bluuebunny/crossref_metadata_2025_split huggingface dataset:
memerna: Sparse RNA Folding Including Coaxial Stacking
Authors: Courtney Eliot , Datta Amitava , Mathews David H. , Ward Max 
Published: August 2023

AbstractDetermining RNA secondary structure is a core problem in computational biology. Fast algorithms for predicting secondary structure are fundamental to this task. We describe a modified formulation of the Zuker-Stiegler algorithm with coaxial stacking, a stabilizing interaction in which the ends of multi-loops are stacked. In particular, optimal coaxial stacking is computed as part of the dynamic programming state, rather than inline. We introduce a new notion of sparsity, which we callreplaceability. The modified formulation along with replaceability allows sparsification to be applied to coaxial stacking as well, which increases the speed of the algorithm. We implemented this algorithm in software we callmemerna, which we show to have the fastest exact RNA folding implementation out of several popular RNA folding packages supporting coaxial stacking. We also introduce a new notation for secondary structure which includes coaxial stacking, terminal mismatches, and dangles (CTDs) information.
Genetic crosses within and between species ofCryptosporidium
Authors: Shaw Sebastian , Cohn Ian S. , Baptista Rodrigo P. , Xia Guoqin , Melillo Bruno , Agyabeng-Dadzie Fiifi , Kissinger Jessica C. , Striepen Boris 
Published: August 2023

AbstractParasites and their hosts are engaged in rapid coevolution that balances competing mechanisms of virulence, resistance, and evasion. This often leads to host specificity, but genomic reassortment between different strains can enable parasites to jump host barriers and conquer new niches. In the apicomplexan parasiteCryptosporidiumgenetic exchange has been hypothesized to play a prominent role in adaptation to humans. The sexual lifecycle of the parasite provides a potential mechanism for such exchange; however, the boundaries ofCryptosporidiumsex are currently undefined. To explore this experimentally, we established a model for genetic crosses. Drug resistance was engineered using a mutated phenylalanyl tRNA synthetase gene and marking strains with this and the previously used Neo transgene enabled selection of recombinant progeny. This is highly efficient, and genomic recombination is evident and can be continuously monitored in real time by drug resistance, flow cytometry, and PCR mapping. Using this approach multiple loci can now be modified with ease. We demonstrate that essential genes can be ablated by crossing a Cre recombinase driver strain with floxed strains. We further find that genetic crosses are also feasible between species. CrossingC. parvum,a parasite of cattle and humans, andC. tyzzeria mouse parasite resulted in progeny with a recombinant genome derived from both species that continues to vigorously replicate sexually. These experiments have important fundamental and translational implications for the evolution ofCryptosporidiumand open the door to reverse- and forward-genetic analysis of parasite biology and host specificity.Significance statementThe parasiteCryptosporidiumis a leading cause of diarrheal disease. While infection is common all around the world, young children experiencing malnutrition are impacted most profoundly, and the disease is an important contributor to early childhood mortality. This study experimentally demonstrates that different strains and even species ofCryptosporidiumcan recombine their genomes through sex. The progeny of such genetic crosses shows combined features of both parents, with resistance to multiple drugs being one example. Sex thus provides a critical mechanism for the parasite to rapidly adapt to changing environments and hosts.Genetic crosses as an experimental tool may also be harnessed in the future to discover the genes underlying differences in virulence, drug sensitivity, and immunogenicity between parasite isolates.
The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress
Authors: Keszthelyi Andrea , Whale Alex , Houseley Jon , Baxter Jonathan 
Published: August 2023

SUMMARYTof1/Timeless protects eukaryotic cells from DNA replication stress as part of the Fork Protection Complex (FPC). Tof1 supports rapid DNA replication, fork pausing, and resolution of DNA topological stress. Here, we show that disruption of FPC function through loss of either Tof1 or Mrc1 results in DNA damage in long replicons. Despite increasing DNA damage in long replicons, loss of either Tof1 or Mrc1 concurrently reduces DNA damage in regions prone to damage caused by DNA topological stress, indicating that the rapid replication promoted by the FPC fosters completing DNA replication at the cost of increased vulnerability to DNA topological stress. Supporting this we find that atof1mutation that selectively inhibits DNA topological stress resolution increases DNA damage in contexts prone to DNA topological stress. Our data indicates that the FPC balances rapid replication with recruitment of topoisomerase I to resolve the topological stress generated by increased DNA unwinding.
Crop diversity, sustainable food and nutritional security among smallholder farmers in Ghana
Authors: Fremmpong Raymond Boadi , Gross Elena , Owusu Victor 
Published: August 2023

PurposeThe nexus between sustainable agri-food production and food security outcomes of farm households in sub-Saharan Africa is attracting policy attention. This study analyzes the effects of crop diversity on the incidence of food scarcity, dietary diversity, and the sale and consumption of own crops.Design/methodology/approachThe study uses panel data collected in 2015 and 2018 on a randomly selected sample of 2553 households from 49 villages in northern Ghana. The study employed a fixed effects modeling approach in the empirical analysis.FindingsThe study finds that crop diversity is positively associated with better dietary diversity, reduced hunger, lower food expenditure, and higher consumption of own produce. The results show positive effects of crop diversity on the total harvested output and sale of agricultural production. Whilst sales improved sustainable food and nutrition security by providing purchasing power to buy nutritional inputs in the market, consumption of own produce rather improved food availability by reducing food scarcity and malnutrition.Practical implicationsCrop diversity is one of the pathways for promoting sustainable agri-food production systems to ensure the food and nutritional security of vulnerable populations and promote biodiversity to achieve environmental goals in sub-Saharan Africa. Crop diversity reduces food expenditure and raises rural incomes through improved outputs and sales, which empowers farm households to diversify their dietary options to be able to overcome incidences of hunger and malnutrition in periods of food scarcity.Originality/valueThe present study improves the understanding of sustainable agri-food production through crop diversity and its implications on food and nutrition security outcomes. The panel data and fixed effects modelling approach address the endogeneity problem between crop diversity and household tastes and preferences.
Pricing model, engagement model and firm performance: evidence from Indian data science industry
Authors: Jhamb Deepika , Kaur Sukhpreet , Pandey Saurabh , Mittal Amit 
Published: August 2023

PurposeData science industry is a multidisciplinary field that deals with a large amount of data and derives useful information for taking routine and strategic business decisions. The purpose of this article is to examine the relationship between pricing models, engagement models, and firm performance (FP). This study also aims at uncovering the most effective pricing model and engagement model for improving FP.Design/methodology/approachIndian data scientists were the respondents of the study. A total of 213 responses were carefully chosen. The data were analyzed using structural equations on Statistical Package for Social Sciences-Analysis of Moment Structures (SPSS-AMOS) version 25 software.FindingsThe findings of the study suggested the positive and significant impact of pricing models and engagement models on FP. Value-based pricing strategies have the maximum impact on FP. On the other hand, managed services have a higher influence on FP.Originality/valueBy developing a multi-faceted framework, this study is a novel contribution to the field of business strategy, especially for the data science industry.
An operationalization of antifragility in inventory management
Authors: Munoz Albert , Zhou Quan Spring 
Published: August 2023

PurposeThe paper explores and characterizes antifragility in simple inventory systems exposed to demand variability, providing the initial inroads to operationalizing antifragility in the context of inventory management. Antifragility refers to the feature of a system that can benefit from uncertainty, rather than suffer from it. The paper expands the concept of inventory beyond that of risk mitigation and towards one of enabling antifragility.Design/methodology/approachThe study employs analytical and simulation modelling of an inventory system with two classes of demand. To separate the influence of factors, a simple inventory policy with a range of fixed order quantities is modelled, allowing for the identification of antifragile regions in an experimental space.FindingsOutputs uncover a variety of performance outcomes, ranging from settings where additional inventory yields no benefit, to areas where additional inventory results in increasing normalized profit with increasing uncertainty, demonstrating antifragility. In between these regions, increases in normalized profit are bounded, and confined to specific regions.Research limitations/implicationsThis research expands academic understanding of inventory as a vehicle to achieving antifragile outcomes. Although this paper does not solve for an optimal policy as typical inventory research does, it instead characterizes the antifragile outcomes within simple inventory systems. Further research should be carried out to investigate antifragility in settings of greater complexity and design ordering policies leveraging inventory towards a gain from uncertainty.Practical implicationsTypically, inventory is used to buffer against uncertainty, and, with a given amount of inventory, the performance is expected to degrade with increasing variability. In this paper, the authors demonstrate that certain levels of additional inventory can result in antifragility and increase profitability as uncertainty increases, extending beyond traditional conceptualizations of inventory and uncertainty.Originality/valueEmpirical research into designing antifragile outcomes is limited, with very few examples of increasing performance with increases in uncertainty. This article presents an initial empirical exploration of how additional inventory can result in antifragility.
CEO's self-oriented perfectionism, strategic decision comprehensiveness and firm resilience
Authors: Wang Qian , Wu Qin , Xie Luqun , Zhang Xiao 
Published: August 2023

PurposeFirm resilience is critical for firm survival and development. The purpose of this study is to investigate whether chief executive officer's (CEO) self-oriented perfectionism affects firm resilience by taking into consideration of the mediating role of strategic decision comprehensiveness and the moderating effect of competitive uncertainty.Design/methodology/approachThis study adopts the survey method and uses two-wave survey data collected from 140 CEOs in different industries in China. The ordinary least square (OLS) regression model and path analysis are adopted to test the authors' theoretical hypotheses.FindingsThe results show that self-oriented perfectionism drives CEOs to pay attention to thoroughness and detail, which helps enhance strategic decision comprehensiveness and further facilitates firm resilience. Furthermore, the positive effect of CEO's self-oriented perfectionism on strategic decision comprehensiveness is weakened when competitive uncertainty is high.Practical implicationsTo promote firm resilience, self-oriented perfectionism can be considered when hiring or promoting key decision-makers. When making strategic decisions, top managers need to search for adequate information, consider various factors and seek more alternative plans to improve strategic decision comprehensiveness to further facilitate firm resilience.Originality/valueThis study pioneers the influence of CEO's perfectionism on firm resilience and further tackles the underlying mechanism behind the influence, which contributes to extending the micro-foundation of firm resilience and enriching perfectionism literature in the strategic leadership field.
Differences in reproductive function between terminal and lateral flowers in the capitulum of Albizia julibrissin (Fabaceae) based on female fertility, ovule number, and pistil and polyad size
Authors: Mizusawa Leiko , Kato Saori , Kurosawa Takahide 
Published: August 2023

AbstractThe division of labor between florets responsible for reproduction and special functions occurs widely in condensed inflorescences. The capitulum of Albizia julibrissin consists of approximately 10–20 lateral flowers and usually one nectar‐secreting terminal flower; the two flower types are morphologically distinct, but the differences in reproductive function have not been revealed. To determine the differences in reproductive function between terminal and lateral flowers, we compared the ratio of terminal and lateral flowers at the flowering and young pod stages. Additionally, ovule number, stigma size, polyad size, and the ratio of flower abscission were compared between the two flower types. Significant differences were detected only in female fertility between the two flower types. At the flowering stage, 6.8% of flowers were terminal flowers, whereas at the young pod stage, all young fruits were obtained from lateral flowers. At the final stage of blooming, based on the generalized linear model analysis, the ratio of surviving terminal flowers was lower than that of the lateral flowers in a capitulum. These results suggest that the terminal flowers of A. julibrissin had female sterility or, at least, female fertility was lower than in lateral flowers. Therefore, it is necessary to reexamine some previous studies that assumed A. julibrissin to be andromonoecious with hermaphroditic terminal flowers and male lateral flowers. Further comparisons of the quality of ovules and polyads are necessary to clarify whether there is a division of labor between the terminal and lateral flowers in A. julibrissin.
Bone calcification rate as a factor of craniofacial transformations in salmonid fish: Insights from an experiment with hormonal treatment of calcium metabolism
Authors: Markevich Grigorii N. , Pavlova Nadezhda S. , Kapitanova Daria V. , Esin Evgeny V. 
Published: August 2023

AbstractAdaptation to different environments can be achieved by physiological shifts throughout development. Hormonal regulators shape the physiological and morphological traits of the evolving animals making them fit for the particular ecological surroundings. We hypothesized that the artificially induced hypersynthesis of calcitonin and parathyroid hormone mutually influencing calcium metabolism could affect bone formation during early ontogeny in fish imitating the heterochrony in craniofacial ossification in natural adaptive morphs. Conducting an experiment, we found that the long‐standing treatment of salmonid juveniles with high doses of both hormones irreversibly shifts the corresponding hormone status for a period well beyond the time scale for total degradation of the injected hormone. The hormones program the ossification of the jaw suspension bones and neurocranial elements in a specific manner affecting the jaws position and pharingo‐branchial area stretching. These morphological shifts resemble the adaptive variants found in sympatric pelagic and demersal morphs of salmonids. We conclude that solitary deviations in the regulators of calcium metabolism could determine functional morphological traits via transformations in skeletal development.
Performance and field host range of the life stages of Cornops aquaticum, a biological control agent of water hyacinth
Authors: Franceschini M. Celeste , Hill Martin , Fuentes‐Rodríguez Daniela , Gervazoni Paula B. , Sabater Lara M. , Coetzee Julie A. 
Published: August 2023

AbstractHost specificity determination of weed biocontrol agents has historically relied on evidence generated through quarantine trials in the region of introduction. These trials could give ‘false positive’ results due to a maximum type I error probability, and where possible, more research under field conditions should be conducted in the region of origin. The oligophagous, semiaquatic grasshopper, Cornops aquaticum Bruner (Orthoptera: Acrididae, Tetrataeniini), was released in South Africa for the biological control of Pontederia crassipes Pellegrini and Horn (Pontederiaceae). The aim of this study was to assess how the performance and field host range of C. aquaticum varies according to its stages of development, and how this contributes to the understanding of the relationship between the fundamental (laboratory‐based) and the ecological (field‐based) host range of this grasshopper, and its implications for water hyacinth biocontrol. We conducted post‐release laboratory no‐choice trials, confining early instars (instars 1 and 2), later instars (instars 3–6), and adult females and males in mesh cages, to determine insect performance on wetland plants growing in sympatry with P. crassipes. Also, gut analysis from field‐collected C. aquaticum was done to determine the ecological host range of this insect, identifying epidermal tissue of consumed plants. In no‐choice trials, survival rates of the later instars and adult C. aquaticum were similar on Pistia stratiotes L. (Araceae), Oxycaryum cubense (Poepp. & Kunth) Lye (Cyperaceae), and P. crassipes. However, under field conditions, P. crassipes and the congeneric Pontederia azurea Sw. were the only plant contents in the guts of early instars and the most abundant species in later instars and adults. The results support the hypothesis that C. aquaticum is an oligophagous insect on the genus Pontederia, and that different life stages should be considered when conducting host‐specificity trials in externally feeding mobile herbivore species. Diet composition of field‐collected insects thus could help detect false positives in laboratory trials, being an additional and realistic approach in understanding and predicting the selection processes of the insect in the new environment. Retrospective analysis of potential agents that were rejected due to lack of host‐specificity, using the methods from this study, could add a suite of additional agents to programs where invasive weeds remain unmanaged.
Cancer in Victorian prisoners: a description of cancer diagnoses, demographics, risk factors and barriers to optimal care
Authors: Newnham Genni M. , Munton Karen , Shaw Mark , McLachlan Sue A. 
Published: August 2023

AbstractBackgroundThe Victorian prison population is growing and ageing. Little has been documented about this group's cancer incidence, presentation or treatment.AimsTo conduct a retrospective review of Victorian prisoners with cancer, including assessment of change over 15 years and adequacy of treatment delivery.MethodsDetailed demographic, cancer and treatment data were collected for all prisoners with malignancy treated at St Vincent's Hospital Melbourne from 2002 to 2017. Detailed analysis of adherence to Optimal Care Guidelines was undertaken for a subset. Descriptive statistics were used.ResultsWe identified 200 cancers in 191 prisoners. The population was predominantly male (185 of 191, 93%), with a median age of 54 years. Rates of cigarette smoking (118 of 191, 59%), mental illness (92 of 191, 46%) and intravenous drug use (59 of 191, 29.5%) were high. Exposure‐related cancers predominated (nonmelanoma skin cancer, lung cancer and hepatoma). Most were symptomatic (154 of 191, 77%) and almost one‐third had incurable disease at diagnosis (64 of 191, 32%). The number of prisoners with cancer increased over time (2002–2006 [T1], n = 31 vs 2012–2016 [T3], n = 101), as did the median age (45 years in T1 vs 55 years in T3) and rates of mental illness (10 of 31 [32%] in T1 vs 55 of 101 [54%] in T3). Delayed treatment initiation occurred in eight of 12 (66%) assessable patients, largely because of nonattendance.ConclusionsVictorian prisoners with cancer are at risk of poor outcomes because of late presentation, delayed treatment initiation and medical comorbidities. Tailored interventions are urgently required to improve the provision of timely, comprehensive cancer care to this vulnerable and growing population.
A novel mutation in PCD‐associated gene DNAAF3 causes male infertility due to asthenozoospermia
Authors: Wan Feng , Yu Lan , Qu Xiaowei , Xia Yanqing , Feng Ke , Zhang Lei , Zhang Na , Zhao Guihua , Zhang Cuilian , Guo Haibin 
Published: August 2023

AbstractPrimary ciliary dyskinesia (PCD) is a rare autosomal‐recessive disease manifested with recurrent infections of respiratory tract and infertility. DNAAF3 is identified as a novel gene associated with PCD and different mutations in DNAAF3 results in different clinical features of PCD patients, such as situs inversus, sinusitis and bronchiectasis. However, the sperm phenotypic characteristics of PCD males are generally poorly investigated. Our reproductive medicine centre received a case of PCD patient with infertility, who presented with sinusitis, recurrent infections of the lower airway and severe asthenozoospermia; However, no situs inversus was found in the patient. A novel homozygous mutation in DNAAF3(c.551T>A; p.V184E) was identified in the PCD patient by whole‐exome sequencing. Subsequent Sanger sequencing further confirmed that the DNAAF3 had a homozygous missense variant in the fifth exon. Transmission electron microscopy and immunostaining analysis of the sperms from the patient showed a complete absence of outer dynein arms and partial absence of inner dynein arms, which resulted in the reduction in sperm motility. However, this infertility was overcome by intracytoplasmic sperm injections, as his wife achieved successful pregnancy. These findings showed that the PCD‐associated pathogenic mutation within DNAAF3 also causes severe asthenozoospermia and male infertility ultimately due to sperm flagella axoneme defect in humans. Our study not only contributes to understand the sperm phenotypic characteristics of patients with DNAAF3 mutations but also expands the spectrum of DNAAF3 mutations and may contribute to the genetic diagnosis and therapy for infertile patient with PCD.
Family practice with fathers, social care, and capabilities
Authors: Perez‐Vaisvidovsky Nadav 
Published: August 2023

AbstractThe aim of this article is to offer a novel theoretical perspective on family practitioners' engagement with fathers, through the lens of theories of social care and capabilities. The paper shows how research on low engagement of fathers in family‐ and child‐related social interventions has advanced along three main axes: (a) giving voice to fathers, (b) analyzing workers' perceptions, and (c) what works analysis of father‐oriented programs. I point to several problems in existing research: the absence of a unifying theoretical framework and the lack of sufficient attention to issues of relationality and agency. Theories of care and the capabilities approach are offered as a framework. Applying these theoretical frameworks to existing research on father engagement raises new questions and directions for further studies, mainly in two directions: first, relationality and the configurations of relations and power within families and within welfare systems, and second, the effect of agency on father engagement.