bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explaining the texture properties of whey protein isolate/starch co-gels from fracture structures
Authors: Fu Wei , Nakamura Takashi 
Published: January 2017

Abstract
The effects of tapioca starch (TS) and potato starch (PS) on texture properties of whey protein isolate (WPI)/starch co-gels were investigated for fracture structures. We focused on two types of WPI network structures. In a fine-stranded structure at pH 6.8, the WPI/TS co-gel fractured similarly to the WPI single gel. The WPI/PS co-gel was broken at a lower strain and lower stress. In a random aggregation at pH 5.8, the WPI/TS co-gel reached a yielding point at a lower strain, whereas the WPI/PS co-gel fractured at a higher strain and higher stress. In the fracture structures, it was revealed that breaks occurred in different places in these cases, which could explain the different texture properties of samples. This study tries to explain the texture properties of WPI/starch co-gels from fracture structures and provides a reference to predict texture properties of the WPI/starch food system.
Soil Conservation Management Systems Under Uncertainty
Authors: Setia Parveen P. , Johnson Gary V. 
Published: January 2017

AbstractSuccess of a soil conservation program depends on the number of acres on which recommended practices are implemented. If risk considerations are introduced in formulating plans to control soil loss, whether individuals will implement the desired management system(s) to achieve conservation objectives established for the region is an unclear factor. This paper illustrates how expected utility maximization and safety‐first decision criteria influence the selection of a soil conservation management system under uncertainty.
Farm Family Resources and the Adoption of No‐Plow Tillage in Southwestern Wisconsin
Authors: Belknap John , Saupe William E. 
Published: January 2017

AbstractA probit model identifies variables related to the probability that a farm operator used a conservation tillage practice. Data from a 1983 survey of 529 randomly selected Wisconsin farmers were used to determine maximum likelihood estimates. Voluntary no‐plow adopters were significantly different from traditional moldboard tillers in these respects: they were more likely to be risk takers; more aware of the effect of erosion damage on property values and yields; operated larger farms in areas that had less precipitation and a warmer climate; and were more often owners than renters. Several other variables, cited elsewhere in the literature, did not appear to be significant but are also reported.
Risk, Diversification, and Vegetables as an Alternative Crop for Midwestern Agriculture
Authors: Weimar Mark R. , Hallam Arne 
Published: January 2017

AbstractA quasi‐spatial substitution model is developed to investigate the opportunities for Iowa to substitute local vegetable production for that of current distant suppliers. This quasi‐spatial equilibrium approach determines not only if crops can be grown profitably at current prices, but whether they would remain profitable after equilibrium price adjustments. Thirteen fresh vegetable crops are studied as alternatives to current row crops such as corn and soybeans. The results indicate that although more than half of these crops could be grown profitably within the state of Iowa, they would replace only about 3,900 acres of current corn and soybean acreage.
Dynamics of IRES-mediated translation
Authors: Johnson Alex G. , Grosely Rosslyn , Petrov Alexey N. , Puglisi Joseph D. 
Published: January 2017

Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of cap-binding and scanning. Owing to their simplicity and ribosomal affinity, the CrPV and HCV IRES have been important models for structural and functional studies of the eukaryotic ribosome during initiation, serving as excellent targets for recent technological breakthroughs in cryogenic electron microscopy (cryo-EM) and single-molecule analysis. High-resolution structural models of ribosome : IRES complexes, coupled with dynamics studies, have clarified decades of biochemical research and provided an outline of the conformational and compositional trajectory of the ribosome during initiation. Here we review recent progress in the study of HCV- and CrPV-type IRESs, highlighting important structural and dynamics insights and the synergy between cryo-EM and single-molecule studies.
This article is part of the themed issue ‘Perspectives on the ribosome’.
Ribosome dynamics during decoding
Authors: Rodnina Marina V. , Fischer Niels , Maracci Cristina , Stark Holger 
Published: January 2017

Elongation factors Tu (EF-Tu) and SelB are translational GTPases that deliver aminoacyl-tRNAs (aa-tRNAs) to the ribosome. In each canonical round of translation elongation, aa-tRNAs, assisted by EF-Tu, decode mRNA codons and insert the respective amino acid into the growing peptide chain. Stop codons usually lead to translation termination; however, in special cases UGA codons are recoded to selenocysteine (Sec) with the help of SelB. Recruitment of EF-Tu and SelB together with their respective aa-tRNAs to the ribosome is a multistep process. In this review, we summarize recent progress in understanding the role of ribosome dynamics in aa-tRNA selection. We describe the path to correct codon recognition by canonical elongator aa-tRNA and Sec-tRNASecand discuss the local and global rearrangements of the ribosome in response to correct and incorrect aa-tRNAs. We present the mechanisms of GTPase activation and GTP hydrolysis of EF-Tu and SelB and summarize what is known about the accommodation of aa-tRNA on the ribosome after its release from the elongation factor. We show how ribosome dynamics ensures high selectivity for the cognate aa-tRNA and suggest that conformational fluctuations, induced fit and kinetic discrimination play major roles in maintaining the speed and fidelity of translation.This article is part of the themed issue ‘Perspectives on the ribosome’.
A non-catalytic role of RecBCD in Homology Directed Gap Repair and Translesion Synthesis
Authors: Laureti Luisa , Lee Lara , Philippin Gaëlle , Pagès Vincent 
Published: January 2017

ABSTRACTThe RecBCD complex is a key factor in DNA metabolism. This protein complex harbors a processive nuclease and two helicases activities that give it the ability to process duplex DNA ends. These enzymatic activities make RecBCD a major player in double strand break repair, conjugational recombination and degradation of linear DNA. In this work, we unravel a new role of the RecBCD complex in the processing of DNA single-strand gaps that are generated at DNA replication-blocking lesions. We show that independently of its nuclease or helicase activities, the entire RecBCD complex is required for recombinational repair of the gap and efficient translesion synthesis. Since none of the catalytic functions of RecBCD are required for those processes, we surmise that the complex acts as a structural element that stabilizes the blocked replication fork, allowing efficient DNA damage tolerance.
A tandem simulation framework for predicting mapping quality
Authors: Langmead Ben 
Published: January 2017

AbstractRead alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality: the probability the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. We describe a framework for predicting mapping qualities that works by simulating a set of tandem reads, similar to the input reads in important ways, but for which the true point of origin is known. We implement this in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.
Gender-specific brain activation during visual art perception
Authors: de Gelder Beatrice , Watson Rebecca , Zhana Minye , Diano Matteo , Tamietto Marco , Vaessena Maarten J. 
Published: January 2017

AbstractThe human body is the most common object of pictorial representation in western art. The goal of this study was to probe its evolutionary basis of visual art perception by investigating neural markers of gender-specific brain activity triggered by paintings of male and female images. Our results show significant activity in brain areas other than those recently associated with visual arts perception. Novel findings concern participant-general as well as gender specific brain activity. Although our participants were fully aware that they were viewing artworks, the inferior parietal lobule - known for its role in the perception of emotional body images - and the somatosensory cortex – which is related to touch - were selectively active for female body paintings in all participants. The most interesting finding as regards gender was that the sight of female bodies activates the subgenual anterior cingulate cortex in males, an area known to subserve autonomic arousal. In contrast, in females the sight of the male body activated reward and control related parts of the dorsal anterior cingulate cortex. This supports the notion that basic evolutionary processes operate when we view body images, also when they are paintings far removed from daily experience.
Wide-Scale Comparative Analysis of Longevity Genes and Genetic Interventions
Authors: Yanai Hagai , Budovsky Arie , Barzilay Thomer , Tacutu Robi , Fraifeld Vadim E. 
Published: January 2017

AbstractHundreds of genes have been identified as being involved in the control of lifespan in the four common model organisms (yeast, worm, fruit fly and mouse). A major challenge is to determine if longevity-associated genes (LAGs) are model-specific or may play a universal role as longevity regulators across diverse taxa. A wide-scale comparative analysis of the 1,805 known LAGs across 205 species revealed that (i) LAG orthologs are substantially over-represented, from bacteria to mammals, especially noted for essential LAGs; (ii) the effects on lifespan, when manipulating orthologous LAGs in different model organisms, were mostly concordant, despite of a high evolutionary distance between them; (iii) the most conserved LAGs were enriched in translational processes, energy metabolism, development, and DNA repair. The least conserved LAGs were enriched in autophagy (Fungi), G-proteins (Nematodes), and neuroactive ligand-receptor interactions (Chordata). The results also suggest that antagonistic pleiotropy is a conserved principle of aging.
Fiber tractography using machine learning
Authors: Neher Peter F. , Côté Marc-Alexandre , Houde Jean-Christophe , Descoteaux Maxime , Maier-Hein Klaus H. 
Published: January 2017

AbstractWe present a fiber tractography approach based on a random forest classification and voting process, guiding each step of the streamline progression by directly processing raw diffusion-weighted signal intensities. For comparison to the state-of-the-art, i.e. tractography pipelines that rely on mathematical modeling, we performed a quantitative and qualitative evaluation with multiple phantom andin vivoexperiments, including a comparison to the 96 submissions of the ISMRM tractography challenge 2015. The results demonstrate the vast potential of machine learning for fiber tractography.
Toxoplasma gondiiAP2IX-4 regulates gene expression during bradyzoite development
Authors: Huang Sherri , Holmes Michael J. , Radke Joshua B. , Hong Dong-Pyo , Liu Ting-Kai , White Michael W. , Sullivan William J. 
Published: January 2017

ABSTRACTToxoplasma gondiiis a protozoan parasite of great importance to human and animal health. In the host, this obligate intracellular parasite persists as a tissue cyst form that is invisible to the immune response and unaffected by current therapies. The tissue cysts facilitate transmission through predation and give rise to chronic cycles of toxoplasmosis in immune compromised patients. Transcriptional changes accompany conversion of the rapidly replicating tachyzoites into the encysted bradyzoites, yet the mechanisms underlying these alterations in gene expression are not well-defined. Here we show that AP2IX-4 is a nuclear protein exclusively expressed in tachyzoites and bradyzoites undergoing division. Knockout of AP2IX-4 had no discernible effect on tachyzoite replication, but resulted in a reduced frequency of tissue cyst formation following alkaline stress induction – a defect that is reversible by complementation. AP2IX-4 has a complex role in regulating bradyzoite gene expression, as many bradyzoite mRNAs dramatically increased beyond normal stress-induction in AP2IX-4 knockout parasites exposed to alkaline media. The loss of AP2IX-4 also resulted in a modest virulence defect and reduced cyst burden in chronically infected mice, which was also reversed by complementation. These findings illustrate that the transcriptional mechanisms responsible for tissue cyst development operate across the intermediate life cycle from the dividing tachyzoite to the dormant bradyzoite.
Consistent local dynamics in the brain across sessions are revealed by whole brain modeling of resting state activity
Authors: Kehoe Patricio Donnelly , Saenger Victor M. , Lisofsky Nina , Kühn Simone , Kringelbach Morten L. , Schwarzbach Jens , Deco Gustavo 
Published: January 2017

AbstractResting state fMRI has been the primary tool for studying the functional organization of the human brain. However, even at so-called “rest”, ongoing brain activity and its underlying physiological organization is highly dynamic and yet most of the information generated so far comes from group analysis. Here we developed an imaging-based technique capable of portraying information of local dynamics at a single-subject level reliably by using a whole-brain model that estimates a local bifurcation parameter, which reflects if a brain region presents stable, asynchronous or transitory oscillations. Using 50 longitudinal resting state sessions of one single subject and single resting state sessions from a group of 50 participants we demonstrated that individual global and local brain dynamics can be estimated consistently with respect to a reference group using only a scanning time of 15 to 20 minutes. We also showed that brain hubs are closer to a transition point between synchronous and asynchronous oscillatory dynamics and that dynamics in frontal areas have larger variations compared to other regions. Finally, we analyzed the variability and error of these dynamics and found high symmetry between hemispheres, which interestingly was reduced by adding more sessions. The framework presented here can be used to study functional brain dynamics on an individual level, opening new avenues for possible clinical applications.Bullet pointsLocal brain dynamics are consistent across scans.Four scans of five minutes each are enough to get highly reliable and consistent results.Hub areas are in a transition point between a synchronous and asynchronous regime.Variability and error of local dynamics presented high symmetry between hemispheres.
Investigations of mutual thermal coupling between SiC Schottky diodes situated in the common case
Authors: Górecki Krzysztof , Bisewski Damian , Zarębski Janusz , Kisiel Ryszard , Myśliwiec Marcin 
Published: January 2017

Purpose
This paper aims to present the results of measurements and calculations illustrating mutual thermal coupling between power Schottky diodes made of silicon carbide situated in the common case.

Design/methodology/approach
The idea of measurements of mutual transient thermal impedances of the investigated device is described.

Findings
The results of measurements of mutual transient thermal impedances between the considered diodes are shown. The experimentally verified results of calculations of the internal temperature waveforms of the considered diodes obtained with mutual thermal coupling taken into account are presented and discussed. The influence of mutual thermal coupling and a self-heating phenomenon on the internal temperature of the considered diodes is pointed out.

Research limitations/implications
The presented methods of measurements and calculations can be used for constructing the investigated diodes made of other semiconductor materials.

Originality/value
The presented results prove that mutual thermal coupling between diodes mounted in the common case must be taken into account to calculate correctly the waveforms of the device internal temperature.
Investigation of nano-inks’ behaviour on flexible and rigid substrates under various conditions
Authors: Lukacs Peter , Pietrikova Alena , Ballokova Beata , Jakubeczyova Dagmar , Kovac Ondrej 
Published: January 2017

Purpose
This paper aims to find the optimal deposition conditions for achieving the homogenous structure of the silver layers onto three types of polymeric substrates as well as on the rigid substrates. For this reason, the detailed investigation of the silver-based layers deposited at different technological conditions by microscopic methods is presented in this paper.

Design/methodology/approach
The special test pattern has been designed and deposited at different substrate temperatures by using two types of generally available silver-based nano-inks. Cross-sections and 3D profiles of the deposited silver layers have been profoundly analysed by using the optical profiler Sensofar S Neox on the generally used polymeric (PI, PET and PEN) and rigid substrates (951 and 9K7 LTCC, glass and alumina).

Findings
The results prove the strong correlation between the substrate temperature during the deposition process and the final shape of the created structure which has the a direct impact on the layers’ homogeneity. The results also prove the theory of the coffee ring effect creation in the inkjet printing technology.

Originality/value
The main benefit of this paper lies in the possibility of the homogeneity achievement of the deposited silver-based layers on the several polymeric and rigid substrates by managing the temperature during the deposition. The paper also offers the comparative study of nano-inks’ behaviour on several polymeric and rigid substrates.
Mentoring for pre-service teachers and the use of inquiry-oriented feedback
Authors: McGraw Amanda , Davis Robert 
Published: January 2017

Purpose
The purpose of this paper is to examine the nature of feedback offered by school mentors in three primary and secondary rural schools during pre-service teachers’ (PSTs’) professional placements. In the context of discussions about the need for more integrated theory/practice connections for PSTs which are “mutually reinforced by all programme components” (Teacher Education Ministerial Advisory Group, 2014, p. ix), it aims to examine whether certain contextual features of school environments have an impact on the nature of feedback offered to PSTs.

Design/methodology/approach
Through a phenomenological analysis of semi-structured interviews, this paper explores the relationship between certain contextual features of school environments and their impact on the effectiveness of mentor feedback practices.

Findings
It is suggested that teacher mentors are more likely to offer inquiry-oriented feedback informed by well-developed personal theories and values if they teach in schools where feedback processes are promoted as a central part of teachers’ ongoing professional learning. Professional learning experiences, which include classroom observations, peer feedback and a focus on using feedback to enhance students’ learning, extend and deepen teachers’ understandings and beliefs about feedback as well as their repertoire of strategies. Consequently, they are more informed and better able to work with PSTs using inquiry-oriented approaches.

Originality/value
Through an examination of teacher narratives, this paper presents two frameworks for considering the nature of feedback offered to PSTs by their teacher mentors: inquiry-oriented and instructional-oriented feedback. It argues that teacher mentors are better equipped to use inquiry-oriented feedback approaches and build growth-fostering relationships if they are engaged in ongoing professional learning experiences in their schools based on classroom observations and non-judgemental peer feedback.
Mentors’ behavioral profiles and college adjustment in young adults participating in an academic mentoring program
Authors: Brodeur Pascale , Larose Simon , Tarabulsy George M. , Feng Bei 
Published: January 2017

PurposeThe purpose of this paper is to explore associations between different mentor behavioral profiles and mentees’ perceptions of the quality of mentoring relationship, the usefulness of the mentoring, and their college adjustment during the first year of college.Design/methodology/approachThe study used a quasi-experimental design and involved the participation of 253 student mentees and 246 students from a control group. Cluster analysis on the responses of mentees on the mentor behavior scale was used to identify behavioral profiles of academic mentors.FindingsFour distinct behavioral profiles were identified: optimal (high scores on mentor structure, involvement, autonomy support, and competence support); sufficient (moderate on all scales); controlling (low on autonomy support but high on other scales); and inadequate (low on all scales). Compared to mentees exposed to sufficient and inadequate profiles, mentees exposed to the optimal profile perceived the mentoring relationship and its usefulness as more positive. Furthermore, they reported better social adjustment in college compared to a control group, whereas mentees exposed to the inadequate profile reported poorer adjustment. Interestingly, mentees exposed to the controlling profile found the mentoring relationship useful.Research limitations/implicationsThis study provides new empirical bases for the behavioral profiles of mentors that best meet mentees’ academic adjustment challenges. Limitations of the study include the absence of the mentors’ perceptions in the creation of behavioral profiles and the fact that the profiles were analyzed based on a single program.Originality/valueBehavioral profiles of academic mentors were examined through the lens of a strong theoretical model that emphasizes the important role of structure, involvement, autonomy support, and competence support in the academic adjustment of mentees.