bluuebunny/crossref_metadata_2025 huggingface dataset:
Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes
Authors: McDonough-Goldstein Caitlin E , Borziak Kirill , Pitnick Scott , Dorus Steve
Published: January 2021

Sexual reproduction in internally fertilizing species requires complex coordination between female and male reproductive systems and among the diverse tissues of the female reproductive tract (FRT). Here, we report a comprehensive, tissue-specific investigation of Drosophila melanogaster FRT gene expression before and after mating. We identified expression profiles that distinguished each tissue, including major differences between tissues with glandular or primarily nonglandular epithelium. All tissues were enriched for distinct sets of genes possessing secretion signals that exhibited accelerated evolution, as might be expected for genes participating in molecular interactions between the sexes within the FRT extracellular environment. Despite robust transcriptional differences between tissues, postmating responses were dominated by coordinated transient changes indicative of an integrated systems-level functional response. This comprehensive characterization of gene expression throughout the FRT identifies putative female contributions to postcopulatory events critical to reproduction and potentially reproductive isolation, as well as the putative targets of sexual selection and conflict.
biotoolsSchema: a formalized schema for bioinformatics software description
Authors: Ison Jon , Ienasescu Hans , Rydza Emil , Chmura Piotr , Rapacki Kristoffer , Gaignard Alban , Schwämmle Veit , van Helden Jacques , Kalaš Matúš , Ménager Hervé
Published: January 2021

Background

Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information used to describe life-scientific digital resources presents an obstacle to their utilization. Although several standardization efforts are emerging, no information schema has been sufficiently detailed to enable uniform semantic and syntactic description—and cataloguing—of bioinformatics resources.

Findings

Here we describe biotoolsSchema, a formalized information model that balances the needs of conciseness for rapid adoption against the provision of rich technical information and scientific context. biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with >17,000 machine-readable and human-understandable descriptions of software and other digital life-science resources. We compare our approach to related initiatives and provide alignments to foster interoperability and reusability.

Conclusions

biotoolsSchema supports the formalized, rigorous, and consistent specification of the syntax and semantics of bioinformatics resources, and enables cataloguing efforts such as bio.tools that help scientists to find, comprehend, and compare resources. The use of biotoolsSchema in bio.tools promotes the FAIRness of research software, a key element of open and reproducible developments for data-intensive sciences.
Is the routine health information system ready to support the planned national health insurance scheme in South Africa?
Authors: Nicol Edward , Hanmer Lyn A , Mukumbang Ferdinand C , Basera Wisdom , Zitho Andiswa , Bradshaw Debbie
Published: January 2021

Implementation of a National Health Insurance (NHI) in South Africa requires a reliable, standardized health information system that supports Diagnosis-Related Groupers for reimbursements and resource management. We assessed the quality of inpatient health records, the availability of standard discharge summaries and coded clinical data and the congruence between inpatient health records and discharge summaries in public-sector hospitals to support the NHI implementation in terms of reimbursement and resource management. We undertook a cross-sectional health-records review from 45 representative public hospitals consisting of seven tertiary, 10 regional and 28 district hospitals in 10 NHI pilot districts representing all nine provinces. Data were abstracted from a randomly selected sample of 5795 inpatient health records from the surgical, medical, obstetrics and gynaecology, paediatrics and psychiatry departments. Quality was assessed for 10 pre-defined data elements relevant to NHI reimbursements, by comparing information in source registers, patient folders and discharge summaries for patients admitted in March and July 2015. Cohen's/Fleiss’ kappa coefficients (κ) were used to measure agreements between the sources. While 3768 (65%) of the 5795 inpatient-level records contained a discharge summary, less than 835 (15%) of diagnoses were coded using ICD-10 codes. Despite most of the records having correct patient identifiers [κ: 0.92; 95% confidence interval (CI) 0.91–0.93], significant inconsistencies were observed between the registers, patient folders and discharge summaries for some data elements: attending physician’s signature (κ: 0.71; 95% CI 0.67–0.75); results of the investigation (κ: 0.71; 95% CI 0.69–0.74); patient’s age (κ: 0.72; 95% CI 0.70–0.74); and discharge diagnosis (κ: 0.92; 95% CI 0.90–0.94). The strength of agreement for all elements was statistically significant (P-value ≤ 0.001). The absence of coded inpatient diagnoses and identified data inaccuracies indicates that existing routine health information systems in public-sector hospitals in the NHI pilot districts are not yet able to sufficiently support reimbursements and resource management. Institutional capacity is needed to undertake diagnostic coding, improve data quality and ensure that a standard discharge summary is completed for every inpatient.
Promoting healthy and sustainable diets: barriers and enablers for successful policy activities in Australia
Authors: Denniss Emily , Woods Julie , Lawrence Mark
Published: January 2021

Consumption of healthy and sustainable diets (HSD) provides opportunities to co-benefit human health and adapt to and mitigate climate change. Despite robust evidence and policy recommendations from authoritative groups to reorientate the food system to favour consumption of HSD there has been limited policy action. This study investigated potential barriers and enablers for successful HSD policies in Australia. A review of HSD policy recommendations and of current Australian policies was undertaken. Results from the reviews informed a Delphi study, which investigated Australian stakeholder opinions on the effectiveness of HSD policy recommendations and barriers and enablers to creating successful HSD policies. Nine participants completed two Delphi iterations. A lack of consensus was reached on the effectiveness of policy recommendations. Consensus was reached on the effect of five barriers and three enablers. Key barriers were: the complex nature of the food system, competing interests of stakeholders, pressure from industry, government silos and lack of political will. Key enablers were: building relationships with key stakeholders across multiple disciplines and sectors, understanding the policy making process and developing a clear and coherent solution. Most of the identified barriers fall under the broad category of lack of political will. Interrelationships between barriers are likely worsening the impact of inadequate political will. There is a need to act on the identified barriers and enablers to secure the HSD policies that are required. Interactions between barriers may present an opportunity to address them simultaneously.
Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Authors: Laskar Ruhina S , Li Peng , Ecsedi Szilvia , Abedi-Ardekani Behnoush , Durand Geoffroy , Robinot Nivonirina , Hubert Jean-Noël , Janout Vladimir , Zaridze David , Mukeria Anush , Mates Dana , Holcatova Ivana , Foretova Lenka , Swiatkowska Beata , Dzamic Zoran , Milosavljevic Sasa , Olaso Robert , Boland Anne , Deleuze Jean-François , Muller David C , McKay James D , Brennan Paul , Le Calvez-Kelm Florence , Scelo Ghislaine , Chanudet Estelle
Published: January 2021

Sexual dimorphism in cancer incidence and outcome is widespread. Understanding the underlying mechanisms is fundamental to improve cancer prevention and clinical management. Sex disparities are particularly striking in kidney cancer: across diverse populations, men consistently show unexplained 2-fold increased incidence and worse prognosis.

We have characterized genome-wide expression and regulatory networks of 609 renal tumors and 256 non-tumor renal tissues. Normal kidney displayed sex-specific transcriptional signatures, including higher expression of X-linked tumor suppressor genes in women. Sex-dependent genotype–phenotype associations unraveled women-specific immune regulation. Sex differences were markedly expanded in tumors, with male-biased expression of key genes implicated in metabolism, non-malignant diseases with male predominance and carcinogenesis, including markers of tumor infiltrating leukocytes. Analysis of sex-dependent RCC progression and survival uncovered prognostic markers involved in immune response and oxygen homeostasis.

In summary, human kidney tissues display remarkable sexual dimorphism at the molecular level. Sex-specific transcriptional signatures further shape renal cancer, with relevance for clinical management.
Law enforcement access to electronic evidence across borders: mapping policy approaches and emerging reform initiatives
Authors: Abraha Halefom H.
Published: January 2021

With the ubiquity of cloud computing, criminal investigations today—including exclusively domestic ones—often require access to data across borders. However, the traditional system of cross-border legal cooperation—the Mutual Legal Assistance system—is ill-suited to this development. There is a growing consensus that this system is unsustainable and needs to be reformed or replaced with new alternatives. That is where the consensus ends, however. Despite the shared understanding of the problem and repeated calls for reform or replacement of the traditional system, there is little agreement on what these reforms or alternative approaches should look like. What one can witness instead is the proliferation of uncoordinated initiatives that could lead to further jurisdictional conflict and legal uncertainty.

The purpose of the present contribution is to map and examine these various initiatives based on the approaches they follow in addressing the challenges in obtaining electronic evidence across borders—issues that are referred to broadly in this article as ‘cross-border data access [CBDA] problem’. It tries to answer two questions: what approaches can best explain the proliferation of initiatives aimed at improving law enforcement access to electronic evidence across borders? To what extent are these initiatives apt to address the CBDA problem? This article develops and distinguishes between four approaches—reformist, unilateralist, internationalist and nuanced—that can best explain the current and emerging initiatives. It then examines the suitability and sustainability of these approaches against their stated objectives and some key principles that have enjoyed extensive support in policy and academic discussions.
Asylum Decisions as Performances: Intertextuality in Internal Credibility Assessment
Authors: Bodström Erna
Published: January 2021

This article shows how the Finnish Immigration Service approaches internal credibility assessment in asylum decisions. The internal credibility assessment is one of the most important parts of the asylum process, since it aims to assess the truthfulness of the asylum applicant’s account, customarily through evaluation of the level of detail, coherence, and sense of personal telling. If the account is not accepted as truthful, the applicant may not be granted asylum. In general, the internal credibility assessment is based on the asylum interview documented in the asylum record. The current study analyses 44 asylum decisions and the corresponding interview records to see how the internal credibility assessment is intertextually constructed in the decisions. The article shows that referring to detail seems to be used as a shorthand in the decisions to reject the applicant’s account, since it is used both in cases where the questions of the interviewer have been general, and in cases where the issue seems rather to be one of consistency in either the interview or the decision. The article further shows how the decisions portray the assumptions of the decision maker as more neutral, objective, and credible than those of the asylum applicant. Overall, the article argues that the asylum decisions become performances in which the form and internal argumentation may become more important than the intertextual coherence of the asylum case.
Bifurcation and chaos of BNNT-reinforced piezoelectric plate under complex load
Authors: Yang Jinhua , Fu Guo , Sun Gaofeng
Published: January 2021

By employing piezoelectric theory with thermal effects and von Kármán nonlinear plate theory, the constitutive equations of the boron nitride nanotube (BNNT)-reinforced piezoelectric plate under complex load are set up. The material constants are calculated by using the “XY” rectangle model. Referring to the Reissner variational principle, the nonlinear motion governing equations of the structure are deduced and resolved by the fourth-order Runge–Kutta method. The numerical results show that decreasing voltage and temperature and increasing volume ratio can delay the chaotic or multiple periodic motions of BNNT-reinforced piezoelectric plates, thus improving the dynamic stability of the structure.
Polysemy, synonymy, and metaphor: The use of theHistorical Thesaurus of Englishin translation studies
Authors: Corbett John , Li Li
Published: January 2021

This article proposes that the consideration of translation equivalences for lexical items in English benefits from reference to the diachronic digital resources of Historical Thesaurus of English and its offshoot projects, Mapping Metaphor with the Historical Thesaurus, and the Semantic Annotation and Mark-Up for Enhancing Lexical Searches semantic tagger. These resources are the result of a long-term endeavour to code every sense of every headword in the lexicographical record of the English language. There has hitherto been little research into the relevance of these resources to the translation challenges raised by synonymy, polysemy, and the semantic radiation of lexical items. The relevance of these resources and their potential application to the study of equivalence in translation is illustrated with reference to a selection of semantic domains in a Portuguese and a Chinese translation of Jack London’s The Call of the Wild.
Chromospheric activity in 55 Cancri – I. Results from theoretical wave studies
Authors: Fawzy Diaa E , Cuntz Manfred
Published: January 2021

We present theoretical models of chromospheric heating for 55 Cancri, an orange dwarf of relatively low activity. Self-consistent, non-linear, and time-dependent ab initio numerical computations are pursued encompassing the generation, propagation, and dissipation of waves. We consider longitudinal waves operating among arrays of flux tubes as well as acoustic waves pertaining to non-magnetic stellar regions. Additionally, flux enhancements for the longitudinal waves are also taken into account as supplied by transverse tube waves. The Ca ii K fluxes are computed (multi-ray treatment) assuming partial redistribution as well as time-dependent ionization (TDI). The self-consistent treatment of TDI (especially for hydrogen) greatly impacts the atmospheric temperatures and electron densities (especially behind the shocks); it also affects the emergent Ca  ii fluxes. Particularly, we focus on the influence of magnetic heating on the stellar atmospheric structure and the emergent Ca ii emission, as well as the impact of non-linearities. Our study shows that a higher photospheric magnetic filling factor entails a larger Ca ii emission; however, an increased initial wave energy flux (e.g. associated with mode coupling) is of little difference. Comparisons of our theoretical results with observations will be conveyed in forthcoming Paper II.
The effect of emission lines on the performance of photometric redshift estimation algorithms
Authors: Csörnyei Géza , Dobos László , Csabai István
Published: January 2021

We investigate the effect of strong emission line galaxies on the performance of empirical photometric redshift estimation methods. In order to artificially control the contribution of photometric error and emission lines to total flux, we develop a PCA-based stochastic mock catalogue generation technique that allows for generating infinite signal-to-noise ratio model spectra with realistic emission lines on top of theoretical stellar continua. Instead of running the computationally expensive stellar population synthesis and nebular emission codes, our algorithm generates realistic spectra with a statistical approach, and – as an alternative to attempting to constrain the priors on input model parameters – works by matching output observational parameters. Hence, it can be used to match the luminosity, colour, emission line and photometric error distribution of any photometric sample with sufficient flux-calibrated spectroscopic follow-up. We test three simple empirical photometric estimation methods and compare the results with and without photometric noise and strong emission lines. While photometric noise clearly dominates the uncertainty of photometric redshift estimates, the key findings are that emission lines play a significant role in resolving colour space degeneracies and good spectroscopic coverage of the entire colour space is necessary to achieve good results with empirical photo-z methods. Template-fitting methods, on the other hand, must use a template set with sufficient variation in emission line strengths and ratios, or even better, first estimate the redshift empirically and fit the colours with templates at the best-fit redshift to calculate the K-correction and various physical parameters.
EDTAKI: a Nephrology and Public Policy Committee platform call for more European involvement in acute kidney injury
Authors: Vanholder Raymond , Rondeau Eric , Anders Hans-Joachim , Carlson Nicholas , Fliser Danilo , Kanbay Mehmet , Lopes José António , Murray Patrick T , Ortiz Alberto , Sanz Ana B , Selby Nicholas M , Wiecek Andrzej , Massy Ziad A
Published: January 2021

Background

Acute kidney injury (AKI) is an often neglected but crucial element of clinical nephrology. The aim of the Nephrology and Public Policy Committee (NPPC) of the European Renal Association–European Dialysis and Transplant Association is to promote several key aspects of European nephrology. One of the targets proposed by the NPPC was to advance European nephrology involvement in AKI.

Methods

We undertook a literature analysis to define the current position of European nephrology in the field of AKI compared with other regions and to determine how different European countries compare with each other.

Results

It appeared that vis-à-vis countries with a comparable socio-economic status (the USA, Australia, New Zealand and Canada), the European contribution was almost 50% less. Within Europe, Central and Eastern Europe and countries with a lower gross domestic product showed lower scientific output. Nephrologists contributed to less than half of the output. There was no trend of a change over the last decade.

Conclusions

There is room to improve the contribution of European nephrology in the field of AKI. We propose a model on how to promote clinical collaboration on AKI across Europe and the creation of a pan-European nephrology network of interested units to improve clinical outcomes, increase nephrologist involvement and awareness outside nephrology and stimulate research on AKI in Europe. Accordingly, we also propose a list of research priorities and stress the need for more European funding of AKI research.
Clinical utility of genetic testing in early-onset kidney disease: seven genes are the main players
Authors: Domingo-Gallego Andrea , Pybus Marc , Bullich Gemma , Furlano Mónica , Ejarque-Vila Laia , Lorente-Grandoso Laura , Ruiz Patricia , Fraga Gloria , López González Mercedes , Piñero-Fernández Juan Alberto , Rodríguez-Peña Lidia , Llano-Rivas Isabel , Sáez Raquel , Bujons-Tur Anna , Ariceta Gema , Guirado Lluis , Torra Roser , Ars Elisabet
Published: January 2021

Background

Inherited kidney diseases are one of the leading causes of chronic kidney disease (CKD) that manifests before the age of 30 years. Precise clinical diagnosis of early-onset CKD is complicated due to the high phenotypic overlap, but genetic testing is a powerful diagnostic tool. We aimed to develop a genetic testing strategy to maximize the diagnostic yield for patients presenting with early-onset CKD and to determine the prevalence of the main causative genes.

Methods

We performed genetic testing of 460 patients with early-onset CKD of suspected monogenic cause using next-generation sequencing of a custom-designed kidney disease gene panel in addition to targeted screening for c.428dupC MUC1.

Results

We achieved a global diagnostic yield of 65% (300/460), which varied depending on the clinical diagnostic group: 77% in cystic kidney diseases, 76% in tubulopathies, 67% in autosomal dominant tubulointerstitial kidney disease, 61% in glomerulopathies and 38% in congenital anomalies of the kidney and urinary tract. Among the 300 genetically diagnosed patients, the clinical diagnosis was confirmed in 77%, a specific diagnosis within a clinical diagnostic group was identified in 15%, and 7% of cases were reclassified. Of the 64 causative genes identified in our cohort, 7 (COL4A3, COL4A4, COL4A5, HNF1B, PKD1, PKD2 and PKHD1) accounted for 66% (198/300) of the genetically diagnosed patients.

Conclusions

Two-thirds of patients with early-onset CKD in this cohort had a genetic cause. Just seven genes were responsible for the majority of diagnoses. Establishing a genetic diagnosis is crucial to define the precise aetiology of CKD, which allows accurate genetic counselling and improved patient management.
Magnetic Resonance Imaging-Guided Laser Thermal Ventral Capsulotomy for Intractable Obsessive-Compulsive Disorder
Authors: McLaughlin Nicole C R , Lauro Peter M , Patrick Morgan T , Pucci Francesco G , Barrios-Anderson Adriel , Greenberg Benjamin D , Rasmussen Steven A , Asaad Wael F
Published: January 2021

BACKGROUND

Obsessive-compulsive disorder (OCD) is a disabling condition characterized by intrusive thoughts and repetitive behaviors. A subset of individuals have severe, treatment-resistant illness and are nonresponsive to medication or behavioral therapies. Without response to conventional therapeutic options, surgical intervention becomes an appropriate consideration.

OBJECTIVE

To report clinical outcomes and the safety profile of bilateral ventral anterior capsulotomy for OCD using magnetic resonance (MR)-guided laser interstitial thermal therapy (LITT) in 10 patients followed for 6 to 24 mo.

METHODS

A total of 10 patients underwent LITT for severe OCD; 1 patient withdrew prior to follow-up. LITT is a minimally invasive ablative technique performed with precise targeting and use of thermography under MR guidance. Lesions of the ventral anterior limb of the internal capsule by other techniques have been shown to be efficacious in prior studies.

RESULTS

A total of 7 of the 9 patients were considered full responders (77.8%; Yale-Brown Obsessive-Compulsive Scale change ≥35%). Adverse effects included transient apathy/amotivation postsurgery (2 patients). One patient had a small tract hemorrhage where the laser fiber traversed the cerebral cortex as well as persistent insomnia postsurgery. One individual died after a drug overdose 7 mo postsurgery, which was judged unrelated to the surgery.

CONCLUSION

LITT ventral capsulotomy was generally well tolerated, with promising evidence of effectiveness in the largest such series to date. Results were comparable to those after gamma knife ventral capsulotomy, as well as ventral anterior limb deep brain stimulation.
Targeting HSPA1A in ARID2-deficient lung adenocarcinoma
Authors: Wang Xue , Wang Yuetong , Fang Zhaoyuan , Wang Hua , Zhang Jian , Zhang Longfu , Huang Hsinyi , Jiang Zhonglin , Jin Yujuan , Han Xiangkun , Hou Shenda , Zhou Bin , Meng Feilong , Chen Luonan , Wong Kwok-Kin , Liu Jinfeng , Zhang Zhiqi , Zhang Xin , Chen Haiquan , Sun Yihua , Hu Liang , Ji Hongbin
Published: January 2021

Somatic mutations of the chromatin remodeling gene ARID2 are observed in ∼7% of human lung adenocarcinomas (LUADs). However, the role of ARID2 in the pathogenesis of LUADs remains largely unknown. Here we find that ARID2 expression is decreased during the malignant progression of both human and mice LUADs. Using two KrasG12D-based genetically engineered murine models, we demonstrate that ARID2 knockout significantly promotes lung cancer malignant progression and shortens overall survival. Consistently, ARID2 knockdown significantly promotes cell proliferation in human and mice lung cancer cells. Through integrative analyses of ChIP-Seq and RNA-Seq data, we find that Hspa1a is up-regulated by Arid2 loss. Knockdown of Hspa1a specifically inhibits malignant progression of Arid2-deficient but not Arid2-wt lung cancers in both cell lines as well as animal models. Treatment with an HSPA1A inhibitor could significantly inhibit the malignant progression of lung cancer with ARID2 deficiency. Together, our findings establish ARID2 as an important tumor suppressor in LUADs with novel mechanistic insights, and further identify HSPA1A as a potential therapeutic target in ARID2-deficient LUADs.
Planned Obsolescence in the Context of a Holistic Legal Sphere and the Circular Economy
Authors: Malinauskaite Jurgita , Erdem Fatih Buğra
Published: January 2021

Businesses may take advantage of rapid technological developments to increase sales by designing products with a short lifespan and encouraging consumers to buy a replacement more quickly than they otherwise might have to, which is commonly known as planned obsolescence. While employing a holistic approach and exploring planned obsolescence from three different angles—the demand side, supply side and environmental side—the article argues that the current measures in the fields of unfair competition and consumer protection law, competition law and environmental law are quite insufficient to deal with planned obsolescence. Therefore, there is a need for an EU measure outlawing planned obsolescence in the context of the circular economy.
Single-Position Surgery: Prone Lateral Lumbar Interbody Fusion: 2-Dimensional Operative Video
Authors: Ohiorhenuan Ifije E , Godzik Jakub , Uribe Juan S
Published: January 2021

Lateral lumbar interbody fusion (LLIF) is a widely used technique for anterior fusion. However, posterior decompression or instrumentation often requires repositioning the patient, which increases operative time. This video describes the prone LLIF as a modification of the standard surgical technique. The prone LLIF facilitates simultaneous decompression and fusion, which avoids the need for repositioning the patient, increasing operative efficiency. Positioning, fluoroscopic considerations, and operative nuances involved in performing the LLIF in the prone position are described, and an illustrative case is presented. The patient provided informed consent for the procedure and videography. LLIF in the prone position can decrease operative time and increase operative efficiency. The prone position is a viable alternative to the conventional lateral decubitus position.

Video used with permission from Barrow Neurological Institute, Phoenix, Arizona.
The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice
Authors: Huang Luojiang , Hua Kai , Xu Ran , Zeng Dali , Wang Ruci , Dong Guojun , Zhang Guozheng , Lu Xueli , Fang Na , Wang Dekai , Duan Penggen , Zhang Baolan , Liu Zupei , Li Na , Luo Yuehua , Qian Qian , Yao Shanguo , Li Yunhai
Published: January 2021

Panicle size and grain number are important agronomic traits and influence grain yield in rice (Oryza sativa), but the molecular and genetic mechanisms underlying panicle size and grain number control remain largely unknown in crops. Here we report that LARGE2 encodes a HECT-domain E3 ubiquitin ligase OsUPL2 and regulates panicle size and grain number in rice. The loss of function large2 mutants produce large panicles with increased grain number, wide grains and leaves, and thick culms. LARGE2 regulates panicle size and grain number by repressing meristematic activity. LARGE2 is highly expressed in young panicles and grains. Biochemical analyses show that LARGE2 physically associates with ABERRANT PANICLE ORGANIZATION1 (APO1) and APO2, two positive regulators of panicle size and grain number, and modulates their stabilities. Genetic analyses support that LARGE2 functions with APO1 and APO2 in a common pathway to regulate panicle size and grain number. These findings reveal a novel genetic and molecular mechanism of the LARGE2-APO1/APO2 module-mediated control of panicle size and grain number in rice, suggesting that this module is a promising target for improving panicle size and grain number in crops.
Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood
Authors: Liu Baoguang , Liu Juan , Yu Jing , Wang Zhifeng , Sun Yi , Li Shuang , Lin Ying-Chung Jimmy , Chiang Vincent L , Li Wei , Wang Jack P
Published: January 2021

Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF–DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF–DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
Gaussian Primes in Narrow Sectors
Authors: Stucky Joshua
Published: January 2021

We generalize a Theorem of Ricci and count Gaussian primes $\mathfrak{p}$ with short interval restrictions on both the norm and the argument of $\mathfrak{p}$. We follow Heath-Brown’s method for counting rational primes in short intervals.
Artificial Intelligence and Deep Learning in Diagnostic Radiology—Is This The Next Phase of Scientific and Technological Development?
Authors: Moores B Michael
Published: January 2021

This paper is concerned with the role of science and technology in helping to create change in society. Diagnostic radiology is an example of an activity that has undergone significant change due to such developments, which over the past 40 years have led to a huge increase in the volume of medical imaging data generated. However, these developments have by and large left the human elements of the radiological process (referrer, radiographer and radiologist) intact.

Diagnostic radiology has now reached a stage whereby the volume of information generated cannot be fully utilised solely by employing human observers to form clinical opinions, a process that has not changed in over 100 years. In order to address this problem, the potential application of Artificial Intelligence (AI) in the form of Deep Learning (DL) techniques to diagnostic radiology indicates that the next technological development phase may already be underway. The paper outlines the historical development of AI techniques, including Machine Learning and DL Neural Networks and discusses how such developments may affect radiological practice over the coming decades. The ongoing growth in the world market for radiological services is potentially a significant driver for change.

The application of AI and DL learning techniques will place quantification of diagnostic outcomes at the heart of performance evaluation and quality standards. The effect this might have on the optimisation process will be discussed and in particular the possible need for automation in order to meet more stringent and standardised performance requirements that might result from these developments. Changes in radiological practices would also impact upon patient protection including the associated scientific support requirements and these are discussed.
Associations of the residential built environment with adolescent sleep outcomes
Authors: Mayne Stephanie L , Morales Knashawn H , Williamson Ariel A , Grant Struan F A , Fiks Alexander G , Basner Mathias , Dinges David F , Zemel Babette S , Mitchell Jonathan A
Published: January 2021

Study Objectives

Over 75% of US high school students obtain insufficient sleep, placing them at risk for adverse health outcomes. Identification of modifiable determinants of adolescent sleep is needed to inform prevention strategies, yet little is known about the influence of the built environment on adolescent sleep.

Methods

In this prospective study, actigraphy was used to assess sleep outcomes among 110 adolescents for 14 days each in eighth and ninth grades: duration (hours/night), onset and offset, and sleeping ≥8 hours. Home addresses were linked to built environment exposures: sound levels, tree canopy cover, street density, intersection density, population density, and housing density. Mixed-effects regression estimated associations of built environment measures with sleep outcomes, adjusting for sex, race, parent education, household income, household size, grade, weeknight status, and neighborhood poverty.

Results

A 1-standard deviation (SD) increase in neighborhood sound was associated with 16 minutes later sleep onset (β = 0.28; 95% confidence interval (CI): 0.06, 0.49) and 25% lower odds of sleeping for ≥8 hours (odds ratio (OR) = 0.75, 95% CI: 0.59, 0.96). A 1-SD increase in neighborhood tree canopy was associated with 18 minutes earlier sleep onset (β = −0.31, 95% CI: −0.49, −0.13) and 10 minutes earlier sleep offset (β= −0.17, 95% CI: −0.28, −0.05). No associations were observed for density-based exposures.

Conclusions

Higher neighborhood sound level was associated with lower odds of sufficient sleep, while higher tree canopy cover was associated with more favorable sleep timing. Neighborhood sound levels and tree canopy cover are potential targets for policies and interventions to support healthier sleep among adolescents.
Working Memory Capacities Neurally Dissociate: Evidence from Acute Stroke
Authors: Martin Randi C , Ding Junhua , Hamilton A Cris , Schnur Tatiana T
Published: January 2021

Substantial behavioral evidence implies the existence of separable working memory (WM) components for maintaining phonological and semantic information. In contrast, only a few studies have addressed the neural basis of phonological versus semantic WM using functional neuroimaging and none has used a lesion-symptom mapping (LSM) approach. Here, we address this gap, reporting a multivariate LSM study of phonological and semantic WM for 94 individuals at the acute stage of left hemisphere stroke. Testing at the acute stage avoids issues of brain reorganization and the adoption of patient strategies for task performance. The LSM analyses for each WM component controlled for the other WM component and semantic and phonological knowledge at the single word level. For phonological WM, the regions uncovered included the supramarginal gyrus, argued to be the site of phonological storage, and several cortical and subcortical regions plausibly related to inner rehearsal. For semantic WM, inferior frontal regions and the angular gyrus were uncovered. The findings thus provide converging evidence for separable systems for phonological and semantic WM that are distinguished from the systems supporting long-term knowledge representations in those domains.
Does Malaria Co-Infection Alter the Clinical Course in Children Infected with Dengue? Analysis from 623 Indian Children Admitted with Dengue Infection
Authors: Bhakhri Bhanu Kiran , Singh Dharmendra Kumar , Singh Nupur , Rai Ruchi
Published: January 2021

Background

Dengue and malaria co-infection has been reported in several case reports. We aim to study effect of malaria co-infection on clinical outcomes of dengue infection.

Methods

Records of 623 children with dengue infection, based on NS-1 antigen and IgM ELISA testing, were collected. Malaria co-infection was identified in 20 cases, based on peripheral blood smear examination. Clinical and hematological parameters were compared in two groups (malaria co-infection vs. dengue mono-infection).

Results

Duration of hospitalization was significantly higher in co-infected group. Significantly higher proportion of malaria co-infection cases had hepatosplenomegaly, hemoglobin ≤8 g/dl, serum albumin ≤3 g/dl, serum bilirubin ≥1 mg/dl, serum aspartate aminotransferase ≥500 U/l and serum alanine aminotransferase ≥300 U/l. Number of transfusions (PRBC and platelets) required in malaria co-infection group was higher.

Conclusion

Malaria co-infection in dengue impacts clinical presentation, hematological parameters, requirement of blood transfusion and morbidity. High index of suspicion is warranted while evaluating febrile patients.
Maize Plants Chimeric for an Autoactive Resistance Gene Display a Cell-Autonomous Hypersensitive Response but Non–Cell Autonomous Defense Signaling
Authors: Karre Shailesh , Kim Saet-Byul , Kim Bong-Suk , Khangura Rajdeep S. , Sermons Shannon M. , Dilkes Brian , Johal Guri , Balint-Kurti Peter
Published: January 2021

The maize gene Rp1-D21 is a mutant form of the gene Rp1-D that confers resistance to common rust. Rp1-D21 triggers a spontaneous defense response that occurs in the absence of the pathogen and includes a programed cell death called the hypersensitive response (HR). Eleven plants heterozygous for Rp1-D21, in four different genetic backgrounds, were identified that had chimeric leaves with lesioned sectors showing HR abutting green nonlesioned sectors lacking HR. The Rp1-D21 sequence derived from each of the lesioned portions of leaves was unaltered from the expected sequence whereas the Rp1-D21 sequences from nine of the nonlesioned sectors displayed various mutations, and we were unable to amplify Rp1-D21 from the other two nonlesioned sectors. In every case, the borders between the sectors were sharp, with no transition zone, suggesting that HR and chlorosis associated with Rp1-D21 activity was cell autonomous. Expression of defense response marker genes was assessed in the lesioned and nonlesioned sectors as well as in near-isogenic plants lacking and carrying Rp1-D21. Defense gene expression was somewhat elevated in nonlesioned sectors abutting sectors carrying Rp1-D21 compared with near-isogenic plants lacking Rp1-D21. This suggests that, whereas the HR itself was cell autonomous, other aspects of the defense response initiated by Rp1-D21 were not.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Temporal Progress of Huanglongbing Epidemics and the Effect of Noncommercial Inoculum Sources on Citrus Orchards in São Paulo State, Brazil
Authors: Pazolini Kelly , Arruda Josicléa H. , Chinelato Gressa A. , Filho Armando Bergamin , Belasque José
Published: January 2021

Huanglongbing (HLB) incidence is increasing and threatening citrus production in São Paulo State, Brazil, despite multiple efforts to control the disease and its vector, the Asian citrus psyllid (ACP) (Diaphorina citri). The objective of this research was to study the temporal dynamics of HLB epidemics, under intensive disease management, in 177 individual commercial citrus blocks on a single property in São Paulo State. The effect of internal and external sources of HLB-associated bacteria and its vector were explored based on the disease epidemics and vector dynamics in the studied area. To manage HLB, the property owner used healthy nursery plants, eradicated symptomatic trees, and used insecticides to control ACPs. Logistic and Gompertz models were fitted to the data to describe dynamics of HLB incidence for all blocks. The average number of ACPs per yellow sticky trap was determined for the same blocks for a period of four consecutive years. Both logistic and Gompertz models described the HLB epidemics well, although the Gompertz model provided a slightly better fit. Disease progress rates, HLB incidences, and average ACP count per trap in the 177 blocks were low compared with reports in the literature. HLB incidence and number of ACPs per trap were higher (P ≤ 0.05) in some citrus blocks located on the periphery of the property. A large number of noncommercial trees were found near the property and were a potential primary inoculum source of HLB-associated bacteria, accounting for the higher incidence of HLB and ACPs per trap in blocks located on the periphery of the property. These results support the recommended preventive measures to HLB management and the necessity of external actions, to include trees in commercial orchards, and noncommercial trees located near commercial citrus properties, in an attempt to maximize the effectiveness of these preventive measures.
Analysing the impact of global demographic characteristics over the COVID-19 spread using class rule mining and pattern matching
Authors: Khan Wasiq , Hussain Abir , Khan Sohail Ahmed , Al-Jumailey Mohammed , Nawaz Raheel , Liatsis Panos
Published: January 2021

Since the coronavirus disease (COVID-19) outbreak in December 2019, studies have been addressing diverse aspects in relation to COVID-19 and Variant of Concern 202012/01 (VOC 202012/01) such as potential symptoms and predictive tools. However, limited work has been performed towards the modelling of complex associations between the combined demographic attributes and varying nature of the COVID-19 infections across the globe. This study presents an intelligent approach to investigate the multi-dimensional associations between demographic attributes and COVID-19 global variations. We gather multiple demographic attributes and COVID-19 infection data (by 8 January 2021) from reliable sources, which are then processed by intelligent algorithms to identify the significant associations and patterns within the data. Statistical results and experts' reports indicate strong associations between COVID-19 severity levels across the globe and certain demographic attributes, e.g. female smokers, when combined together with other attributes. The outcomes will aid the understanding of the dynamics of disease spread and its progression, which in turn may support policy makers, medical specialists and society, in better understanding and effective management of the disease.
Signal processing basics applied to Ecoacoustics
Authors: Sanchez-Gendriz Ignacio
Published: January 2021

Ecoacoustics is a research field that has attracted attention of researchers from areas as diverse as ecology, biology, engineering, and human sciences, to cite a few. Ecoacoustics studies the sounds that emanates from the environments, by gaining insights of landscape dynamics from acoustic patterns and particularities at different places. With recent advance in technology, it is common to obtain sound datasets recorded 24-h a day for several months. The analysis of these long-term sound recordings represents several challenges. Investigators already involved in acoustic are familiar with signal processing methods, which are essential tools for sound analysis. However, in general beginners interested in Ecoacoustics do not share this background formation. The present work illustrates basic topics of digital signal processing in a comprehensible style, and an effective pipeline for long-term sound explorative data analysis (EDA) is presented. Finally, the described signal processing fundamentals are applied for EDA of 1-month underwater acoustic data recorded in a Brazilian marine protected area. The Matlab codes used for the analysis will be available as supplementary material.
Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer
Authors: Saif Rashid , Ejaz Aniqa , Mahmood Tania , Zia Saeeda
Published: January 2021

Advances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-developed pipelines using computational tools/softwares has allowed researchers to reveal ground-breaking discoveries in multi-omics data analysis. However, there is still uncertainty due to massive upsurge in parallel tools and difficulty in choosing best practiced pipeline for expression profiling of RNA sequenced (RNA-seq) data. Here, we detail the optimized pipeline that works at a fast pace with enhanced accuracy on personal computer rather than using cloud or high-performance computing clusters (HPC). The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially expressed features and visualization of the data. The tools FastQC, Trimmomatic, Salmon and some other scripts in Trinity toolkit were applied on two paired-end datasets. An extension of this pipeline may also be formulated in future for the gene ontology enrichment analysis and functional annotation of the differential expression matrix to make this data biologically more significant.
ModifiedE. colistrains enhance baculovirus production by elimination of aberrant transposition events
Authors: Grose Carissa , Wright Chelsea , Mehalko Jennifer , Esposito Dominic
Published: January 2021

Baculovirus technology has been the most commonly used expression system for insect cells both due to its potential to generate a large amount of recombinant protein as well as the benefit of post-translational modifications. The most commonly used system to generate recombinant baculoviruses is the Tn7 transposition-based technology known as Bac-to-Bac. Although improvements have been made to this system to further improve quality and reproducibility of baculovirus production, recent data suggests that improved strains still have potential issues with contamination of non-recombinant baculovirus caused by improper transposition into a Tn7 site in theE. colichromosome. Here we describe a new option for alteration of theE. coligenome to completely block the native Tn7 attachment site, leading to far fewer false positive bacmid colonies being selected and eliminating all risk of non-recombinant baculovirus production.