bluuebunny/crossref_metadata_2025 huggingface dataset:
Pedestrian-Friendly for Redesign Leuwipanjang Integrated Terminal with Wayfinding Approach
Authors: Hanissa A N , Paramita B , Megayanti T , Koerniawan M D
Published: June 2020

This research is about the importance of user comfort in Leuwipanjang terminal, especially pedestrians, while in it. Leuwipanjang Terminal is a type A bus terminal in Bandung which will be one of the 14 proposed Transit-Oriented Development (TOD) planning points. The terminal controls the movement of traffic, namely pedestrian and vehicle traffic. Integrated Terminal Planning at Leuwipanjang Bus Terminal will accommodate many types of transportation modes so that there is an overlapping circulation when switching between modes. While passengers who have just arrived at the terminal usually feel confused to find a destination. The Leuwipanjang terminal does not currently provide clarity on circulation and does not give a pedestrian way. So Leuwipanjang terminal is needed to redesign, pedestrian-friendly terminal by providing safe and comfortable direct access to all the characteristics of users at the terminal.
The prototypes of energy-efficient residential Building with metal roof in Gorontalo, Indonesia
Authors: Jahja M , Gunawan A , Syamsul A N F , Arifin Y I , Koerniawan M D
Published: June 2020

To optimize Gorontalo’s residential building design to a sequential search technique is being used to minimize their life-cycle energy cost while improving their energy efficiency. Certain design features are included like air-conditioned, house orientation, window material, wall exterior finish, roof insulation, lighting fixtures, cooling system efficiencies, and photovoltaic while also considering the neighbor displacement. The outcomes of the sequential search methodology are contrasted with those achieved through a more time-consuming approach to brute-force optimization. Alternatively, for selected locations in Gorontalo, the best design features for residential building is determined. By using specific measures resulted from the optimization technique can cost-effectively reduce the annual energy saving by 59%, while adding the photovoltaic as a measure, we can increase the annual energy use saving percentage up to 117% compared to the reference design in the residential building in Gorontalo.
Sustainability Potential for Renewable Energy System in Isolated Area that Supports Nantu Boliyohuto Wildlife Reserve
Authors: Pontoiyo F , Sulaiman M , Budiarto R , Novitasari D
Published: June 2020

It is still a challenging task to fulfill power demand of Tumba Hamlet in Tamaila Utara Village, which is an isolated area in the buffer zone of Nantu Boliyohuto Wildlife Reserve. The efforts to fulfill the demand had been carried out by the local government by distributing the Solar Home System (SHS) to all households in 2013. However, the SHS performance quickly declined because the solar panels in the rooftop covered by dense and lush trees, and then it did not work at all in 2018. This research performs pre-feasibility in building the micro-hydro powerplant (MHPP) and its sustainability potential in Tumba Hamlet to fulfill the community’s electrical energy needs without disrupting the Nantu Boliyohuto Wildlife Reserve. A basic survey was performed in exploring river resources and topographical conditions in this hamlet. Sustainability study, including technical, social, and environmental aspects, was conducted by interviewing the residents. The results show that the power needs in Tumba Hamlet are 48.5 kW. This demand can be fulfilled by the MHPP with head and water discharge of 10 meters and 0.706 m3/s, respectively. It was found that positive feedback in the technical, social, and environmental aspects of sustainability is dominant.
Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts
Authors: Ding Hongxu , Bailey Andrew D , Jain Miten , Olsen Hugh , Paten Benedict
Published: June 2020

Motivation

Nucleotide modification status can be decoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current signals. Although various algorithms have been developed for nanopore-sequencing-based modification analysis, more detailed characterizations, such as modification numbers, corresponding signal levels and proportions are still lacking.

Results

We present a framework for the unsupervised determination of the number of nucleotide modifications from nanopore-sequencing readouts. We demonstrate the approach can effectively recapitulate the number of modifications, the corresponding ionic current signal levels, as well as mixing proportions under both DNA and RNA contexts. We further show, by integrating information from multiple detected modification regions, that the modification status of DNA and RNA molecules can be inferred. This method forms a key step of de novo characterization of nucleotide modifications, shedding light on the interpretation of various biological questions.

Availability and implementation

Modified nanopolish: https://github.com/adbailey4/nanopolish/tree/cigar_output. All other codes used to reproduce the results: https://github.com/hd2326/ModificationNumber.

Supplementary information

Supplementary data are available at Bioinformatics online.
Loss of myosin VI expression affects acrosome/acroplaxome complex morphology during mouse spermiogenesis†
Authors: Zakrzewski Przemysław , Rędowicz Maria Jolanta , Buss Folma , Lenartowska Marta
Published: June 2020

During spermiogenesis in mammals, actin filaments and a variety of actin-binding proteins are involved in the formation and function of highly specialized testis-specific structures. Actin-based motor proteins, such as myosin Va and VIIa, play a key role in this complex process of spermatid transformation into mature sperm. We have previously demonstrated that myosin VI (MYO6) is also expressed in mouse testes. It is present in actin-rich structures important for spermatid development, including one of the earliest events in spermiogenesis—acrosome formation. Here, we demonstrate using immunofluorescence, cytochemical, and ultrastructural approaches that MYO6 is involved in maintaining the structural integrity of these specialized actin-rich structures during acrosome biogenesis in mouse. We show that MYO6 together with its binding partner TOM1/L2 is present at/around the spermatid Golgi complex and the nascent acrosome. Depletion of MYO6 in Snell’s waltzer mice causes structural disruptions of the Golgi complex and affects the acrosomal granule positioning within the developing acrosome. In summary, our results suggest that MYO6 plays an anchoring role during the acrosome biogenesis mainly by tethering of different cargo/membranes to highly specialized actin-related structures.
HIV, progestins, genital epithelial barrier function, and the burden of objectivity†
Authors: Vicetti Miguel Rodolfo D , Quispe Calla Nirk E , Cherpes Thomas L
Published: June 2020

Contributions from a diverse set of scientific disciplines will be needed to help individuals make fully informed decisions regarding contraceptive choices least likely to promote HIV susceptibility. This commentary recaps contrasting interpretations of results from the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial, a study that compared HIV risk in women using the progestin-only injectable contraceptive depot medroxyprogesterone acetate (DMPA) vs. two other contraceptive choices. It also summarizes results from basic and translational research that establish biological plausibility for earlier clinical studies that identified enhanced HIV susceptibility in women using DMPA.
Cytogenetic diversity in the polyploid complexLinum suffruticosum s.l. (Linaceae)
Authors: Afonso Ana , Loureiro João , Arroyo Juan , Olmedo-Vicente Erika , Castro Sílvia
Published: June 2020

Polyploidy plays a significant role in the evolution and diversification of flowering plants. In several polyploid complexes, high morphological variability and plasticity coupled with cytogenetic diversity make it difficult to disentangle their evolutionary history. The main goal of this study was to gain insights into the role of whole genome duplications as one of the factors shaping the evolution of flowering plants. Linum suffruticosum s.l. has been described as a polyploid complex, with high morphological variability, but nothing is known about current cytogeographical patterns. We investigated cytotype diversity and distribution patterns in 151 populations covering most of the distribution range, in the Iberian Peninsula, south-eastern France, north-western Italy and Morocco, using flow cytometric analyses complemented with chromosome counts. A high cytogenetic diversity was found with five major cytotypes being detected (diploids, tetraploids, hexaploids, octoploids and decaploids) and with new ploidy levels being reported for the first time. The different ploidies were distributed parapatrically, with geographical structure and several contact zones. Most of the populations comprised one cytotype, but a few mixed-ploidy populations were observed. Our results suggest that whole genome duplications are one of the key mechanisms, alone or together with hybridization, governing the diversification of L. suffruticosum s.l. Genome size and/or chromosome counts might be useful tools for identifying specimens of L. suffruticosum s.l. Also, geographical overlap and high cytogenetic diversity suggest multiple origins of the polyploids. The diversity observed here has been mostly neglected to date and should be accounted when studying the biosystematics of this complex.
Central bankers and the rationale for unconventional monetary policies: reasserting, renouncing or recasting monetarism?
Authors: Fiebiger Brett , Lavoie Marc
Published: June 2020

The purpose of this paper is to examine the rationale for the unconventional monetary policies adopted by central banks in response to the Global Financial Crisis. Quantitative easing appears to be a return to monetarist principles. Indeed, the Bank of England emphasised a causal chain running from increases in broad money to spending and inflation, while the Bank of Japan later pointed to a theorised relation between base money and expected inflation. Some aspects of monetarism have been renounced, albeit not necessarily with convincing reasoning. Monetarist principles can also be discerned in the ‘credit view’ associated with the research of two-term US Federal Reserve Chair, Ben Bernanke. An understanding of the banking system and the channels of monetary transmission is still a work in progress.
Novel non-cystic features of polycystic kidney disease: having new eyes or seeking new landscapes
Authors: Van Laecke Steven , Van Biesen Wim
Published: June 2020

For decades, researchers have been trying to decipher the complex pathophysiology of autosomal dominant polycystic kidney disease (ADPKD). So far these efforts have led to clinical trials with different candidate treatments, with tolvaptan being the only molecule that has gained approval for this indication. As end-stage kidney disease due to ADPKD has a substantial impact on health expenditures worldwide, it is likely that new drugs targeting kidney function will be developed. On the other hand, recent clinical observations and experimental data, including PKD knockout models in various cell types, have revealed unexpected involvement of many other organs and cell systems of variable severity. These novel non-cystic features, some of which, such as lymphopenia and an increased risk to develop infections, should be validated or further explored and might open new avenues for better risk stratification and a more tailored approach. New insights into the aberrant pathways involved with abnormal expression of PKD gene products polycystin-1 and -2 could, for instance, lead to a more directed approach towards early-onset endothelial dysfunction and subsequent cardiovascular disease. Furthermore, a better understanding of cellular pathways in PKD that can explain the propensity to develop certain types of cancer can guide post-transplant immunosuppressive and prophylactic strategies. In the following review article we will systematically discuss recently discovered non-cystic features of PKD and not well-established characteristics. Overall, this knowledge could enable us to improve the outcome of PKD patients apart from ongoing efforts to slow down cyst growth and attenuate kidney function decline.
Systematic Review of Curriculum-Based Measurement with Students Who Are Deaf
Authors: Lam Elizabeth A , McMaster Kristen L , Rose Susan
Published: June 2020

This review systematically identified and compared the technical adequacy (reliability and validity evidence) of reading curriculum-based measurement (CBM) tasks administered to students who are deaf and hard of hearing (DHH). This review included all available literature written in English. The nine studies identified used four CBM tasks: signed reading fluency, silent reading fluency, cloze (write in missing words given blank lines within a passage), and maze (circle the target word given multiple choice options within a passage). Data obtained from these measures were generally found to be internally consistent and stable with validity evidence varying across measures. Emerging evidence supports the utility of CBM for students who are DHH. Further empirical evidence is needed to continue to explore technical properties, identify if student scores are sensitive to growth over short periods of time, and examine whether CBM data can be used to inform instructional decision-making to improve student outcomes.
Goodnight Gorilla: Deaf Student American Sign Language Narrative Renditions After Viewing a Model
Authors: Beal Jennifer S , Scott Jessica A , Spell Kelly
Published: June 2020

The present study used an observational learning framework to investigate changes in non-native signing deaf children’s narrative renditions before (Time 1) and after (Time 2) a single viewing of a signing adult’s rendition of the same story. The deaf adult model rendered the picture book Goodnight Gorilla in American Sign Language (ASL) with the pages of the book displayed behind her. We analyzed the details children aged 6–13 years included within their narratives and how they rendered those details. Specifically, we compared their use of depicting constructions (DCs), constructed action (CA), simultaneous use of both DCs and CA, and only lexical signs before and after viewing the model. The deaf adult predominantly and equally used CA and constructed actin paired with DCs and rarely used lexical signs alone during her rendition. After watching the adult rendition, children’s renditions were longer and they included more details. Children increased their use of DCs, CA, and to a lesser extent, combinations of DCs and CA. However, half of the children never used DCs paired with CA. Suggestions for pairing ASL content standards with viewings of deaf adult sign language models are discussed.
Binary classification with covariate selection through ℓ0-penalised empirical risk minimisation
Authors: Chen Le-Yu , Lee Sokbae
Published: June 2020

We consider the problem of binary classification with covariate selection. We construct a classification procedure by minimising the empirical misclassification risk with a penalty on the number of selected covariates. This optimisation problem is equivalent to obtaining an ℓ0-penalised maximum score estimator. We derive probability bounds on the estimated sparsity as well as on the excess misclassification risk. These theoretical results are nonasymptotic and established in a high-dimensional setting. In particular, we show that our method yields a sparse solution whose ℓ0-norm can be arbitrarily close to true sparsity with high probability and obtain the rates of convergence for the excess misclassification risk. We implement the proposed procedure via the method of mixed-integer linear programming. Its numerical performance is illustrated in Monte Carlo experiments and a real data application of the work-trip transportation mode choice.
Prognostic impact of transcatheter mitral valve repair in patients with exercise-induced secondary mitral regurgitation
Authors: Izumo Masaki , Kuwata Shingo , Ishibashi Yuki , Suzuki Tomomi , Ohara Hiroshi , Watanabe Mika , Sato Yukio , Nishikawa Haruka , Okuyama Kazuaki , Kamijima Ryo , Takai Manabu , Kou Seisyo , Harada Tomoo , Akashi Yoshihiro J
Published: June 2020

Aims

Although exercise-induced secondary mitral regurgitation (MR) is known to have a poor prognosis, the therapeutic strategy towards this condition remains to be investigated. In the present study, we aimed to investigate the prognostic impact of transcatheter mitral valve repair (TMVr) using the MitraClip in patients with exercise-induced secondary MR.

Methods and results

Of the 200 consecutive patients with secondary MR who underwent exercise stress echocardiography, 46 (23%) that presented with exercise-induced secondary MR [i.e. increase in effective regurgitant orifice area (EROA) of ≥ 0.13 cm2] were enrolled in the present investigation. The composite endpoints of all-cause mortality and hospitalization for heart failure were evaluated. Of the 46 patients included in the current cohort, 19 (41%) underwent TMVr and 27 (59%) were medically managed (control group). Although the TMVr group tended to present with a greater EROA at rest (0.26 ± 0.10 vs. 0.20 ± 0.08 cm2, P = 0.047), there were no differences in the EROA changes during exercise between the two groups (0.18 ± 0.10 vs. 0.18 ± 0.04 cm2, P = 0.940). While the TMVr group reported a higher event-free survival rate after the 13-month follow-up period (log-rank P = 0.017), the Cox proportional-hazard analysis suggested the TMVr to be associated with clinical outcomes (hazard ratio: 0.419, P = 0.044).

Conclusion

As opposed to the medical management, TMVr treatment was associated with a lower risk of composite endpoints in patients with exercise-induced secondary MR. Exercise stress echocardiography is considered to have played an important role in decision-making for secondary MR.
Public Capital and Economic Development
Authors: Cubas German
Published: June 2020

Public capital is sizable and its share in total capital is higher in poor countries. The standard development accounting approach does not distinguish it from private capital, ignoring its public good features. The goal of this paper is to measure public capital stocks for a wide range of countries, and then develop and implement a development accounting framework that explicitly includes its non-rival aspects. The paper finds that factors of production account for a significantly greater share of cross-country differences in output per worker compared to the standard framework. With both non-rivalry and congestion, the contribution of factors of production decreases.
One-year mortality increases four-fold in frail patients undergoing cardiac surgery
Authors: Bäck Caroline , Hornum Mads , Jørgensen Morten Buus , Lorenzen Ulver Spangsberg , Olsen Peter Skov , Møller Christian H
Published: June 2020

OBJECTIVES

An increased focus on biological age, ‘frailty’, is important in an ageing population including those undergoing cardiac surgery. None of the existing surgery risk scores European System for Cardiac Operative Risk Evaluation II or Society of Thoracic Surgeons score incorporates frailty. Therefore, there is a need for an additional risk score model including frailty and not simply the chronological age. The aim of this study was to evaluate the impact of frailty assessment on 1-year mortality and morbidity for patients undergoing cardiac surgery.

METHODS

A total of 604 patients aged ≥65 years undergoing non-acute cardiac surgery were included in this single-centre prospective observational study. We compared 1-year mortality and morbidity in frail versus non-frail patients. The Comprehensive Assessment of Frailty (CAF) score was used: This is a score of 1–35 determined via minor physical tests. A CAF score ≥11 indicates frailty.

RESULTS

The median age was 73 years and 79% were men. Twenty-five percent were deemed frail. Frail patients had four-fold, odds ratios 4.63, 95% confidence interval (CI) 2.21–9.69; P < 0.001 increased 1-year mortality and increased risk of postoperative complications, i.e. surgical wound infections and prolonged hospital length of stay. A univariable Cox proportional hazards regression showed that an increased CAF score was a risk factor of mortality at any time after undergoing cardiac surgery (hazards ratios 1.11, 95% CI 1.07–1.14; P < 0.001).

CONCLUSIONS

CAF score identified frail patients undergoing cardiac surgery and was a good predictor of 1-year mortality.

Clinical trial registration number

NCT02992587.
Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health
Authors: Zeineldin Mohamed , A. Elolimy Ahmed , Barakat Radwa
Published: June 2020

Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.
Finance Beyond the Bounds of the Fiscal-Military State: Debt, Speculation and the Renovation of Nineteenth-Century French Financial Capitalism
Authors: Leuchter Tyson
Published: June 2020

Focusing on the Paris Stock Exchange in the early nineteenth century, this article examines the renovation of public debt and speculation following financial, political and military collapse. Though financial capitalism at the Exchange in the eighteenth century had been located mostly within the architecture of the fiscal-military state, the fallout of the Revolution and the defeat of the Napoleonic regime eliminated this option. Rather than military competition, financial capitalism at the Exchange in the nineteenth century was rebuilt by focusing inwards, by being linked to political values such as defined property rights, a particular vision of liberty and theories of representative government. Financial capitalism was still connected to empire, however; the reconstruction of financial capitalism at home helped to establish the conditions for exporting capital abroad, in the pursuit of informal empire. The article thus shows how financial capitalism came to be aligned with the political good in the post-revolutionary world.
The democratization of bioinformatics: A software engineering perspective
Authors: Lawlor Brendan , Sleator Roy D
Published: June 2020

Today, thanks to advances in cloud computing, it is possible for small teams of software developers to produce internet-scale products, a feat that was previously the preserve of large organizations. Herein, we describe how these advances in software engineering can be made more readily available to bioinformaticians. In the same way that cloud computing has democratized access to distributed systems engineering for generalist software engineers, access to scalable and reproducible bioinformatic engineering can be democratized for generalist bioinformaticians and biologists. We present solutions, based on our own efforts, to achieve this goal.
Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat
Authors: Lu Fu-Hao , McKenzie Neil , Gardiner Laura-Jayne , Luo Ming-Cheng , Hall Anthony , Bevan Michael W
Published: June 2020

Background

Polyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood.

Results

Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ~40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression.

Conclusions

Our pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.
Functional Tradeoffs Carry Phenotypes Across the Valley of the Shadow of Death
Authors: Polly P David
Published: June 2020

Synopsis

Functional tradeoffs are often viewed as constraints on phenotypic evolution, but they can also facilitate evolution across the suboptimal valleys separating performance peaks. I explore this process by reviewing a previously published model of how disruptive selection from competing functional demands defines an intermediate performance optimum for morphological systems that cannot simultaneously be optimized for all of the functional roles they must play. Because of the inherent tradeoffs in such a system, its optimal morphology in any particular environmental context will usually be intermediate between the performance peaks of the competing functions. The proportional contribution of each functional demand can be estimated by maximum likelihood from empirically observed morphologies, including complex ones measured with multivariate geometric morphometrics, using this model. The resulting tradeoff weight can be mapped onto a phylogenetic tree to study how the performance optimum has shifted across a functional landscape circumscribed by the function-specific performance peaks. This model of tradeoff evolution is sharply different from one in which a multipeak Ornstein–Uhlenbeck (OU) model is applied to a set of morphologies and a phylogenetic tree to estimate how many separate performance optima exist. The multi-peak OU approach assumes that each branch is pushed toward one of two or more performance peaks that exist simultaneously and are separated by valleys of poor performance, whereas the model discussed here assumes that each branch tracks a single optimal performance peak that wanders through morphospace as the balance of functional demands shifts. That the movements of this net performance peak emerge from changing frequencies of selection events from opposing functional demands are illustrated using a series of computational simulations. These simulations show how functional tradeoffs can carry evolution across putative performance valleys: even though intermediate morphologies may not perform optimally for any one function, they may represent the optimal solution in any environment in which an organism experiences competing functional demands.
Steep Rebound of Chloroquine-SensitivePlasmodium falciparumin Zimbabwe
Authors: Mharakurwa Sungano , Matsena-Zingoni Zvifadzo , Mudare Nobert , Matimba Charmaine , Gara Tanatswa Xuxa , Makuwaza Aramu , Maponga Gladys , Munyati Shungu , Gwanzura Lovemore , Mutambu Susan L , Mason Peter , Kobayashi Tamaki , Midzi Nicholas , Moss William J , Ippolito Matthew M
Published: June 2020

Removal of chloroquine from national malaria formularies can lead to the reversion of resistant Plasmodium falciparum to wild-type. We report a steep decline in chloroquine-resistant P falciparum within 10 years of national discontinuation of chloroquine monotherapy in Zimbabwe. Drug resistance surveillance is a vital component of malaria control programs, and the experience with chloroquine in Zimbabwe and elsewhere in sub-Saharan Africa is illustrative of the potentially rapid and dramatic impact of drug policy on antimalarial resistance.
Using informatics to improve cancer surveillance
Authors: Blumenthal Wendy , Alimi Temitope O , Jones Sandra F , Jones David E , Rogers Joseph D , Benard Vicki B , Richardson Lisa C
Published: June 2020

Objectives

This review summarizes past and current informatics activities at the Centers for Disease Control and Prevention National Program of Cancer Registries to inform readers about efforts to improve, standardize, and automate reporting to public health cancer registries.

Target audience

The target audience includes cancer registry experts, informaticians, public health professionals, database specialists, computer scientists, programmers, and system developers who are interested in methods to improve public health surveillance through informatics approaches.

Scope

This review provides background on central cancer registries and describes the efforts to standardize and automate reporting to these registries. Specific topics include standardized data exchange activities for physician and pathology reporting, software tools for cancer reporting, development of a natural language processing tool for processing unstructured clinical text, and future directions of cancer surveillance informatics.
Macroevolutionary Patterns of Sexual Size Dimorphism Among African Tree Frogs (Family: Hyperoliidae)
Authors: Portik Daniel M , Blackburn David C , McGuire Jimmy A
Published: June 2020

Sexual size dimorphism (SSD) is shaped by multiple selective forces that drive the evolution of sex-specific body size, resulting in male or female-biased SSD. Stronger selection on one sex can result in an allometric body size scaling relationship consistent with Rensch’s rule or its converse. Anurans (frogs and toads) generally display female-biased SSD, but there is variation across clades and the mechanisms driving the evolution of SSD remain poorly understood. We investigated these topics in a diverse family of African treefrogs (Hyperoliidae). Hyperoliids display traits considered rare among amphibians, including sexual dichromatism and protogynous sex change. Using phylogenetic comparative methods, we tested if adult ecology, sexual dichromatism, and sex change were predictors of body size or SSD. We also tested whether hyperoliids displayed allometric interspecific body size scaling relationships. We found a majority of hyperoliid taxa display female-biased SSD, but that adult ecology and sexual dichromatism are poor predictors of sex-specific body size and SSD. Regardless of the groupings analyzed (partitioned by clades or traits), we found support for isometric body size scaling. However, we found that sex change is a significant predictor of SSD variation. Species in the Hyperolius viridiflavus complex, which putatively display this trait, show a significant reduction in SSD and are frequently sexually monomorphic in size. Although protogynous sex change needs to be validated for several of these species, we tentatively propose this trait is a novel mechanism influencing anuran body size evolution. Beyond this association, additional factors that shape the evolution of anuran body size and SSD remain elusive.
Silicon: its ameliorative effect on plant defense against herbivory
Authors: Singh Archana , Kumar Amit , Hartley Susan , Singh Indrakant Kumar
Published: June 2020

Plants protect themselves against pest attack utilizing both direct and indirect modes of defense. The direct mode of defense includes morphological, biochemical, and molecular barriers that affect feeding, growth, and survival of herbivores whereas the indirect mode of defense includes release of a blend of volatiles that attract natural enemies of the pests. Both of these strategies adopted by plants are reinforced if the plants are supplied with one of the most abundant metalloids, silicon (Si). Plants absorb Si as silicic acid (Si(OH)4) and accumulate it as phytoliths, which strengthens their physical defense. This deposition of Si in plant tissue is up-regulated upon pest attack. Further, Si deposited in the apoplast, suppresses pest effector molecules. Additionally, Si up-regulates the expression of defense-related genes and proteins and their activity and enhances the accumulation of secondary metabolites, boosting induced molecular and biochemical defenses. Moreover, Si plays a crucial role in phytohormone-mediated direct and indirect defense mechanisms. It is also involved in the reduction of harmful effects of oxidative stress resulting from herbivory by accelerating the scavenging process. Despite increasing evidence of its multiple roles in defense against pests, the practical implications of Si for crop protection have received less attention. Here, we highlight recent developments in Si-mediated improved plant resistance against pests and its significance for future use in crop improvement.
Significance of silicon uptake, transport, and deposition in plants
Authors: Mandlik Rushil , Thakral Vandana , Raturi Gaurav , Shinde Suhas , Nikolić Miroslav , Tripathi Durgesh K , Sonah Humira , Deshmukh Rupesh
Published: June 2020

Numerous studies have shown the beneficial effects of silicon (Si) for plant growth, particularly under stress conditions, and hence a detailed understanding of the mechanisms of its uptake, subsequent transport, and accumulation in different tissues is important. Here, we provide a thorough review of our current knowledge of how plants benefit from Si supplementation. The molecular mechanisms involved in Si transport are discussed and we highlight gaps in our knowledge, particularly with regards to xylem unloading and transport into heavily silicified cells. Silicification of tissues such as sclerenchyma, fibers, storage tissues, the epidermis, and vascular tissues are described. Silicon deposition in different cell types, tissues, and intercellular spaces that affect morphological and physiological properties associated with enhanced plant resilience under various biotic and abiotic stresses are addressed in detail. Most Si-derived benefits are the result of interference in physiological processes, modulation of stress responses, and biochemical interactions. A better understanding of the versatile roles of Si in plants requires more detailed knowledge of the specific mechanisms involved in its deposition in different tissues, at different developmental stages, and under different environmental conditions.
Bringing Evidence to the Point of Care: TriService Nursing Research Program Battlefield and Disaster Nursing Pocket Guide
Authors: Bridges Elizabeth , McNeill Margaret
Published: June 2020

Care under operational conditions is complex and unique. Although there is a growing body of evidence to inform this care, very few resources address operational nursing care. To address this issue and the lack of a compilation of relevant studies and evidence-based guidelines, the TriService Nursing Research Program Battlefield and Disaster Nursing Pocket Guide was created. The pocket guide has been updated and incorporates new and emerging evidence and also showcases the focused operational research of military nurse scientists. Eight thousand copies of the second edition of the guide, which curates a comprehensive body of literature related to operational nursing care, are being distributed to the three services. Military nurse scientists and multidisciplinary clinical experts contributed to the guide, with the content undergoing critical review by experts in operational care. This article summarizes the development of the pocket guide, summarizes some of the updates from the first edition, and demonstrates the integration of the guide into the major phases of evidence translation: knowledge, creation, and distillation; diffusion and dissemination; and adoption, implementation, and institutionalization. The incorporation of the pocket guide into readiness training reflects a goal of TriService Nursing Research Program to “develop and strengthen the Triservice community of nurse scholars to generate new knowledge in military nursing and translate it into practice” and an unending commitment to bring world class care to those in harm’s way.
Asteroseismic masses of four evolved planet-hosting stars using SONG and TESS: resolving the retired A-star mass controversy
Authors: Malla Sai Prathyusha , Stello Dennis , Huber Daniel , Montet Benjamin T , Bedding Timothy R , Fredslund Andersen Mads , Grundahl Frank , Jessen-Hansen Jens , Hey Daniel R , Palle Pere L , Deng Licai , Zhang Chunguang , Chen Xiaodian , Lloyd James , Antoci Victoria
Published: June 2020

The study of planet occurrence as a function of stellar mass is important for a better understanding of planet formation. Estimating stellar mass, especially in the red giant regime, is difficult. In particular, stellar masses of a sample of evolved planet-hosting stars based on spectroscopy and grid-based modelling have been put to question over the past decade with claims they were overestimated. Although efforts have been made in the past to reconcile this dispute using asteroseismology, results were inconclusive. In an attempt to resolve this controversy, we study four more evolved planet-hosting stars in this paper using asteroseismology, and we revisit previous results to make an informed study of the whole ensemble in a self-consistent way. For the four new stars, we measure their masses by locating their characteristic oscillation frequency, νmax, from their radial velocity time series observed by SONG. For two stars, we are also able to measure the large frequency separation, Δν, helped by extended SONG single-site and dual-site observations and new Transiting Exoplanet Survey Satellite observations. We establish the robustness of the νmax-only-based results by determining the stellar mass from Δν, and from both Δν and νmax. We then compare the seismic masses of the full ensemble of 16 stars with the spectroscopic masses from three different literature sources. We find an offset between the seismic and spectroscopic mass scales that is mass dependent, suggesting that the previously claimed overestimation of spectroscopic masses only affects stars more massive than about 1.6 M⊙.
X-ray properties of He ii λ 1640 emitting galaxies in VANDELS
Authors: Saxena A , Pentericci L , Schaerer D , Schneider R , Amorin R , Bongiorno A , Calabrò A , Castellano M , Cimatti A , Cullen F , Fontana A , Fynbo J P U , Hathi N , McLeod D J , Talia M , Zamorani G
Published: June 2020

We explore X-ray emission from a sample of 18 He ii λ1640 emitting star-forming galaxies at z ∼ 2.3–3.6 from the VANDELS survey in the Chandra Deep Field South, to set constraints on the role of X-ray sources in powering the He ii emission. We find that 4 He ii emitters have tentative detections with S/N ∼ 2 and have X-ray luminosities, LX = 1.5−4.9 × 1041 erg s−1. The stacked luminosity of all 18 He ii emitters is 2.6 × 1041 erg s−1, and that of a subset of 13 narrow He ii emitters (FHWM(He ii) < 1000 km s−1) is 3.1 × 1041 erg s−1. We also measure stacked LX for non-He ii emitters through bootstrapping of matched samples, and find LX = 2.5 × 1041 erg s−1, which is not significantly different from LX measured for He ii emitters. The LX per star formation rate for He ii emitters (log (LX/SFR) ∼ 40.0) and non-emitters (log (LX/SFR) ∼ 39.9) are also comparable and in line with the redshift evolution and metallicity dependence predicted by models. Due to the non-significant difference between the X-ray emission from galaxies with and without He ii, we conclude that X-ray binaries or weak or obscured active galactic nuclei are unlikely to be the dominant producers of He ii ionizing photons in VANDELS star-forming galaxies at z ∼ 3. Given the comparable physical properties of both He ii emitters and non-emitters reported previously, alternative He ii ionizing mechanisms such as localized low-metallicity stellar populations, Pop-III stars, etc. may need to be explored.
Detecting multiple DLAs per spectrum in SDSS DR12 with Gaussian processes
Authors: Ho Ming-Feng , Bird Simeon , Garnett Roman
Published: June 2020

We present a revised version of our automated technique using Gaussian processes (GPs) to detect damped Lyman α absorbers (DLAs) along quasar (QSO) sightlines. The main improvement is to allow our GP pipeline to detect multiple DLAs along a single sightline. Our DLA detections are regularized by an improved model for the absorption from the Lyman α forest that improves performance at high redshift. We also introduce a model for unresolved sub-DLAs that reduces misclassifications of absorbers without detectable damping wings. We compare our results to those of two different large-scale DLA catalogues and provide a catalogue of the processed results of our GP pipeline using 158 825 Lyman α spectra from SDSS data release 12. We present updated estimates for the statistical properties of DLAs, including the column density distribution function, line density (dN/dX), and neutral hydrogen density (ΩDLA).
Stellar spectral interpolation using machine learning
Authors: Sharma Kaushal , Singh Harinder P , Gupta Ranjan , Kembhavi Ajit , Vaghmare Kaustubh , Shi Jianrong , Zhao Yongheng , Zhang Jiannan , Wu Yue
Published: June 2020

Theoretical stellar spectra rely on model stellar atmospheres computed based on our understanding of the physical laws at play in the stellar interiors. These models, coupled with atomic and molecular line databases, are used to generate theoretical stellar spectral libraries (SSLs) comprising of stellar spectra over a regular grid of atmospheric parameters (temperature, surface gravity, abundances) at any desired resolution. Another class of SSLs is referred to as empirical spectral libraries; these contain observed spectra at limited resolution. SSLs play an essential role in deriving the properties of stars and stellar populations. Both theoretical and empirical libraries suffer from limited coverage over the parameter space. This limitation is overcome to some extent by generating spectra for specific sets of atmospheric parameters by interpolating within the grid of available parameter space. In this work, we present a method for spectral interpolation in the optical region using machine learning algorithms that are generic, easily adaptable for any SSL without much change in the model parameters, and computationally inexpensive. We use two machine learning techniques, Random Forest (RF) and Artificial Neural Networks (ANN), and train the models on the MILES library. We apply the trained models to spectra from the CFLIB for testing and show that the performance of the two models is comparable. We show that both the models achieve better accuracy than the existing methods of polynomial based interpolation and the Gaussian radial basis function (RBF) interpolation.
Free Will and Quantum Mechanics
Authors: De Caro Mario , Putnam Hilary
Published: June 2020

In the last few decades, the relevance of quantum mechanics to the free-will debate has been discussed at length, especially in relation to the prospects of libertarianism (the view according to which humans enjoy an indeterministic kind of free will). Basing his interpretation on Anscombe’s seminal work, Putnam argued in 1979 that, given that quantum mechanical indeterminacy is holistic at the macrolevel—i.e., it is not traceable to atomistic events such as quantum jumps of single atoms—it can provide libertarians with the kind of freedom they seek. As shown in this article, however, Putnam ultimately reached the conclusion—together with the other author of this article—that his argument was wrong due to problems with the way it appealed to the Uncertainty Principle.**
Acute hepatitis C treatment in advanced renal failure using 8 weeks of pan-genotypic daclatasvir and reduced-dose sofosbuvir
Authors: Goel Amit , Bhadauria Dharmendra S , Kaul Anupma , Verma Abhai , Tiwari Prachi , Rungta Sumit , Rai Praveer , Gupta Amit , Aggarwal Rakesh
Published: June 2020

Background

Sofosbuvir is not recommended in persons with estimated glomerular filtration rate (eGFR) <30 mL/min. We report the results of treatment with an off-label 8-week regimen of daclatasvir and half-dose sofosbuvir in patients with acute infection with hepatitis C virus ( HCV) and eGFR <30 mL/min.

Methods

Clinic records were searched to identify treatment-naïve, noncirrhotic adults with acute hepatitis C (HCV viremia and a ≥10-fold elevation of serum alanine aminotransferase activity) and eGFR <30 mL/min, who had been treated with a sofosbuvir-based regimen. Treatment response was assessed using serum HCV RNA testing at 4 weeks of treatment, end of the 8-week treatment and 12 weeks after stopping treatment.

Results

Of the 31 patients with acute hepatitis C, 27 [median age (range): 36 (18–74) years; 20 (74%) male] were started on treatment with 200 mg sofosbuvir and 60 mg daclatasvir daily for 8 weeks, irrespective of HCV genotype. All the 27 completed the planned 8-week treatment. One patient died 10 weeks after completing the treatment of an unrelated cause. All the 27 patients had undetectable HCV RNA after 4 weeks of and at the end of treatment. At 12 weeks after completion of treatment, only one tested HCV RNA positive and 25 were negative, with sustained virological response rate of 25/27 (92.6%) and 25/26 (96.2%) on intention-to-treat and per-protocol basis, respectively.

Conclusion

Eight-week course of daclatasvir and half-dose sofosbuvir is effective for acute hepatitis C in patients with eGFR <30 mL/min and could be a useful alternative to costly, kidney-safe anti-HCV oral drugs in resource-constrained settings.