bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical transitions in malaria transmission models are consistently generated by superinfection
Authors: Alonso David , Dobson Andy , Pascual Mercedes 
Published: May 2019

The history of modelling vector-borne infections essentially begins with the papers by Ross on malaria. His models assume that the dynamics of malaria can most simply be characterized by two equations that describe the prevalence of malaria in the human and mosquito hosts. This structure has formed the central core of models for malaria and most other vector-borne diseases for the past century, with additions acknowledging important aetiological details. We partially add to this tradition by describing a malaria model that provides for vital dynamics in the vector and the possibility of super-infection in the human host: reinfection of asymptomatic hosts before they have cleared a prior infection. These key features of malaria aetiology create the potential for break points in the prevalence of infected hosts, sudden transitions that seem to characterize malaria’s response to control in different locations. We show that this potential for critical transitions is a general and underappreciated feature of any model for vector-borne diseases with incomplete immunity, including the canonical Ross–McDonald model. Ignoring these details of the host’s immune response to infection can potentially lead to serious misunderstanding in the interpretation of malaria distribution patterns and the design of control schemes for other vector-borne diseases.This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.
Ectopic hepatocyte transplantation cures the pig model of tyrosinemia
Authors: Nicolas Clara T , Hickey Raymond D , Allen Kari L , Du Zeji , VanLith Caitlin J , Guthman Rebekah M , Amiot Bruce , Suksanpaisan Lukkana , Han Bing , Francipane Maria Giovanna , Cheikhi Amin , Jiang Huailei , Bansal Aditya , Pandey Mukesh K , Garg Ishan , Lowe Val , Bhagwate Aditya , O’Brien Daniel , Kocher Jean-Pierre A , DeGrado Timothy R , Nyberg Scott L , Kaiser Robert A , Lagasse Eric , Lillegard Joseph B 
Published: May 2019

AbstractThe effectiveness of cell-based therapies to treat liver failure is limited by the diseased liver environment. Herein we provide preclinical proof-of-concept for the treatment of liver failure through hepatocyte transplantation into lymph nodes in a large-animal model of hereditary tyrosinemia type 1 (HT1), a metabolic liver disease caused by deficiency of fumarylacetoacetate hydrolase (FAH) enzyme. FAH-deficient pigs received autologous hepatocyte transplantation into mesenteric lymph nodes afterex vivotransduction with a lentiviral vector carrying the pigFahgene. Hepatocytes showed early (6 hour) and durable (8 month) engraftment in lymph nodes, with reproduction of vascular and hepatic microarchitecture. Subsequently, hepatocytes migrated to and repopulated the native diseased liver. The corrected cells generated enough liver mass to clinically ameliorate disease as early as 97 days post-transplantation, with complete normalization of tyrosine levels and liver function tests. Integration site analysis defined the corrected hepatocytes in the liver as a subpopulation of hepatocytes in the lymph nodes, indicating that the lymph nodes served as a source for healthy hepatocytes to repopulate a diseased liver. Ectopic transplantation of hepatocytes cures the pig model of HT1 and presents a promising approach to the treatment of liver disease in patients with pre-existing liver damage and fibrosis.One Sentence SummaryTransplantation of corrected hepatocytes in mesenteric lymph nodes can cure fatal metabolic liver disease by providing organized liver tissue and by repopulating the diseased liver in the pig tyrosinemia model.
Division of labor increases with colony size, regardless of group composition, in the social spiderStegodyphus dumicola
Authors: Wright Colin M. , Lichtenstein James L. L. , Holbrook C. Tate , Pretorius Justin , Pinter-Wollman Noa , Pruitt Jonathan N. 
Published: May 2019

AbstractDivision of labor (DOL) is a pattern of work organization where individual group members specialize on different tasks. DOL is argued to have been instrumental for the success of eusocial insects, where it scales positively with group size both within and across species. Here we evaluate whether DOL scales positively with group size in a society of cooperative breeders (social spiders) and whether this pattern is impacted by the behavioral composition of the group. To do this we engineered experimental colonies of contrasting group sizes and behavioral compositions and tracked individuals participation in two colony maintenance tasks: prey capture and web construction. As with some eusocial insects, we found that larger groups exhibited DOL metrics up to 10-times greater than smaller groups, conveying that individuals specialize on particular tasks more in larger colonies. This scalar relationship did not differ by a groups behavioral composition, though groups composed of only bold spiders exhibited reduced DOL relative to all-shy or mixed groups. We also found that per capita participation in prey capture, but not web construction, decreased as a function of group size. This suggests that individuals in larger groups may save energy by reducing their involvement in some tasks. Together, our results convey that similar scalar relationships between DOL and group size can emerge both inside and outside the eusocial insects. Thus, theory developed for understanding DOL in eusocial societies may inform our understanding of group function in a larger swath of animal social diversity than is broadly appreciated.SignificanceStatementDivision of labor (DOL) has been a major area of research in the eusocial insects for decades, and is argues to underlie their ecological success. Only recently have other social arthropods, such as social spiders, been considered for studies concerning DOL. Given their smaller colony sizes, and absence of morphological castes, DOL was not thought to be an important facet of spider societies. However, we found that spider societies do indeed exhibit high degrees of DOL that is positively correlated to colony size, as seen in many eusocial insects. These findings suggest that the scalar relationship between group size and social organization seen in social insects is likely generalizable to a larger diversity of social taxa, and that cooperative breeders can show levels of division of labor equaling or exceeding those of eusocial systems evaluated to date.
Spasticity reduction in children with cerebral palsy is not associated with reduced energy consumption during walking
Authors: Zaino Nicole L. , Steele Katherine M. , Donelan J. Maxwell , Schwartz Michael H. 
Published: May 2019

AbstractBackgroundThe average energy consumption during walking of children with cerebral palsy (CP) is over two times of that of typically developing (TD) children and fatigue is one of the top complaints of children with CP and their families. Spasticity has been theorized to contribute to increased energy consumption during walking in CP, but its role remains unclear.MethodsWe retrospectively compared the energy consumption of walking in children with diplegic CP before and after selective dorsal rhizotomy (SDR), a surgery that reduces spasticity. A control group of participants with CP who also underwent gait analysis but did not undergo SDR was matched to the SDR group by pre-surgery age, spasticity, and energy consumption. Energy consumption and spasticity were compared at baseline and follow-up for both groups.FindingsAs expected, the SDR group has a significantly greater decrease (−44%) in spasticity compared to matched peers with CP who did not undergo SDR (−16%,P<0.001). While both groups had a reduction in energy consumption between visits (12 % SDR and 14% no-SDR), there was no difference in the change in energy consumption between groups (P=0.4).Interpretation: Reducing spasticity did not contribute to greater reductions in energy consumption, suggesting that spasticity has minimal impact on elevated energy consumption during walking for children with CP. Energy consumption and spasticity decrease with age among children with CP. Identifying matched control groups of peers with CP is critical for research involving children with CP to account for changes due to development.HighlightsEnergy consumption is not reduced after rhizotomy compared to matched peersSpasticity has minimal contribution to elevated energy during walkingMatched control groups are critical in cerebral palsy research
Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3’ processing and transcription termination
Authors: Sanchez Ana M. , Garg Angad , Shuman Stewart , Schwer Beate 
Published: May 2019

ABSTRACTFission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here we show that phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3’-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of the Asp1 and Aps1 IPP pyrophosphatases is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1Δ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3’-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.
Spatial cell disparity in the colonial choanoflagellateSalpingoeca rosetta
Authors: Naumann Benjamin , Burkhardt Pawel 
Published: May 2019

AbstractChoanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellateSalpingoeca rosettathat exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity ofS. rosettacells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial and food vacuole volumes of 40 individual cells from four differentS. rosettarosette colonies and compared our findings to previously published data on sponge choanocytes. Our analysis show that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria and food vacuoles. Furthermore, cell disparity withinS. rosettacolonies is higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.
Quantitative physiology of non-energy-limited retentostat cultures ofSaccharomyces cerevisiaeat near-zero specific growth rates
Authors: Liu Yaya , el Masoudi Anissa , Pronk Jack T. , van Gulik Walter M. 
Published: May 2019

AbstractSo far, the physiology ofSaccharomyces cerevisiaeat near-zero growth rates has been studied in retentostat cultures with a growth-limiting supply of the carbon and energy source. Despite its relevance in nature and industry, the near-zero growth physiology ofS. cerevisiaeunder conditions where growth is limited by the supply of non-energy substrates remains largely unexplored. This study analyses the physiology ofS. cerevisiaein aerobic chemostat and retentostat cultures grown under either ammonium or phosphate limitation. To compensate for loss of extracellular nitrogen- or phosphorus-containing compounds, establishing near-zero growth rates (μ < 0.002 h-1) in these retentostats required addition of low concentrations of ammonium or phosphate to reservoir media. In chemostats as well as in retentostats, strongly reduced cellular contents of the growth-limiting element (nitrogen or phosphorus) and high accumulation levels of storage carbohydrates were observed. Even at near-zero growth rates, culture viability in non-energy-limited retentostats remained above 80 % and ATP synthesis was still sufficient to maintain an adequate energy status and keep cells in a metabolic active state. Compared to similar glucose-limited retentostat cultures, the nitrogen- and phosphate-limited cultures showed a partial uncoupling of catabolism and anabolism and aerobic fermentation. The possibility to achieve stable, near-zero growth cultures ofS. cerevisiaeunder nitrogen- or phosphorus-limitation offers interesting prospects for high-yield production of bio-based chemicals.ImportanceThe yeastSaccharomyces cerevisiaeis a commonly used microbial host for production of various bio-chemical compounds. From a physiological perspective, biosynthesis of these compounds competes with biomass formation in terms of carbon and/or energy equivalents. Fermentation processes functioning at extremely low or near-zero growth rates would prevent loss of feedstock to biomass production. EstablishingS. cerevisiaecultures in which growth is restricted by the limited supply of a non-energy substrate could therefore have a wide range of industrial applications, but remains largely unexplored. In this work we accomplished near-zero growth ofS. cerevisiaethrough limited supply of a non-energy nutrient, namely the nitrogen or phosphorus source and carried out a quantitative physiology study of the cells under these conditions. The possibility to achieve near-zero-growthS. cerevisiaecultures through limited supply of a non-energy nutrient may offer interesting prospects to develop novel fermentation processes for high-yield production of bio-based chemicals.
Implicit micelle model for membrane proteins using super-ellipsoid approximation
Authors: Mori Takaharu , Sugita Yuji 
Published: May 2019

AbstractSurfactant micelles are often utilized as membrane mimetics for structure determination and functional analysis of membrane proteins. Although curved-surface effects of the micelle can perturb their structure, it is difficult to assess such effects and membrane mimetic artifacts by experimental and theoretical methods. Here, we propose an implicit micelle model (IMIC) to be used in molecular dynamics (MD) simulations of membrane proteins. IMIC is an extension of the IMM1 implicit membrane model by introducing a super-ellipsoid approximation to represent the curved-surface effects. Most of the parameters for IMIC are obtained from all-atom explicit solvent MD simulations of twelve membrane proteins in various micelles. In simulations of the HIV envelop protein gp41, M13 major coat protein gp8, and amyloid precursor protein (APP) dimer, curved-surface and compact hydrophobic-core effects are exhibited. The MD simulations with IMIC provide accurate structure predictions of membrane proteins in various micelle environments quickly with smaller computational cost than that necessary for explicit solvent/micelle model.
PAM recognition by miniature CRISPR nucleases triggers programmable double-stranded DNA target cleavage
Authors: Karvelis Tautvydas , Bigelyte Greta , Young Joshua K. , Hou Zhenglin , Zedaveinyte Rimante , Budre Karolina , Paulraj Sushmitha , Djukanovic Vesna , Gasior Stephen , Silanskas Arunas , Venclovas Česlovas , Siksnys Virginijus 
Published: May 2019

ABSTRACTIn recent years, CRISPR-associated (Cas) nucleases have revolutionized the genome editing field. Being guided by an RNA to cleave double-stranded (ds) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer unprecedented flexibility, however, more compact versions would simplify delivery and extend application. Here, we present a collection of 10 exceptionally compact (422-603 amino acids) CRISPR-Cas nucleases that recognize and cleave dsDNA in PAM dependent manner. Categorized as class 2 type V-F they come from the Cas14 family and distantly related type V-U3 Cas proteins found in bacteria. Using biochemical methods, we demonstrate that a 5’ T- or C-rich PAM sequence triggers double stranded (ds) DNA target cleavage. Based on this discovery, we evaluated whether they can protect against invading dsDNA in E. coli and find that some but not all can. Altogether, our findings show that miniature Cas nucleases are functional CRISPR-Cas defense systems and have the potential to be harnessed as programmable nucleases for genome editing.
Assessing the sustainability content of the Nigerian engineering curriculum
Authors: Akeel Usman Umar , Bell Sarah Jayne , Mitchell John E. 
Published: May 2019

PurposeThe purpose of this study is to present an assessment of the sustainability content of the Nigerian engineering curriculum in universities.Design/methodology/approachContent analysis is used to generate and analyse data from three engineering documents, namely, the Benchmark Minimum Academic Standards for Engineering Programmes in Nigeria and the engineering handbooks of two Nigerian higher education institutions.FindingsThe Nigerian engineering curriculum is revealed to have a low sustainability content, with environmental concepts being the most cited themes and social topics as the least stated issues.Research limitations/implicationsThe sustainability assessment approach adopted in the study is constrained by the question of what constitutes a sustainability syllabus. Expert-derived sustainability themes used in the study are unavoidably incomplete and may limit the conduct of an exhaustive sustainability content assessment.Practical implicationsBased on the research outcome, the Council for the Regulation of Engineering in Nigeria and other stakeholders can consider ways to adequately incorporate sustainability themes in the Nigerian engineering curriculum.Originality/valueThe research is an effort to determine the presence of sustainability issues in the Nigerian engineering education, which has hitherto been scarcely documented. This study provides a baseline and a rationale for sustainability education interventions in the Nigerian engineering curriculum. It also presents a methodology for analysing sustainability content in university curriculum and contributes to the continuing sustainability education discourse, especially in relation to sub-Saharan Africa.
The educational impact of using mobile technology in a database course in college
Authors: Sakibayev Spartak , Sakibayev Razakh , Sakibayeva Bela 
Published: May 2019

Purpose
Nowadays, when mobile devices are actively evolving and penetrating the various spheres of human activity they have a potential to modernize and facilitate the sphere of IT education as well. This paper aims to test the hypothesis stating that introduction of mobile technology to the college-level database course for future IT specialists has a positive academic impact on students.

Design/methodology/approach
The main theoretical premises for the present study were the general findings of the surveys by Hinze et al. (2017) and Bowen and Pistilli (2012) indicating that: using mobile tools to work on classroom projects improves student’s academic success students, especially those from computing specialties, actively turn to mobile tools in their academic activity students favor the Android and iPhone platforms and prefer native mobile apps to Web-based mobile apps The key idea of the present study was to validate these general premises in the specific case of the college-level database class. Namely, the authors formulated a hypothesis that Android-based mobile devices have a positive impact on the IT students’ academic performance and interest in the subject at the college-level introductory database lessons. Throughout the study, the authors examined both quantitative (students’ scores and attendance rate) and qualitative aspects (students’ and teachers’ opinions) of the hypothesis.

Findings
Based on the experiment’s positive outcome resulting in students’ increased academic performance and interest in the subject, the authors conclude that in the context of the college-level database course mobile devices can successfully substitute traditional desktop computers and positively affect students’ academic activity.

Originality/value
Based on the experiment’s positive outcome resulting in students’ increased academic performance and interest in the subject, the authors conclude that in the context of the college-level database course mobile devices can successfully substitute traditional desktop computers and positively affect students’ academic activity.
Identification of factors affecting productivity in Thailand’s construction industry and proposed maturity model for improvement of the productivity
Authors: Pornthepkasemsant Patraporn , Charoenpornpattana Santi 
Published: May 2019

Purpose
Low productivity is one of the main challenges facing the Thai construction industry. The purpose of this study is to identify factors affecting the productivity of Thailand’s construction industry and to develop a maturity model for improvement of the productivity.

Design/methodology/approach
Data were collected quantitatively through questionnaire surveys targeting different Thai construction companies to identify factors affecting the productivity in the Thai construction industry. Based on the identified factors and opinions of experts, a maturity model was then developed and validated.

Findings
The top five factors affecting the productivity are labor skills, material management, equipment management, site management and safety. A maturity model for the productivity improvement has been developed, and its performance is satisfactory.

Research limitations/implications
The productivity maturity model is based on data collected in Thailand, and the model is valid only in Thailand or other countries which have similar social and economic circumstance.

Practical implications
Construction companies may use the proposed maturity model as a framework for improving their productivity.

Originality/value
Unlike other studies, which usually rely on an issue-based approach, this study uses a systematic company-wide approach to improve the productivity.