bluuebunny/crossref_metadata_2025_split huggingface dataset:
PyFolding: An open-source software package for graphing, simulation and analysis of the biophysical properties of proteins
Authors: Lowe Alan R. , Perez-Riba Albert , Itzhaki Laura S. , Main Ewan R.G. 
Published: September 2017

Abstract]For many years, curve fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large datasets. One field that is relient on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we presentPyFolding, a free, open source, and extensible Python framework for graphing, analysis and simulation of the biophysical properties of proteins. To demonstrate the utility ofPyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: (i) multi-phase kinetic folding fitted to linked equations, (ii) global fitting of multiple datasets and (iii) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate howPyfoldingis easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show thatPyFoldingcan be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and amongst research teams.
Targeting histone deacetylase activity to arrest cell growth and promote neural differentiation in Ewing sarcoma
Authors: Souza Bárbara Kunzler , Costa Lopez Patrícia Luciana da , Menegotto Pâmela Rossi , Vieira Igor Araujo , Kersting Nathalia , Abujamra Ana Lúcia , Brunetto André T. , Brunetto Algemir L. , Gregianin Lauro , de Farias Caroline Brunetto , Thiele Carol J. , Roesler Rafael 
Published: September 2017

AbstractThere is an urgent need for advances in the treatment of Ewing sarcoma (EWS), an aggressive childhood tumor with possible neuroectodermal origin. Inhibition of histone deacetylases (HDAC) can revert aberrant epigenetic states and reduce growth in different experimental cancer types. Here, we investigated whether the potent HDAC inhibitor, sodium butyrate (NaB) has the ability to reprogram EWS cells towards a more differentiated state and affect their growth and survival. Exposure of two EWS cell lines to NaB resulted in rapid and potent inhibition of HDAC activity (1 h, IC501.5 mM) and a significant arrest of cell cycle progression (72 h, IC500.68-0.76 mM), marked by G0/G1 accumulation. Delayed cell proliferation and reduced colony formation ability were observed in EWS cells after long-term culture. NaB-induced effects included suppression of cell proliferation accompanied by reduced transcriptional expression of theEWS-FLI1fusion oncogene, decreased expression of key survival and pluripotency-associated genes, and re-expression of the differentiation neuronal marker ²III-tubulin. Finally, NaB reduced c-MYC levels and impaired survival in putative EWS cancer stem cells. Our findings support the use of HDAC inhibition as a strategy to impair cell growth and survival and to reprogram EWS tumors towards differentiation. These results are consistent with our previous studies indicating that HDis can inhibit the growth and modulate differentiation of cells from other types of childhood pediatric tumors possibly originating from neural stem cells.
A simplified electronic circuit for combined single-cell stimulation and recording using loose cell-attached electrodes
Authors: Strowbridge Ben W. , Todd Pressler R. 
Published: September 2017

AbstractWhile tight-seal patch clamp recordings have found wide use in neuroscience and in other fields, the requirement to replace the glass pipette after every attempted recording represents an impediment to high throughput studies such as searching for monosynaptically connected pairs of neurons. Loose cell-attached recording was introduced in 2000 to circumvent this problem since it enabled combined recording and stimulation of visually-identified neurons without necessitating a tight (gigaohm) seal. Since the stimulus voltages required to evoke action potentials through low resistance seals are beyond the capacity of most commercial amplifiers, Barbour and Isope introduced a variation of classic patch clamp amplifier circuit that is able to deliver stimulus voltages that are effective in triggering action potentials under the loose cell-attached patch clamp configuration. The present report presents the design and operation of a simpler amplifier that contains only two integrated circuits and is able to effectively stimulate and record action potentials in mitral cells in rodent olfactory bulb slices. The addition of an accessory analog gating circuit enables manual control of the stimulus voltage with pulse timing controlled by a digital output from a computer. This system may be useful in studies that require surveying many potential pairs of neurons for synaptic connections and for sampling and manipulating single-cell activity in in vivo electrophysiology experiments.
Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways ofNicotiana tabacumRubisco activase
Authors: Wang Quan , Serban Andrew J. , Wachter Rebekka M. , Moerner W.E. 
Published: September 2017

ABSTRACTOligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently-developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior ofNicotiana tabacum(Nt) rubisco activase (Nt-Rca), a chaperone-like, AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers and a tetramer/hexamer mixture, and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time, and from there estimated the rate of subunit exchange to be ~0.1s-1with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.
Human mobility in the context of climate change and disasters: a South American approach
Authors: Yamamoto Lilian , Serraglio Diogo Andreola , Cavedon-Capdeville Fernanda de Salles 
Published: September 2017

Purpose
This paper aims to assess to what extent South American countries have integrated recommendations of the international agenda to address human mobility in the context of disasters and climate change in their national laws and policies.

Design/methodology/approach
This research sought to find the level of discussions around human mobility in disaster laws, NDCs and National Adaptation Plans (NAPs) by looking for a range of search terms connected to human mobility in the context of disasters and climate change, followed by the content analysis of these terms.

Findings
Some advances with regards to human mobility are already confirmed in the domestic level of South American countries through humanitarian visas to disaster displaced persons and the inclusion of the topic in the DRR, climate change laws, NAPs and INDCs/NDCs. But they have not developed specific strategies with regards to it. Hence, their advances still require that national norms and policies are harmonized with the international guidelines. This will enable to fill the protection gap of people in context of disasters and climate change.

Originality/value
The results assess the level of harmonization above-mentioned between international instruments with national policies on human mobility in the context of disasters and climate change in South America.
Who takes responsibility for the climate refugees?
Authors: Ahmed Bayes 
Published: September 2017

Purpose
“No climate change, no climate refugees”. On the basis of this theme, this paper aims to propose a method for undertaking the responsibility for climate refugees literally uprooted by liable climate polluting countries. It also considers the historical past, culture, geopolitics, imposed wars, economic oppression and fragile governance to understand the holistic scenario of vulnerability to climate change.

Design/methodology/approach
This paper is organized around three distinct aspects of dealing with extreme climatic events – vulnerability as part of making the preparedness and response process fragile (past), climate change as a hazard driver (present) and rehabilitating the climate refugees (future). Bangladesh is used as an example that represents a top victim country to climatic extreme events from many countries with similar baseline characteristics. The top 20 countries accounting for approximately 82 per cent of the total global carbon dioxide (CO2) emissions are considered for model development by analysing the parameters – per capita CO2 emissions, ecological footprint, gross national income and human development index.

Findings
Results suggest that under present circumstances, Australia and the USA each should take responsibility of 10 per cent each of the overall global share of climate refugees, followed by Canada and Saudi Arabia (9 per cent each), South Korea (7 per cent) and Russia, Germany and Japan (6 per cent each). As there is no international convention for protecting climate refugees yet, the victims either end up in detention camps or are refused shelter in safer places or countries. There is a dire need to address the climate refugee crisis as these people face greater political risks.

Originality/value
This paper provides a critical overview of accommodating the climate refugees (those who have no means for bouncing back) by the liable countries. It proposes an innovative method by considering the status of climate pollution, resource consumption, economy and human development rankings to address the problem by bringing humanitarian justice to the ultimate climate refugees.
Biomarker of burden: Feather corticosterone reflects energetic expenditure and allostatic overload in captive waterfowl
Authors: Johns David W. , Marchant Tracy A. , Fairhurst Graham D. , Speakman John R. , Clark Robert G. 
Published: September 2017

AbstractAllostatic load describes the interplay between energetic demand and availability and is highly context dependent, varying between seasons and life‐history stages. When energy demands exceed physiological set points modulated by glucocorticoid hormones, individuals may experience allostatic overload and transition between stages in sub‐optimal physiological states.Corticosterone, the major glucocorticoid hormone regulating energy expenditure in birds, is incorporated into growing feathers (CORTf), and it has been suggested that CORTfreflects long‐term records of allostatic load during feather growth. However, relationships between allostatic load and CORTfhave not been adequately evaluated. If such relationships exist, the use of CORTfto investigate cross‐seasonal effects could provide novel insights into impacts of past allostatic load and/or overload events.We tested whether experimental increases in daily workload during two adjacent life‐history stages would be reflected in CORTflevels, and examined if CORTflevels reflected either current energetic demand or allostatic load prior to feather growth.Daily workloads in female mallardAnas platyrhynchosducklings were increased over a 6‐week period using physical obstacles and/or carrying back‐mounted weights. We measured daily energy expenditure, growth, body mass, and CORTfin growing ducklings. Then, we induced feather moult and reapplied combinations of workload treatments for an additional 6 weeks to investigate whether effects of past energetic demands would be detected in future CORTflevels.Ducklings confronted with higher workloads during development had reduced body mass, growth rates and consequently higher daily energy expenditure and CORTfvalues compared to controls. When ducklings were fully developed, CORTfpatterns in birds re‐exposed to workload treatments reflected only current, rather than past, energetic demands. However, under allostatic overload conditions, past levels of CORTfwere positively associated with CORTfin the subsequent moult.Our study confirms the previously untested assumption that CORTfreflects energetic demand during the period of feather growth in a precocial bird. We show that allostatic overload conditions early in life, which temporarily suppress growth, can be detected using CORTf, an event potentially missed in studies which rely solely on measures of body condition alone.We suggest that CORTfcan provide a valuable biomarker of allostatic load and overload conditions during the period of feather growth, but highlight how context should be considered for studies using CORTfto investigate influences of carryover effects. Our study contributes to building a physiological foundation to inform interpretations of ecological patterns using CORTf.Aplain language summaryis available for this article.
Mammalian herbivores affect leafhoppers associated with specific plant functional types at different timescales
Authors: Vandegehuchte Martijn L. , Trivellone Valeria , Schütz Martin , Firn Jennifer , de Schaetzen Frederic , Risch Anita C. 
Published: September 2017

Abstract

Theory predicts that mammalian herbivores affect the quantity and quality of plants on which they preferentially feed in the short term. In the longer term, they can promote either preferred or less preferred plants, depending on whether preferred plants are adapted or sensitive to grazing. Less clear are the short‐ and long‐term responses of herbivorous insects to mammalian herbivory, and how these responses depend on the specific plants or plant functional types on which the insects feed.

We progressively excluded large, medium and small mammals for five growing seasons in two subalpine vegetation types with long‐term differences in mammalian grazing intensity. Short‐grass vegetation has a history of intensive grazing, while tall‐grass vegetation has been grazed less intensively. We tested whether mammals altered the abundance and body size of leafhoppers specialized on specific plant functional types (grasses, sedges, forbs, or legumes/forbs), distinguishing between short‐term (exclosures) and long‐term (vegetation types) differences in mammalian grazing pressure. Furthermore, we assessed whether leafhoppers’ responses were explained by changes in biomass or quality of the plant functional types on which they feed.

In the short term, mammal exclosures increased the abundance of grass‐ and forb‐feeding leafhoppers via increases in the biomass of grasses and forbs, regardless of vegetation type. Both grasses and forbs are preferred food plants of mammals. In the long term, the biomass of sedges, which are less preferred by mammals, increased in the less intensively grazed tall‐grass vegetation. This resulted in a higher abundance of sedge‐feeding leafhoppers. The small size of these sedge feeders lowered the average leafhopper body size in the tall‐grass vegetation. Plant nutritional quality did not explain any effects of exclusions or vegetation types.

Our results demonstrate that both short‐ and long‐term effects of mammalian herbivores on the biomass of specific plant functional types caused concurrent changes in the abundance of specialized herbivorous insects, which scaled up to community‐wide shifts in insect body size, a key life‐history trait. A plant‐functional‐type approach can thus help to predict how overabundance or extinction of mammalian herbivores impacts on other components of the food web at various timescales.

A plain language summary is available for this article.
Thermoregulatory windows in Darwin's finches
Authors: Tattersall Glenn J. , Chaves Jaime A. , Danner Raymond M. 
Published: September 2017

Abstract

Darwin's finches have been the focus of intense study demonstrating how climatic fluctuations coupled with resource competition drive the evolution of a variety of bill sizes and shapes. The bill, as other peripheral surfaces, also plays an important role in thermoregulation in numerous bird species. The avian bill is vascularized, while limbs have specialized vasculature that facilitate heat loss or heat conservation (i.e. they are thermoregulatory windows).

The Galápagos Islands, home to Darwin's finches, have a hot and relatively dry climate for approximately half of the year, during which thermoregulatory windows (i.e. surfaces) could be important for thermoregulation and the linked challenge of water balance.

We hypothesized that Darwin's finch bills have evolved in part for their role in thermoregulation, possibly co‐opted, following adaptation for other functions, such as foraging. We predicted that bills of Darwin's finches are effective thermoregulatory windows, and that species differences in bill morphology, along with physiology and behaviour, lead to differences in thermoregulatory function.

To test these hypotheses, we conducted a field study to assess heat exchange and microclimate use in three ground finch species and sympatric cactus finch (Geospiza spp.). We collected thermal images of free‐living birds during a hot and dry season and recorded microclimate data for each observation. We used individual thermographic data to model the contribution of bills, legs and bodies to overall heat balance and compared surface temperatures to those from dead birds to test physiological control of heat loss from these surfaces. We derived and compared species‐specific threshold environmental temperatures, which are indicative of a species’ thermally neutral temperature.

In all species, the bill surface was an effective heat dissipater during naturally occurring warm temperatures. As expected, we found that finches controlled surface temperatures through physiology and that young birds had higher surface temperatures than adults. Larger bills contributed proportionally more to overall heat loss than smaller bills.

We demonstrate here that related, sympatric species with different bill sizes exhibit different patterns in the use of these thermoregulatory structures, supporting a role for thermoregulation in the evolution and ecology of Darwin's finch morphology.

A plain language summary is available for this article.
Insulin‐like growth factor 1 and life‐history evolution of passerine birds
Authors: Lodjak Jaanis , Mänd Raivo , Mägi Marko 
Published: September 2017

Abstract

Natural selection has generated a diversity of ways in which vertebrates allocate their resources between fundamental life‐history traits. The availability of possible evolutionary trajectories of these traits is limited by various genetic, physiological and phylogenetic constraints. This causes trade‐offs due to shared resource pools for, or genetic linkage of, competing traits. The majority of these trade‐offs are mediated by hormones and create the variability in phenotypes that can be observed in nature.

Insulin‐like growth factor 1 (IGF‐1) is an evolutionarily conserved peptide, which has been shown to be essential in the regulation of body size, the pattern of reproductive investment and life span across a broad taxonomic range of model species in laboratory and domesticated conditions. However, studies addressing corresponding evolutionary hypotheses on a broader scale and in free‐living vertebrates are very rare.

In this phylogenetic comparative study on free‐living passerines (Passeriformes), we explore the way in which plasma IGF‐1 levels underlie the evolution of body size and demographic fitness correlates (clutch size, egg weight, life span).

We showed firstly that IGF‐1 levels were positively associated with the body size of passerines, although smaller birds had larger IGF‐1‐mediated investment into building up their body faster. IGF‐1 levels were negatively associated with life span of passerines, and more so in birds with smaller body weight. Finally, IGF‐1 levels were negatively associated with clutch size in heavier species, and positively associated with egg weight in species with higher body weight and longer duration of parental care. The pattern was opposite in species with smaller body weight and shorter duration of parental care.

The described evolutionary framework indicates that variation in IGF‐1 levels can be regarded as an important mechanism that may underlie life‐history evolution in passerines. IGF‐1 could act as a physiological link mediating the inter‐regulatory growth–reproduction–lifespan “life‐history triangle” on the pace‐of‐life continuum. Interestingly, body weight and investment into parental care have likely imposed a constraining effect on the IGF‐1‐mediated co‐evolution of demographic fitness traits, such as life span or reproductive investment. This has limited the availability of adaptive pathways via which those traits could evolve as passerines diversified.

A plain language summary is available for this article.
The Variegated Financialization of Housing
Authors: Aalbers Manuel B. 
Published: September 2017

AbstractThere is a small but growing literature on the financialization of housing that demonstrates how housing is a central aspect of financialization. Despite the varied analyses of the financialization of housing and the importance of housing to financialization, the relations between housing and financialization remain under‐researched and under‐theorized. The financialization of housing is not really a specific form of financialization, transcending as it does a number of different forms of financialization. Housing systems, in particular, vary widely across the globe, which implies that housing financialization will be inherently variegated, path‐dependent and uneven. In this introduction to the symposium, I will discuss how the articles to follow contribute to the literature on the financialization of housing. Housing has entered a post‐Fordist, neoliberal and financialized regime. Increasingly, both mortgaged homeownership and subsidized rental housing are there to keep financial markets going, rather than being facilitated by those markets. There is little evidence that the global financial crisis has resulted in any de‐financialization of housing. There are common trajectories within uneven and variegated financialization, rather than radically different and completely unrelated forms of housing financialization.