bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forensic post-mortem interval (PMI) estimates: variation in fly developmental times of individuals
Authors: Földvári Mihály 
Published: December 2016

ABSTRACTImmature stages of flies are paramount in establishing the post-mortem interval (PMI) in forensic practice. My focus is on differences in developmental time that can be influenced by genetic differences or individual life history traits, which latter may be interpreted as life history decisions.Data of a calliphorid fly species (Lucilia ampullacea) are presented: one female produced 300 eggs within an hour and the individual developmental time varied subsequently to a great extent – when the first flies emerged from their puparia there were still first instar larvae in the food (pig liver) provided.In conclusion the estimated PMI must be based on a wide range of collected flies (not simply the oldest or largest or widest individual), since a limited sample can be one extremity of a potentially bell shaped (Gaussian) frequency distribution of developmental times — unrepresentative sampling will bias the PMI in an unpredictable way. One possible solution can be to use large, randomized samples and their body measurement means.
Microprocessor dynamics shows co- and post-transcriptional processing of pri-miRNAs
Authors: Louloupi Annita , Ntini Evgenia , Liz Julia , Ørom Ulf Andersson 
Published: December 2016

AbstractmiRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multi-step process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to obtain nascent RNA within a 1-hour window after labeling with bromouridine. We show, that pri-miRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing and provide evidence that pri-miRNA processing can occur both co-transcriptionally and post-transcriptionally.
Environment driven conformational changes modulate H-NS DNA bridging activity
Authors: van der Valk Ramon A. , Vreede Jocelyne , Moolenaar Geri F. , Hofmann Andreas , Goosen Nora , Dame Remus T. 
Published: December 2016

AbstractBacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator inGram-negative bacteria, and is believed to be a crucial player in bacterial chromatin organization via its DNA bridging activity. H-NS activityin vivois modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically it is unclear how functional modulation of H-NS by such factors is achieved. Here, we show that a diverse spectrum of H-NS modulators alter the ability of H-NS to bridge DNA. Changes in monovalent and divalent ion concentrations drive an abrupt switch between a bridging and non-bridging DNA binding mode. Similarly, synergistic and antagonistic co-regulators modulate the DNA bridging efficiency. Structural studies suggest a conserved mechanism: H-NS switches between a “closed” and an “open”, bridging competent, conformation driven by environmental cues and interaction partners.
A new improved and extended version of the multicell bacterial simulatorgro
Authors: Gutiérrez Martín , Gregorio-Godoy Paula , Pérez del Pulgar Guillermo , Muñoz Luis , Sáez Sandra , Rodríguez-Patón Alfonso 
Published: December 2016

Abstractgrois a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits. In this work, we present several extensions made togrothat improve the performance of the simulator, make it easier to use and provide new functionalities. The new version ofgrois between one and two orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 105cells in less than 20 minutes. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version ofgro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented forgrohave made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.
Parallel streams define the temporal dynamics of speech processing across human auditory cortex
Authors: Hamilton Liberty S. , Edwards Erik , Chang Edward F. 
Published: December 2016

AbstractTo derive meaning from speech, we must extract multiple dimensions of concurrent information from incoming speech signals, including phonetic and prosodic cues. Equally important is the detection of acoustic cues that give structure and context to the information we hear, such as sentence boundaries. How the brain organizes this information processing is unknown. Here, using data-driven computational methods on an extensive set of high-density intracranial recordings, we reveal a large-scale partitioning of the entire human speech cortex into two spatially distinct regions that detect important cues for parsing natural speech. These caudal (Zone 1) and rostral (Zone 2) regions work in parallel to detect onsets and prosodic information, respectively, within naturally spoken sentences. In contrast, local processing within each region supports phonetic feature encoding. These findings demonstrate a fundamental organizational property of the human auditory cortex that has been previously unrecognized.
Tandem duplications lead to novel expression patterns through exon shuffling inD. yakuba
Authors: Rogers Rebekah L. , Shao Ling , Thornton Kevin R. 
Published: December 2016

AbstractOne common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample ofDrosophila yakubato test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5ʹ and 3ʹ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30de novogene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.Author SummaryThe enclosed work shows that whole gene duplications rarely affect gene expression, in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number. We further explain how tandem duplications that create shuffled gene structures can force upregulation of gene sequences,de novogene creation, and multifold changes in transcript levels.These results show that tandem duplications can produce new genes that are a source of immediate novelty associated with more extreme expression changes than previously suggested by theory. Further, these gene expression changes are a potential source of both beneficial and pathogenic mutations, immediately relevant to clinical and medical genetics in humans and other metazoans.
Fusing tree-ring and forest inventory data to infer influences on tree growth
Authors: Evans Margaret E. K. , Falk Donald A. , Arizpe Alexis , Swetnam Tyson L. , Babst Flurin , Holsinger Kent E. 
Published: December 2016

AbstractBetter understanding and prediction of tree growth is important because of the many ecosystem services provided by forests and the uncertainty surrounding how forests will respond to anthropogenic climate change. With the ultimate goal of improving models of forest dynamics, here we construct a statistical model that combines complementary data sources – tree-ring and forest inventory data. A Bayesian hierarchical model is used to gain inference on the effects of many factors on tree growth – individual tree size, climate, biophysical conditions, stand-level competitive environment, tree-level canopy status, and forest management treatments – using both diameter at breast height (DBH) and tree-ring data. The model consists of two multiple regression models, one each for the two data sources, linked via a constant of proportionality between coefficients that are found in parallel in the two regressions. The model was applied to a dataset developed at a single, well-studied site in the Jemez Mountains of north-central New Mexico, U. S. A. Inferences from the model included positive effects of seasonal precipitation, wetness index, and height ratio, and negative effects of seasonal temperature, southerly aspect and radiation, and plot basal area. Climatic effects inferred by the model compared well to results from a dendroclimatic analysis. Combining the two data sources did not lead to higher predictive accuracy (using the leave-one-out information criterion, LOOIC), either when there was a large number of increment cores (129) or under a reduced data scenario of 15 increment cores. However, there was a clear advantage, in terms of parameter estimates, to the use of both data sources under the reduced data scenario: DBH remeasurement data for ~500 trees substantially reduced uncertainty about non-climate fixed effects on radial increments. We discuss the kinds of research questions that might be addressed when the high-resolution information on climate effects contained in tree rings are combined with the rich metadata on tree- and stand-level conditions found in forest inventories, including carbon accounting and projection of tree growth and forest dynamics under future climate scenarios.
Skills and earnings in less than bachelor’s occupations
Authors: Yerger David B. 
Published: December 2016

Purpose
The purpose of this paper is to investigate linkages in US labor market between importance of specific skills, education, or training requirements, and private average salary for occupations not characterized as requiring a bachelor’s degree or higher.

Design/methodology/approach
Data set constructed that matches 474 less than bachelor’s occupations to private average salary, education, or training requirements category, and 35 specific skills. Statistical and regression analysis has been done to assess linkages between these variables.

Findings
Highest returns associated with cognitive skills, quantitative skills, and other core academic basic skills set followed by traditional blue-collar technical skills. Interpersonal skills and related social skills set exhibited weak, and sometimes negative, association with private average salary by occupation.

Research limitations/implications
Study of only US labor market at single point of time, findings may not generalize to either non US markets or occupations requiring bachelor’s degree or higher.

Practical implications
Workers in the less than bachelor’s labor market have greater upside salary potential if they obtain postsecondary certificates or associates’ degrees and target occupations placing a greater importance on cognitive skills, quantitative skills, and core academic basic skills than if they target traditional blue-collar technical skill occupations.

Social implications
Social policies to enhance earnings for workers lacking bachelor’s degrees must target improving core generic transferable academic skills as well as vocationally specific training.

Originality/value
This if the first study that links these many specific skills to salary variation across less than bachelor’s occupations.
The rationale of part-time farming: empirical evidence from Norway
Authors: Mittenzwei Klaus , Mann Stefan 
Published: December 2016

PurposeOutside farming, pluriactivity is generally considered as undesirable, whereas agricultural economists tend to recommend part-time farming. This contradiction is to be solved. The paper aims to discuss this issue.Design/methodology/approachLinking tax-payer and statistical farm-level data from Norway, the authors tested how profitable part-time farming is for Norwegian farm households.FindingsThe analysis showed that concentrating on either working on-farm or off-farm generates a higher household income than combining the two.Practical implicationsPart-time farming may be a lifestyle decision, but apparently is not economically optimal for most farms.Originality/valueThe contribution solves an apparent contradiction between the discourses inside and outside agriculture.
Trust-based social capital, economic growth and property rights: explaining the relationship
Authors: Ahmad Mahyudin , Hall Stephen G. 
Published: December 2016

Purpose
The purpose of this paper is to attest whether generalized trust variable is the best proxy for social capital in explaining the latter’s effect on economic growth in a panel setting. Via a specially formulated theoretical framework, the authors also test whether the growth-effect of social capital is direct or indirect, and if it is indirect, can property rights be the link between social capital and growth.

Design/methodology/approach
The authors begin with testing the robustness of generalized trust variable in explaining the effect of social capital on growth and property rights. The authors then propose a number of trust-alternative variables that are shown to contain an element of trust based on theoretical arguments drawn from previous studies, to proxy for social capital and re-estimate its effect on growth and property rights. In this study, the authors use panel estimation technique, hitherto has been limited in social capital studies, which are capable of reducing omitted variable bias and time-invariant heterogeneity compared to the commonly used cross-sectional estimation.

Findings
First, the authors find that generalized trust data obtained by the World Value Survey (WVS) are unable to yield sufficiently robust results in panel estimation due to missing observations problem. Using the proposed trust-alternative variables, the estimation results improve significantly and the authors are able to show that social capital is a deep determinant of growth and it is affecting growth via property rights channel. The findings also give supporting evidence to the primacy of informal rules and constraints as proposed by North (2005) over the political prominence theory by Acemoglu et al. (2005).

Research limitations/implications
Generalized trust data obtained from the WVS, frequently used in majority of social capital studies to measure social capital, yield highly non-robust results in panel estimation due to missing observations problem. Future studies in social capital intending to use panel estimation therefore need to find trust-alternative variables to proxy for social capital, and this paper has proposed four such variables.

Originality/value
The use of panel estimation technique extends the evidence of social capital significance to economic growth and property rights, since the previous social capital studies rely heavily on cross-sectional estimation technique. Due to the availability of annual observations of the trust-alternative variables, this paper is able to find better results as compared to estimation using generalized trust data.
Maintaining hope: the intrinsic role of professional support
Authors: Onnis Leigh-ann L. , Dyer Geraldine 
Published: December 2016

Purpose
The purpose of this paper is to examine the supportive aspects of a team approach for a remote mental health team that report high stability in senior clinical roles, in a region where voluntary turnover is typically high.

Design/methodology/approach
This qualitative research study examines the reflections of team members on their role and job characteristics through informal semi-structured interviews.

Findings
The extant themes identified as supportive aspects of the team approach included engagement and both personal and professional support. The intrinsic role of support in remote work environments, and the impact of intrinsic job satisfaction through client-focussed practices further supported low turnover, improved stability and consistency of service provision.

Originality/value
Continued support for existing experienced health professionals will contribute to workforce stability in remote regions where needs are complex and continuity of care is improved by consistent, reliable services. With health professionals working in remote Australia reporting high levels of job satisfaction; it follows that the next steps involve minimising dissatisfaction through effective workforce support mechanisms. Health professionals already working in remote regions, suggest that this is about engagement and personal and professional support through flexible work systems. While the findings of this study may not be generalisable, the authors suggest that these supportive aspects are transferable to other multi-disciplinary team settings.
Livestock grazing, forest protection and law in Greece
Authors: Kapotas Panagiotis , Maria Efpraxia Aithra 
Published: December 2016

Purpose
The purpose of this paper is to present, from a critical point of view, the current legal framework of livestock grazing in public forests in Greece, to present the implementation problems that have arisen and to suggest possible solutions.

Design/methodology/approach
The authors are trying to combine and implement some of the rangeland ecology results as a tool to explain the legal status and the reform proposals.

Findings
Livestock grazing is a misunderstood activity when it occurs in forests. In fact, when livestock grazing is controlled and based on the capacity of a forest area, it has been proven that it does not degrade an ecosystem; on the contrary, it contributes to biodiversity and to the prevention of forest fires. The prohibition of grazing for a long period of time, along with the establishment of a legal framework by which the forestry service is required to abide, which does not provide for alternatives or compensatory measures to farmers, has resulted in the creation of extremely unpleasant conditions for farmers.

Originality/value
There are hardly any relevant studies in Greek and international literature specifically focused on the Greek legal status of livestock grazing. The scarce contributions on this topic have been investigated and are incorporated in the justification of the study.
Analysis of the stochastic model of the Markov chain on daily rainfall occurrence in the state of Santa Catarina, Brazil
Authors: Back Álvaro José , Miguel Luana Pasini 
Published: December 2016

Purpose
The purpose of this paper is to evaluate the seasonal and spatial variations in the statistical descriptors of the Markov chain model as well as the expected values of the length of dry and wet days and to estimate the probability of dry and rainy sequences in the state of Santa Catarina.

Design/methodology/approach
Daily rainfall data from 1970 to 2013 of five rainfall stations in the state of Santa Catarina were used. To model the sequence of dry and wet days, the first order of the Markov chain was used. The statistical descriptors of the Markov model were evaluated, as well as the expected values of the length of dry and wet days and the number of dry and rainy days for each month. Along with geometric distribution, the probability of occurrence of sequences of dry and rainy days was determined. The adherence of the data to geometric distribution was evaluated using the Kolmogorov-Smirnov test.

Findings
The results showed that there is a seasonal and spatial variation in Markov model descriptors and also in the duration of the dry and rainy periods. These variations may be related to the mechanisms responsible for the formation and distribution of rainfall in the state, such as the air masses and relief. The Lages station, located in the Plateau of Santa Catarina, had the highest P00 values, reflecting more stable conditions of the atmosphere. In autumn and winter, no marked differences were found between the coastal stations and west of the state. The geometric distribution was adequate for estimating the probability of dry and rainy days.

Originality/value
Although some work has already been carried out on the modeling of the Markov chain in the state of Santa Catarina, this study was found to be more complete with the use of various statistical descriptors of the model and its application in estimating the duration of the cycles of dry and wet periods and the number of rainy days in the period.
Enhancing the spatial rainfall uniformity of pressurized nozzle simulators
Authors: Silveira Alexandre , Isidoro Jorge M.G.P. , de Deus Fábio P. , dos Reis Simone Siqueira , Silva Antônio Marciano da , Gonçalves Flávio A. , Menezes Paulo Henrique Bretanha Junker , Tiezzi Rafael de O. 
Published: December 2016

Purpose
Rainfall simulators are used on experimental hydrology, in areas such as, e.g., urban drainage and soil erosion, with important timesaving when compared to real scale hydrological monitoring. The purpose of this paper is to contribute to increase the quality of rainfall simulation, namely, for its use with scaled physical models.

Design/methodology/approach
Two pressurized rainfall simulators are considered. M1 uses three HH-W 1/4 FullJet nozzles under an operating pressure of 166.76 kPa and was tested over a 4.00 m length by 2.00 m width V-shaped surface. M2 was prepared to produce artificial rainfall over an area of 10.00 m length by 10.00 m width. The spatial distribution of rainfall produced from a single nozzle was characterized in order to theoretically find the best positioning for nozzles to cover the full 100 m2 area with the best possible rainfall uniformity.

Findings
Experiments with M1 led to an average rainfall intensity of 76.77-82.25 mm h−1 with a 24.88 per cent variation coefficient and a Christiansen Uniformity Coefficient (CUC) of 78.86 per cent. The best result with M2 was an average rainfall intensity of 75.12-76.83 mm h−1 with a 21.23 per cent variation coefficient and a CUC of 83.05 per cent.

Practical implications
This study contributes to increase the quality of artificial rainfall produced by pressurized rainfall simulators.

Originality/value
M2 is the largest rainfall simulator known by the authors worldwide. Its use on rainfall-runoff studies (e.g. urban areas, erosion, pollutant transport) will allow for a better understanding of complex surface hydrology processes.