natural geometric weighting. We also prove the corresponding Central Limit Theorems describing the further features of the distribution of their weights.

These results have direct applications to a wide variety of examples, including the case of Apollonian Circle Packings, Apollonian Triangle, expanding and parabolic rational functions, Farey maps, continued fractions, Mannenville-Pomeau maps, Schottky groups, Fuchsian groups, and many more. This gives a unified approach which both recovers known results and proves new results.

Our new approach is founded on spectral properties of complexified Ruelle–Perron–Frobenius operators and Tauberian theorems as used in classical problems of prime number theory.
Increased ploidy of Butomus umbellatus in introduced populations is not associated with higher phenotypic plasticity to N and P
Authors: Harms Nathan E , Cronin James T , Gaskin John F
Published: July 2021

Separate introductions or post-introduction evolution may lead to multiple invader genotypes or cytotypes that differ in growth rates, biomass or chemical profile responses (phenotype) to a range of environments. If the invader has high trait plasticity to a range of resource levels, then sediment N or P enrichment may enhance invasiveness. However, the ways in which ploidy, plasticity, and available N or P interact are unknown for most species despite the potential to explain spread and impacts by invaders with multiple introduced lineages. We conducted a common garden experiment with four triploid and six diploid populations of Butomus umbellatus, collected from across its invasive range in the USA. Plants were grown under different N or P nutrient levels (4, 40, 200, 400 mg L−1 N; 0.4, 4, 40 mg L−1 P) and we measured reaction norms for biomass, clonal reproduction and tissue chemistry. Contrary to our expectation, triploid B. umbellatus plants were less plastic to variation in N or P than diploid B. umbellatus in most measured traits. Diploid plants produced 172 % more reproductive biomass and 57 % more total biomass across levels of N, and 158 % more reproductive biomass and 33 % more total biomass across P than triploid plants. Triploid plants had lower shoot:root ratios and produced 30 % and 150 % more root biomass than diploid plants in response to increases in N and P, respectively. Tissue chemistry differed between cytotypes but plasticity was similar; N was 8 % higher and C:N ratio was 30 % lower in triploid than diploid plants across levels of N and plant parts, and N was 22 % higher and C:N ratio 27 % lower across levels of P and plant parts. Our results highlight differences in nutrient response between cytotypes of a widespread invader, and we call for additional field studies to better understand the interaction of nutrients and ploidy during invasion.
The Impact of Breast Symmetry on Eye Movement and Gaze Pattern: An Eye-Tracking Investigation
Authors: Moellhoff Nicholas , Kandelhardt Chiara , Ehrl Denis , Kohler Lukas , Koban Konstantin , Giunta Riccardo E , Guertler Anne , Mardini Samir , Cotofana Sebastian , Frank Konstantin
Published: July 2021

Background

The objective assessment of beauty remains challenging despite ongoing research efforts. A new method of objectively determining the aesthetic appeal of body features by analyzing gaze patterns and eye movements has recently been investigated.

Objectives

The objective of this study was to assess, by means of objective eye-tracking technology, differences in the gaze patterns of observers presented with standardized 3-dimensional images showing different degrees of breast asymmetry.

Methods

A total of 83 Caucasian study participants with a mean age of 38.60 (19.8) years were presented with 5 images depicting varying degrees of breast asymmetry. In addition to the assessment of eye movements, participants were asked to rate the aesthetic appeal and the asymmetry of the breasts on a 5-point Likert scale.

Results

Overall, the data showed that participants’ rating of the breasts’ aesthetic appeal was inversely related to the level of asymmetry. The mean [standard deviation] time until fixation was shortest for the image depicting the greatest breast asymmetry (50 cc) at 0.77 [0.7] seconds (P < 0.001). In addition, the mammary region was also viewed longest in this image at 3.76 [0.5] seconds (P < 0.001). A volume difference of 35 cc between breasts deflected the observers’ gaze significantly toward the larger of the asymmetric breasts (P < 0.001).

Conclusions

Surgeons should focus on achieving symmetric breast volume (ie, differences <35 cc between breasts) to avoid noticeable asymmetry with regard to breast size.
1′-Acetoxychavicol acetate, a potent transient receptor potential ankyrin 1 agonist derived from Thai ginger, prevents visceral fat accumulation in mice fed with a high-fat and high-sucrose diet
Authors: Ikeya Tatsunori , Terada Yuko , Morimitsu Yasujiro , Kubota Kikue , Ito Keisuke , Watanabe Tatsuo
Published: July 2021

1′-Acetoxychavicol acetate (ACA) is found in Thai ginger (Alpinia galanga) and is a powerful agonist of transient receptor potential ankyrin 1 (TRPA1). In a diet-induced obesity mouse model, ACA reduced fat deposition. Sympathetic nerve activation was also indicated in the ACA-fed group. This study is expected to promote the utilization of food containing TRPA1 agonists to treat obesity.
White rice ethanol extract is qualitatively, but not quantitatively, equivalent to that of brown rice as an antioxidant source
Authors: Wu Hongyan , Nakamura Toshiyuki , Guo Yingnan , Hirooka Miho , Zhang Gongliang , Munemasa Shintaro , Murata Yoshiyuki , Fujita Akiko , Nakamura Yoshimasa
Published: July 2021

The purpose of this study is to compare the potentials to exhibit biologically active antioxidant actions between white rice (WR) and brown rice (BR) in in vitro assays and a cellular model. The Trolox equivalent (TE) per 1 mg ethanol extract of WR for the 1,1-diphenyl-2-picrylhydrazyl assay was slightly higher than that of BR, whereas the TE per 1 g whole WR was much lower than that for BR. This tendency was very comparable to those for the oxygen radical absorbance capacity and total polyphenol content. Both of the ethanol extracts also similarly suppressed the hydrogen peroxide-induced cytotoxicity and enhanced the gene expression of drug-metabolizing enzymes. Based on the α-tocopherol quantity, its contribution to the cytoprotective effect of the rice extracts is very limited. Taken together, the ethanol extract of WR might be a qualitatively, but not quantitatively, equivalent source of antioxidative phytochemicals to that of BR.
Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data
Authors: Koch Forrest C , Sutton Gavin J , Voineagu Irina , Vafaee Fatemeh
Published: July 2021

A typical single-cell RNA sequencing (scRNA-seq) experiment will measure on the order of 20 000 transcripts and thousands, if not millions, of cells. The high dimensionality of such data presents serious complications for traditional data analysis methods and, as such, methods to reduce dimensionality play an integral role in many analysis pipelines. However, few studies have benchmarked the performance of these methods on scRNA-seq data, with existing comparisons assessing performance via downstream analysis accuracy measures, which may confound the interpretation of their results. Here, we present the most comprehensive benchmark of dimensionality reduction methods in scRNA-seq data to date, utilizing over 300 000 compute hours to assess the performance of over 25 000 low-dimension embeddings across 33 dimensionality reduction methods and 55 scRNA-seq datasets. We employ a simple, yet novel, approach, which does not rely on the results of downstream analyses. Internal validation measures (IVMs), traditionally used as an unsupervised method to assess clustering performance, are repurposed to measure how well-formed biological clusters are after dimensionality reduction. Performance was further evaluated over nearly 200 000 000 iterations of DBSCAN, a density-based clustering algorithm, showing that hyperparameter optimization using IVMs as the objective function leads to near-optimal clustering. Methods were also assessed on the extent to which they preserve the global structure of the data, and on their computational memory and time requirements across a large range of sample sizes. Our comprehensive benchmarking analysis provides a valuable resource for researchers and aims to guide best practice for dimensionality reduction in scRNA-seq analyses, and we highlight Latent Dirichlet Allocation and Potential of Heat-diffusion for Affinity-based Transition Embedding as high-performing algorithms.
APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures
Authors: Timmons Patrick Brendan , Hewage Chandralal M
Published: July 2021

Good knowledge of a peptide’s tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5–40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.
miRAnno—network-based functional microRNA annotation
Authors: Tokar Tomas , Pastrello Chiara , Abovsky Mark , Rahmati Sara , Jurisica Igor
Published: July 2021

Motivation

Functional annotation is a common part of microRNA (miRNA)-related research, typically carried as pathway enrichment analysis of the selected miRNA targets. Here, we propose miRAnno, a fast and easy-to-use web application for miRNA annotation.

Results

miRAnno uses comprehensive molecular interaction network and random walks with restart to measure the association between miRNAs and individual pathways. Independent validation shows that miRAnno achieves higher signal-to-noise ratio compared to the standard enrichment analysis.

Availability and implementation

miRAnno is freely available at https://ophid.utoronto.ca/miRAnno/.

Supplementary information

Supplementary data are available at Bioinformatics online.
CCIP: predicting CTCF-mediated chromatin loops with transitivity
Authors: Wang Weibing , Gao Lin , Ye Yusen , Gao Yong
Published: July 2021

Motivation

CTCF-mediated chromatin loops underlie the formation of topological associating domains and serve as the structural basis for transcriptional regulation. However, the formation mechanism of these loops remains unclear, and the genome-wide mapping of these loops is costly and difficult. Motivated by the recent studies on the formation mechanism of CTCF-mediated loops, we studied the possibility of making use of transitivity-related information of interacting CTCF anchors to predict CTCF loops computationally. In this context, transitivity arises when two CTCF anchors interact with the same third anchor by the loop extrusion mechanism and bring themselves close to each other spatially to form an indirect loop.

Results

To determine whether transitivity is informative for predicting CTCF loops and to obtain an accurate and low-cost predicting method, we proposed a two-stage random-forest-based machine learning method, CTCF-mediated Chromatin Interaction Prediction (CCIP), to predict CTCF-mediated chromatin loops. Our two-stage learning approach makes it possible for us to train a prediction model by taking advantage of transitivity-related information as well as functional genome data and genomic data. Experimental studies showed that our method predicts CTCF-mediated loops more accurately than other methods and that transitivity, when used as a properly defined attribute, is informative for predicting CTCF loops. Furthermore, we found that transitivity explains the formation of tandem CTCF loops and facilitates enhancer–promoter interactions. Our work contributes to the understanding of the formation mechanism and function of CTCF-mediated chromatin loops.

Availability and implementation

The source code of CCIP can be accessed at: https://github.com/GaoLabXDU/CCIP.

Supplementary information

Supplementary data are available at Bioinformatics online.
What Influences Parents and Practitioners’ Decisions to Share Personal Information within an Early Help (Social Care) Context? Implications for Practice in Sharing Digital Data across Sectors
Authors: Smart Deborah , Jackson Katherine , Alderson Hayley , Foley Thomas , Foreman Stephen , Kaner Ben , Kaner Eileen , Lancaster Helen , Lingam Raghu , Rankin Judith , Rowlands Gill , Spencer Liam , McGovern Ruth
Published: July 2021

Meeting the multiple and often complex needs of families (children, young people and adults) within ‘Early Help’ support is dependent upon practitioners from different sectors sharing relevant and timely information, after gaining a family’s voluntary consent to share information. This article reports on qualitative one-to-one interviews with adults in families (n = 32), one mother/father dyad interview (n = 2) and focus groups with practitioners (n = 47) in five local authority areas in North East England receiving or providing Early Help support. We explored experiences of providing consent to share personal information and consider the usefulness of a digital health data system when providing Early Help support to families. Communication Privacy Management theory was used as a framework to analyse the data. Key themes in participants’ accounts include the degree of need for help and support; the importance of trusting relationships; stronger and structured joint working practices; and understanding how information is shared. This work provides insights into current information sharing practices for some of the most vulnerable families and the wider social contexts. It has implications for the usefulness of a digital data system that shares GP health data with Early Help services and suggests the role this could have in the parent–practitioner relationship.
Bridging the energy gap of India’s residential buildings by using rooftop solar PV systems for higher energy stars
Authors: Dalal Rakesh , Bansal Kamal , Thapar Sapan
Published: July 2021

The residential-building sector in India consumes >25% of the total electricity and is the third-largest consumer of electricity; consumption increased by 26% between 2014 and 2017. India has introduced a star-labelling programme for residential buildings that is applicable for all single- and multiple-dwelling units in the country for residential purposes. The Energy Performance Index (EPI) of a building (annual energy consumption in kilowatt-hours per square metre of the building) is taken as an indicator for awarding the star label for residential buildings. For gauging the EPI status of existing buildings, the electricity consumption of residential buildings (in kWh/m2/year) is established through a case study of the residential society. Two years of electricity bills are collected for an Indian residential society located in Palam, Delhi, analysed and benchmarked with the Indian residential star-labelling programme. A wide EPI gap is observed for existing buildings for five-star energy labels. Based on existing electricity tariffs, the energy consumption of residential consumers and the Bureau of Energy Efficiency (BEE)’s proposed building ENERGY STAR labelling, a grid-integrated rooftop solar photovoltaic (PV) system is considered for achieving a higher star label. This research study establishes the potential of grid-connected rooftop solar PV systems for residential buildings in Indian cities through a case study of Delhi. Techno-economic analysis of a grid-integrated 3-kWp rooftop solar PV plant is analysed by using RETScreen software. The study establishes that an additional two stars can be achieved by existing buildings by using a grid-integrated rooftop solar PV plant. Payback for retrofit of a 3-kWp rooftop solar PV plant for Indian cites varies from 3 to 7 years.

A case study in Delhi, India establishes the potential of grid-connected rooftop solar PV systems for residential buildings. Techno-economic analysis of grid integrated, 3 kWp rooftop solar systems estimates a payback period from 3 to 7 years.
Accuracy of Gastrointestinal Ultrasound and Calprotectin in the Assessment of Inflammation and its Location in Patients with an Ileoanal Pouch
Authors: Ardalan Zaid S , Friedman Antony B , Con Danny , Chandran Sujievvan , Gibson David , Pham Alan , De Cruz Peter , Tay Kwang , Bell Stephen , Rosella Ourania , Sparrow Miles P , Gibson Peter R
Published: July 2021

Background and Aims

In symptomatic patients with ileoanal pouches, pouchoscopy is needed for accurate diagnosis but is invasive. We aimed to assess the utility of non-invasive gastrointestinal ultrasound and faecal calprotectin in ileoanal pouch patients.

Methods

Patients with an ileoanal pouch were consecutively enrolled in this cross-sectional study from clinics in Victoria, Australia. The pouchitis disease activity index was used as a reference standard. Video-recorded pouchoscopies were reviewed by three gastroenterologists. Pouch, pre-pouch, and cuff biopsies were reviewed by a single pathologist. Ultrasound was performed by a single gastroenterologist transabdominally and transperineally. Faecal calprotectin was measured from morning stool samples. All examiners were blinded to patients’ clinical history.

Results

A total of 44 participants had a pouchoscopy, of whom 43 had a faecal calprotectin test and 42 had an ultrasound; 17 had pouchitis, 15 had pre-pouch ileitis, and 16 had cuffitis. Pouch wall thickness of <3 mm was 88% sensitive in excluding pouchitis, and pouch wall thickness of ≥4 mm was 87% specific in diagnosing pouchitis. Transabdominal ultrasound had good utility [area under the curve: 0.78] in diagnosing moderate-severe pre-pouch ileitis. Transperineal ultrasound had good utility for the diagnosis of pouchitis [area under the curve: 0.79]. Faecal calprotectin differentiated inflammatory from non-inflammatory pouch disorders, such as irritable pouch syndrome, with an area under the curve of 0.90. Faecal calprotectin <100 µg/g ruled out inflammatory pouch disorders with a sensitivity of 94%.

Conclusions

Faecal calprotectin and ultrasound are accurate and complementary tests to diagnose and localise inflammation of the ileoanal pouch. Prospective studies are needed to validate proposed sonographic indices and calprotectin levels.
Low-dose rivaroxaban and aspirin among patients with peripheral artery disease: a meta-analysis of the COMPASS and VOYAGER trials
Authors: Anand Sonia S , Hiatt Will , Dyal Leanne , Bauersachs Rupert , Berkowitz Scott D , Branch Kelley R H , Debus Sebastian , Fox Keith A A , Liang Yan , Muehlhofer Eva , Nehler Mark , Haskell Lloyd P , Patel Manesh , Szarek Michael , Yusuf Salim , Eikelboom John , Bonaca Marc P
Published: July 2021

Aims

Peripheral artery disease (PAD) patients suffer a high risk of major cardiovascular (CV) events, with athero-thrombo-embolism as the underlying pathophysiologic mechanism. Recently, two large randomized clinical trials evaluated the efficacy and safety of low-dose rivaroxaban twice daily plus aspirin in stable PAD outpatients and those immediately after peripheral revascularization. We sought to determine if the effects of low-dose rivaroxaban and aspirin compared to aspirin alone are consistent across this broad spectrum of PAD patients.

Methods and results

We conducted a random-effects meta-analysis of the COMPASS and VOYAGER randomized trials among 11 560 PAD patients (4996 from COMPASS and 6564 from VOYAGER) in the primary analysis and 9332 (2768 from COMPASS and 6564 from VOYAGER) with lower extremity (LE)-PAD in the secondary analysis. The hazard ratio (HR) for the composite of CV death, myocardial infarction, ischaemic stroke, acute limb ischaemia, or major vascular amputation was 0.79 (95% confidence interval, CI: 0.65–0.95) comparing low-dose rivaroxaban plus aspirin to aspirin alone. While the risk of major bleeding was increased with low-dose rivaroxaban plus aspirin compared to aspirin alone [HR: 1.51 (95% CI: 1.22–1.87)], there was no significant increase in severe bleeding [HR: 1.18 (95% CI: 0.79–1.76)]. Similar effects were observed in the subset with symptomatic LE-PAD.

Conclusions

Among PAD patients, low-dose rivaroxaban plus aspirin is superior to aspirin alone in reducing CV and limb outcomes including acute limb ischaemia and major vascular amputation. This reduction is offset by a relative increase in major bleeding, but not by an excess of fatal or critical organ bleeding. The consistency of findings of these trials supports the use of combination low-dose rivaroxaban plus aspirin in PAD patients across a broad spectrum of disease.
Applications of virus-induced gene silencing for identification of gene function in fruit
Authors: Liu Gangshuai , Li Hongli , Fu Daqi
Published: July 2021

With the development of bioinformatics, it is easy to obtain information and data about thousands of genes, but the determination of the functions of these genes depends on methods for rapid and effective functional identification. Virus-induced gene silencing (VIGS) is a mature method of gene functional identification developed over the last 20 years, which has been widely used in many research fields involving many species. Fruit quality formation is a complex biological process, which is closely related to ripening. Here, we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.
Chemical rescue of mutant proteins in livingSaccharomyces cerevisiaecells by naturally occurring small molecules
Authors: Hassell Daniel S , Steingesser Marc G , Denney Ashley S , Johnson Courtney R , McMurray Michael A
Published: July 2021

Intracellular proteins function in a complex milieu wherein small molecules influence protein folding and act as essential cofactors for enzymatic reactions. Thus protein function depends not only on amino acid sequence but also on the concentrations of such molecules, which are subject to wide variation between organisms, metabolic states, and environmental conditions. We previously found evidence that exogenous guanidine reverses the phenotypes of specific budding yeast septin mutants by binding to a WT septin at the former site of an Arg side chain that was lost during fungal evolution. Here, we used a combination of targeted and unbiased approaches to look for other cases of “chemical rescue” by naturally occurring small molecules. We report in vivo rescue of hundreds of Saccharomyces cerevisiae mutants representing a variety of genes, including likely examples of Arg or Lys side chain replacement by the guanidinium ion. Failed rescue of targeted mutants highlight features required for rescue, as well as key differences between the in vitro and in vivo environments. Some non-Arg mutants rescued by guanidine likely result from “off-target” effects on specific cellular processes in WT cells. Molecules isosteric to guanidine and known to influence protein folding had a range of effects, from essentially none for urea, to rescue of a few mutants by DMSO. Strikingly, the osmolyte trimethylamine-N-oxide rescued ∼20% of the mutants we tested, likely reflecting combinations of direct and indirect effects on mutant protein function. Our findings illustrate the potential of natural small molecules as therapeutic interventions and drivers of evolution.
“When I Need to Travel, I Feel Feverish”: Everyday Experiences of Transport Inequalities Among Older Adults in Dhaka, Bangladesh
Authors: Jahangir Selim , Bailey Ajay , Hasan Musleh Uddin , Hossain Shanawez , Helbich Marco , Hyde Martin
Published: July 2021

Background and Objectives

Buses are the most common form of public transport for older adults in developing countries. With over 37% of total trips, buses are the principal mode of transport in Dhaka. The majority of older adults are dependent on buses because of their affordability relative to other modes such as auto-rickshaws, rideshares, and taxis. This study aims to investigate key barriers in accessing buses in Dhaka and the consequences of these barriers to the everyday mobility of older adults.

Research Design and Methods

Thirty participants aged 60 and older were recruited from 2 socioeconomically different neighborhoods in Dhaka. We employed a thematic analysis of visual surveys and in-depth interviews to understand older adults’ spatial and cultural context and their experiences using buses in their everyday lives.

Results

Boarding and deboarding buses were common barriers for older adults due to overcrowding and traffic congestion. In addition, older adults faced challenges such as ageism, gender discrimination, and undesirable behavior by transport personnel and co-passengers. These barriers affected their independent mobility and influenced their access to work and social life, contributing to their social exclusion.

Discussion and Implications

This study illustrates the challenges faced by older adults when accessing public transport and the need to improve access to work, health care, and social life. Inclusive transport policies are essential in low- and middle-income countries to improve the well-being of older adults.
A unified description of surface waves and guided waves with relative amplitude dispersion maps
Authors: Sun Chengyu , Wang Zhinong , Wu Dunshi , Cai Ruiqian , Wu Han
Published: July 2021

Compared with surface waves, guided waves are rarely applied in near-surface investigation. The main reason may lie in the complexity of their dispersion curves. Besides, the study and understanding of guided wave dispersion characteristics are now also inadequate and not deep enough. In this paper, we derived the complete theoretical dispersion curves of P–SV-wave and pure P-wave systems in layered media based on the transmission matrix method and obtained the relative displacement amplitude coefficients at the free surface as a function of frequency and phase velocity for both surface and guided waves. By assigning the value of relative displacement amplitude coefficient to the corresponding point (f,v) on dispersion curve, we got a multi-information diagram called relative amplitude dispersion map (RADM). As a unified description of surface and guided waves, RADM not only shows the velocity–frequency relationship but also represents the polarized energy ratio at the free surface by display colours. The accuracy of RADM was proved by synthetic seismic records, in which RADMs fit well with the corresponding dispersion energy of surface and guided waves. In addition, we designed six models with different Poisson's ratio (PR) and different layer numbers for comparison. It shows that the dispersive vertical-to-horizontal amplitude ratio of guided waves is complex and discontinuous in RADM, which brings great difficulty for mode identification and even affects the subsequent inversion. Tests also show that for high PR layers, the trends of guided P–SV-wave dispersion curves are basically consistent with those of pure P wave. With the decrease of PR, dispersion curves of guided P–SV wave gradually deviate from those of pure P wave. However, RADMs can be greatly consistent with the dispersion energy in either case. This is of great significance for the inversion of near-surface P and S velocities by using dispersion relationships of multimode surface and guided waves.
A systematic investigation of piercing-point-dependent seismic azimuthal anisotropy
Authors: Jia Yan , Liu Kelly H , Kong Fansheng , Liu Lin , Gao Stephen S
Published: July 2021

The vast majority of teleseismic XKS (including SKS, SKKS and PKS) shear wave splitting studies interpret the observed splitting parameters (fast orientation and splitting time) based on the assumption of a spatially invariant anisotropy structure in the vicinity of a recording station. For such anisotropy structures the observed splitting parameters are either independent of the arriving azimuth of the seismic ray paths if the medium traversed by the ray paths can be represented by a single layer of anisotropy with a horizontal axis of symmetry (i.e. simple anisotropy), or demonstrate a periodic variation with respect to the arriving azimuth for a more complicated structure of anisotropy (e.g. multiple layers with a horizontal axis of symmetry, or a single layer with a dipping axis). When a recording station is located near the boundary of two or more regions with different anisotropy characteristics, the observed splitting parameters are dependent on the location of the ray piercing points. Such a piercing-point dependence is clearly observed using a total of 360 pairs of XKS splitting parameters at three stations situated near the northeastern edge of the Sichuan Basin in central China. For a given station, the fast orientations differ as much as 90°, and the azimuthal variation of the fast orientations lacks a 90° or 180° periodicity which is expected for double-layered or dipping axis anisotropy. The observed splitting parameters from the three stations are spatially most consistent when they are projected at a depth of ∼250 km, and can be explained by shear strain associated with the absolute plate motion and mantle flow deflected by the cone-shaped lithospheric root of the Sichuan Basin.
A spatial analysis of out-of-pocket payments for healthcare in Malawi
Authors: Mwale Martin Limbikani , Mchenga Martina , Chirwa Gowokani Chijere
Published: July 2021

Out-of-pocket (OOP) expenditures on health remain high in many low- and middle-income countries despite policy efforts aiming to reduce these health costs by targeting their hotspots. Hotspot targeting remains inadequate, particularly where the OOP expenditures are related across geographic regions due to unequal demand, supply and prices of healthcare services. In this paper, we investigate the existence of geographical correlations in OOP health expenditures by employing a spatial Durbin model on data from 778 clusters obtained from the 2016 Malawi’s Integrated Household Survey. Results reveal that Malawian communities face geographical spillovers of OOP health expenditures. Furthermore, we find that factors including household size, education and geographical location are important drivers of the OOP health expenditure’s spatial dependency. The paper calls for policy in low-income countries to improve the quality and quantity of healthcare services in both OOP hotspots and their neighbouring communities.
Discovery of genomic variation across a generation
Authors: Trost Brett , Loureiro Livia O , Scherer Stephen W
Published: July 2021

Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
A long road to recovery: dynamics and ecology of the marbled rockcod (Notothenia rossii, family: Nototheniidae) at South Georgia, 50 years after overexploitation
Authors: Hollyman Philip R , Hill Simeon L , Laptikhovsky Vladimir V , Belchier Mark , Gregory Susan , Clement Alice , Collins Martin A
Published: July 2021

Exploitation is one of the major drivers of change in marine ecosystems. Following discovery in 1775, South Georgia saw sequential overexploitation of living resources, including seals, whales, and fish. Although exploitation is now tightly regulated, the ecosystem is still recovering. Marbled rockcod, Notothenia rossii (Richardson 1844), was the first fish species to be commercially exploited and high catches between 1967 and 1972 resulted in dramatic stock decline. Here, we use 30 years of trawl survey data to provide the first evidence of a sustained increase in the N. rossii population starting two decades after the prohibition of targeted fishing in 1985. The way species respond to change is mediated in part by trophic relationships with other organisms. We present the first multi-year, spatially-resolved comparison of adult N. rossii diet at South Georgia, highlighting a variable diet with less reliance on Antarctic krill than previously thought. Life history factors and possible heavy predation on early life stages might have delayed their recovery while diet plasticity potentially supported recent population growth. Due to the dynamic ecosystem at South Georgia and questions over catch reports from the period of heaviest exploitation, it is unlikely the current ecosystem could support a recovery to estimated pre-exploitation levels.
The limited function of law in transforming rule of law: A reply to Ruiping Ye
Authors: Chang Wen-Chen
Published: July 2021

This article is a reply to Ruiping Ye’s article on China’s journey towards socialist rule of law. Ye argues that despite a string of legal reforms, China remains a system of rule by law rather than rule of law. Ye provides two main observations. One is the Communist Party’s instrumental perception of law, and the other is the Communist Party’s need to maintain legal legitimacy. This article agrees with Ye’s two observations, and extends the discussion further to the future of such a rule by law or what other scholars call authoritarian legality. By highlighting an intensely debated issue on whether to further legalize or constitutionalize the Communist Party’s absolute rule, this article questions the gradual and formative function of law in bringing profound change. Particularly noteworthy are the sustainability of legitimacy generated by authoritarian legality and the efficacy of a legal transformation from within.
Monitoring Emerging Human Immunodeficiency Virus Drug Resistance in Sub-Saharan Africa in the Era of Dolutegravir
Authors: da Silva Juliana , Pals Sherri , Chang Joy , Hackett Stephanie , Godfrey Catherine , Raizes Elliot
Published: July 2021

Dolutegravir-based regimens are now standard of care for human immunodeficiency virus treatment for millions of people around sub-Saharan Africa. To ensure its continued efficacy, monitoring of emerging drug resistance that inform a treatment strategy among those failing is crucial. In this report, we outline the US President’s Emergency Plan for AIDS Relief to leverage viral load infrastructure to implement effective drug resistance surveillance in the countries it supports.
Integration of crop growth model and constraint-based metabolic model predicts metabolic changes over rice plant development under water-limited stress
Authors: Shaw Rahul , Cheung C Y Maurice
Published: July 2021

Rice is a major staple food worldwide and understanding its metabolism is essential for improving crop yield and quality, especially in a changing climate. Constraint-based modelling is an established method for studying metabolism at a systems level, but one of its limitations is the difficulty in directly integrating certain environmental factors, such as water potential, to the model for predicting metabolic changes in response to environmental changes. Here, we developed a framework to integrate a crop growth model and an upgraded diel multi-organ genome-scale metabolic model of rice to predict the metabolism of rice growth under normal and water-limited conditions. Our model was able to predict distinct metabolic adaptations under water-limited stress compared to normal condition across multiple developmental stages. Our modelling results of dynamic changes in metabolism over the whole-plant growth period highlighted key features of rice metabolism under water-limited stress including early leaf senescence, reduction in photosynthesis and significant nitrogen assimilation during grain filling.
Spatiotemporal model of cellular mechanotransduction via Rho and YAP
Authors: Novev Javor K , Heltberg Mathias L , Jensen Mogens H , Doostmohammadi Amin
Published: July 2021

How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio’s time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.