bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionarily informed deep learning methods: Predicting transcript abundance from DNA sequence
Authors: Washburn Jacob D. , Mejia-Guerra Maria Katherine , Ramstein Guillaume , Kremling Karl A. , Valluru Ravi , Buckler Edward S. , Wang Hai 
Published: July 2018

ABSTRACTDeep learning methodologies have revolutionized prediction in many fields, and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two novel approaches that account for evolutionary relatedness in machine learning models: 1) gene-family guided splitting, and 2) ortholog contrasts. The first approach accounts for evolution by constraining the models training and testing sets to include different gene families. The second, uses evolutionarily informed comparisons between orthologous genes to both control for and leverage evolutionary divergence during the training process. The two approaches were explored and validated within the context of mRNA expression level prediction, and have prediction auROC values ranging from 0.72 to 0.94. Model weight inspections showed biologically interpretable patterns, resulting in the novel hypothesis that the 3’ UTR is more important for fine tuning mRNA abundance levels while the 5’ UTR is more important for large scale changes.
Geographic variation in reproductive assurance of Clarkia pulchella
Authors: Bontrager Megan , Muir Christopher D. , Angert Amy L. 
Published: July 2018

AbstractClimate can affect plant populations through direct effects on physiology and fitness, and through indirect effects on their relationships with pollinating mutualists. We therefore expect that geographic variation in climate might lead to variation in plant mating systems. Biogeographic processes, such as range expansion, can also contribute to geographic patterns in mating system traits. We manipulated pollinator access to plants in eight sites spanning the geographic range of Clarkia pulchella to investigate geographic and climatic drivers of fruit production and seed set in the absence of pollinators (reproductive assurance). We examined how reproductive assurance and fruit production varied with the position of sites within the range of the species and with temperature and precipitation. We found that reproductive assurance in C. pulchella was greatest in populations in the northern part of the species’ range, and was not well-explained by any of the climate variables that we considered. In the absence of pollinators, some populations of C. pulchella have the capacity to increase fruit production, perhaps through resource reallocation, but this response is climate-dependent. Pollinators are important for reproduction in this species, and recruitment is sensitive to seed input. The degree of autonomous self-pollination that is possible in populations of this mixed-mating species may be shaped by historic biogeographic processes or variation in plant and pollinator community composition rather than variation in climate.
Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast
Authors: Epstein Alexander E. , Espinoza-Sanchez Sofia , Pollard Thomas D. 
Published: July 2018

AbstractLeClaireet al.presented evidence that phosphorylation of three sites on the Arp2 subunit activates Arp2/3 complex to nucleate actin filaments. We mutated the homologous residues of Arp2 (Y198, T233 and T234) in the fission yeast genome to amino acids that preclude or mimic phosphorylation. Arp2/3 complex is essential for the viability of fission yeast, yet strains unable to phosphorylate these sites grew normally. Y198F/T233A/T234A Arp2 was only nonfunctional if GFP-tagged, as observed by LeClaireet al.inDrosophilacells. Replacing both T233 and T234 with aspartic acid was lethal, suggesting that phosphorylation might be inhibitory. Nevertheless, blocking phosphorylation at these sites had the same effect as mimicking it: slowing assembly of endocytic actin patches. Mass spectrometry revealed phosphorylation at a fourth conserved Arp2 residue, Y218, but both blocking and mimicking phosphorylation of Y218 only slowed actin patch assembly slightly. Therefore, phosphorylation of Y198, T233, T234 and Y218 is not required for the activity of fission yeast Arp2/3 complex.SummaryPrevious research concluded that phosphorylation at three sites on Arp2 is necessary to activate Arp2/3 complex. Epstein et al. make genomic substitutions blocking or mimicking phosphorylation to demonstrate that phosphorylation of these three sites does not regulate Arp2/3 complex in fission yeast.
TISMorph: A tool to quantify texture, irregularity and spreading of single cells
Authors: Alizadeh Elaheh , Xu Wenlong , Castle Jordan , Foss Jacqueline , Prasad Ashok 
Published: July 2018

AbstractA number of recent studies have shown that cell shape and cytoskeletal texture can be used as sensitive readouts of the physiological state of the cell. However, utilization of this information requires the development of quantitative measures that can describe relevant aspects of cell shape. In this paper we develop a toolbox, TISMorph, to calculate set of quantitative measures to address this need. Some of the measures introduced here are used previously and others are new and have desirable properties for shape and texture quantification of cells. These measures, broadly classifiable into the categories of textural, spreading and irregularity measures, are tested by using them to discriminate between osteosarcoma cell lines treated with different cytoskeletal drugs. We find that even though specific classification tasks often rely on a few measures, these are not the same between all classification tasks, thus requiring the use of the entire suite of measures for classification and discrimination. We provide detailed descriptions of the measures, well as TISMorph package to implement them. Image based quantitative analysis has the potential to become a new field of biological data (“image-omics”), providing quantitative insight into cellular processes.
Mixed fruit juices from Cerrado
Authors: Schiassi Maria Cecília Evangelista Vasconcelos , Lago Amanda Maria Teixeira , Souza Vanessa Rios de , Meles Juliana dos Santos , Resende Jaime Vilela de , Queiroz Fabiana 
Published: July 2018

Purpose
The purpose of this paper is to optimize a mixed juice made from Brazilian Cerrado fruits (cagaita, mangaba and marolo).

Design/methodology/approach
The juices were evaluated by rheological, physical, physicochemical, nutritional and sensory acceptance analyses. The mixture design is a widely used tool for product optimization, allowing the determination of factors, combinations and levels that provide best responses.

Findings
The results show that using mangaba pulp negatively contributed to juice acceptance, but resulted in the highest ascorbic acid content. The treatments produced using cagaita and marolo pulps presented a greater acceptance by consumers, and contributed to higher antioxidant activity and phenolic compounds content. The juice prepared with a mixture of equivalent quantities of the three fruits had the highest β-carotene and lycopene contents.

Practical implications
This research has shown that different fruit combinations can improve sensory and nutritional characteristics, adding value to the final product.

Social implications
The processing of mixed juices could increase population access to the nutrients present in Brazilian Cerrado fruits, given that they are seasonal and perishable fruits.

Originality/value
In recent years, there has been an increase in the development of new food products based on Cerrado native fruits, however information on the chemical and nutritional characteristics, rheological behavior, and sensory attributes of the derivative products are still limited, resulting in a lack of scientific investments in this area. In addition, it is necessary to optimize the developed products to offer the consumer a unique product, combining the characteristics of two or more fruits, which adds value to the final product.
An evaluation of Swiss agriculture’s contribution to food security with decision support system for food security strategy
Authors: Ferjani Ali , Mann Stefan , Zimmermann Albert 
Published: July 2018

Purpose
The purpose of this paper is to estimate the domestic agriculture’s contribution to food security in the case of missing imports of food and feed to the food supplies of the country.

Design/methodology/approach
This paper uses the Decision Support System for food Security Strategy and Supply Management (DSS-ESSA) to simulate whether a country with as low a level of self-sufficiency (around 60 per cent) as Switzerland would theoretically be capable of supplying its own population with a sufficient quantity of domestically produced food. The authors try to estimate the short-term and long-term impacts of the missing imports of food and feed on the energy supply in Switzerland.

Findings
Findings are summarised as follows. Starting with the long-term impact, the results show that in the long-term an energy supply of 2,340 kcal/person/day would be possible if the appropriate available cultivated area and optimised production existed. However, in the short-time, the potential and the time required to adapt and expand agricultural production depends primarily on the crop-rotation land available and on the existing infrastructure.

Research limitations/implications
In the present version of DSS-ESSA no economic and environmental module has been integrated.

Originality/value
The current model version has been funded by the Swiss Federal Office for Agriculture and aims at supporting Swiss policy-makers to guide changes. Numerous additional data such as technical production contexts are regularly checked by experts.
Co-creation with customers and suppliers: an exploratory study
Authors: Bettiga Debora , Ciccullo Federica 
Published: July 2018

Purpose
Co-creation along the new product development (NPD) seems the winning approach in nowadays market. The purpose of this paper is to explore the collaboration and interaction flows between suppliers and customers in co-creation initiatives devoted to NPD.

Design/methodology/approach
After developing a classification of demand-side and supply-side involvement in co-creation along the NPD process, 13 cases of co-creation in the consumer goods industry, within the Italian context, have been analyzed.

Findings
Three patterns of co-creation have been identified: supplier-driven approach: companies co-creating with suppliers in multiple NPD phases, while involving customers only in one; customer-driven approach: companies involving customers in multiple phases, while engaging suppliers only in one and firm-driven approach: companies involving both customers and suppliers in one single phase. Further, the locus of relevant knowledge drives to different co-creation approaches.

Research limitations/implications
The work contributes to extant literature by: providing a classification of demand-side and supply-side involvement in NPD; empirically investigating the interaction flows between customers and suppliers in co-creation initiatives along the NPD; highlighting the factors potentially affecting a concurrent involvement of customers and suppliers in NPD.

Practical implications
The findings can help to efficiently and effectively design and manage the relation with both suppliers and customers in co-creation projects devoted to NPD.

Originality/value
The involvement of suppliers and customers in co-creation initiatives has been so far analyzed only separately in literature. This study opens a new stream of research, stressing how the evolution of the market, toward a more participative one, spurs the need to investigate the collaboration and interaction flows between the two actors.
FINRA’s disciplinary actions in 2017: increased restitution ordered with minimal changes in number of cases
Authors: Rubin Brian , Pollet Adam 
Published: July 2018

Purpose
The purpose of this paper is to analyze the Financial Industry Regulatory Authority’s (FINRA) 2017 disciplinary actions, the issues that resulted in the most significant fines and restitution and the emerging enforcement trends from 2017 and beyond.

Design/methodology/approach
The approach of this paper discusses the disciplinary actions in 2017 and prior years, details the top 2017 enforcement issues measured by total fines assessed, including anti-money laundering, trade reporting, electronic communications, books and records, research analysts and research reports, and explains current enforcement trends, including restitution, suitability cases and technological issues.

Findings
In 2017, restitution more than doubled from the prior year, resulting in the fourth highest total sanctions (fines combined with restitution and disgorgement) assessed by FINRA over the past 10 years.

Practical implications
Firms and their representatives should heed the trends in both the substantial restitution FINRA is ordering and the related enforcement issues in the cases FINRA has brought.

Originality/value
This paper provides expert analysis and guidance from experienced securities enforcement lawyers.
“Extracellular matrix remodelling in the liver of rats subjected to dietary choline deprivation and/or thioacetamide administration”
Authors: Al‐Humadi Hussam , Alhumadi Ahmed , Al‐Saigh Rafal , Strilakou Athina , Lazaris Andreas C , Gazouli Maria , Liapi Charis 
Published: July 2018

SummaryCholine deprivation is a recognized experimental approach to nonalcoholic steatohepatitis, while thioacetamide (TAA)‐induced liver fibrosis resembles alcoholic liver fibrogenesis. In order to elucidate the effect of TAA on liver extracellular matrix composition under choline deprivation due to choline‐deficient diet (CDD) administration, we evaluated the transcriptional and immunohistochemical (IHC) pattern of major hepatic matrix metalloproteinases (namely, MMP‐2, ‐9) and their tissue inhibitors (TIMP‐1, ‐2) in adult male albino Wistar rats at 30, 60 and 90 days. In the CDD+TAA group, IHC showed an early progressive increase in MMP‐2 expression, while MMP‐9 initially exhibited a significant increase followed by a gradual decrease; TIMP‐1 and TIMP‐2 IHC expressions showed gradual increase throughout the experiment. The MMPs‐TIMPs regulation at the transcriptional level was found to be increased in all groups throughout the experiment. The increased MMP‐2/TIMP‐2 and suppressed MMP‐9/TIMP‐1 ratios in IHC and in real‐time polymerase chain reaction (RT‐PCR) seemed to correlate with the degree of liver fibrosis. These results support the important role of MMPs and TIMPs in controlling the hepatic pathogenesis and shed more light on the recently described experimental approach to liver disease (steatohepatitis) under the impact of two insults (TAA and CDD).
THE TRADE IN TOOLS: THE MARKET FOR ILLICIT GUNS IN HIGH‐RISK NETWORKS
Authors: HUREAU DAVID M. , BRAGA ANTHONY A. 
Published: July 2018

AbstractIllegal guns circulating among high‐risk networks represent a threat to the security and well‐being of urban neighborhoods. Research findings reveal that illegal firearms are usually acquired through a variety of means, including theft and diversions from legitimate firearms commerce. Little is known, however, about the underground gun markets supplying the gang and drug networks responsible for a large share of gun violence in U.S. cities. In this article, we take a mixed‐methods approach, combining trace analyses of recovered handguns with ethnographic interviews of high‐risk gun users to develop new insights on the entry of guns into three criminal networks in Boston. We find that guns possessed by Boston gang members are of a different character compared with other crime guns; these guns are more likely to be older firearms originating from New Hampshire, Maine, and I‐95 southern states. The results of our qualitative research reveal that gang members and drug dealers pay inflated prices for handguns diverted by traffickers exploiting unregulated secondary market transactions, with significant premiums paid for high‐caliber semiautomatic pistols. Taken together, these findings provide an analytic portrait of the market for illicit guns among those most proximate to violence, yielding novel empirical, theoretical, and practical insights into the problem of criminal gun access.
Metapodials of ancient bison (Bison priscus) of northeast Russia: “stress markers,” sex and withers height
Authors: KIRILLOVA Irina Vladimirovna , SHIDLOVSKIY Fedor Kasperovich , ZINOVIEV Andrei Valerievich 
Published: July 2018

AbstractA total of 175 metapodials (MP) of Pleistocene and early Holocene bison (Bison priscus Boj.) from the vast area of northeast Russia were studied. MP were attributed to males and females both visually and statistically. Data on the withers height of bison from northeast Russia are provided. Stress markers were recorded, including so‐called “buttresses.” With rare exceptions, stress markers were not of a pathological nature. The origin and development of the buttresses are age‐related; their prevalence in bison females can be considered as the response to an increased load during pregnancy. Changes in the periosteum, found in males, are related to their greater activity. Buttresses are also well developed on metatarsals of the red deer and the elk; they are less developed in reindeer and not found in giant deer. A relationship among stress markers, locomotion and the environment is established. Possible peculiarities of the Rauchua River bison locomotion are discussed.
Trimetazidine suppresses oxidative stress, inhibits MMP‐2 and MMP‐9 expression, and prevents cardiac rupture in mice with myocardial infarction
Authors: Gong Wei , Ma Youcai , Li Aobo , Shi Han , Nie Shaoping 
Published: July 2018

SummaryBackground/AimsCardiac rupture (CR) is a catastrophic complication of acute myocardial infarction (MI). At present, there are no effective pharmacological strategies for preventing post‐MI rupture. Here we investigated the effect of trimetazidine (TMZ) on post‐MI CR.MethodsMI models were induced by left coronary artery ligation in male C57BL/6 mice. Animals allocated to the rupture incidence were closely monitored for 7 days; autopsy was performed once animals were found dead to determine the reason of death. Heart function was detected by echocardiography. Oxidative stress markers and matrix metalloproteinases (MMPs) were analyzed by Western Blotting.ResultsTMZ markedly reduced the post‐MI CR incidence of mice. We found that the expression of metalloproteinase (MMP) ‐2 and MMP‐9 in the TMZ‐treated group was significantly lower than the saline‐treated group. Further, TMZ markedly attenuated MI‐induced oxidative stress. To investigate the mechanism of the effect of TMZ on CR, we pretreated H9c2 cells with H2O2 and found that TMZ treatment markedly decreased H2O2‐induced MMP‐2 and MMP‐9 expression. TMZ prevents CR through inhibition of oxidative stress, which is attributable to the down‐regulation of MMP‐2, MMP‐9 expression.ConclusionsOur findings indicate that TMZ suppresses oxidative stress, inhibits MMP‐2 and MMP‐9 expression, and prevents CR in mice with MI.
A Clinical Trial with Combined Transcranial Direct Current Stimulation and Attentional Bias Modification in Alcohol‐Dependent Patients
Authors: den Uyl Tess E. , Gladwin Thomas E. , Lindenmeyer Johannes , Wiers Reinout W. 
Published: July 2018

BackgroundModifying attentional processes with attentional bias modification (ABM) might be a relevant add‐on to treatment in addiction. This study investigated whether influencing cortical plasticity with transcranial direct current stimulation (tDCS) could increase training effects. tDCS could also help alcohol‐dependent patients to overcome craving and reduce relapse, independent of training. These approaches were combined to investigate effects in the treatment of alcoholism.MethodsNinety‐eight patients (analytical sample = 83) were randomly assigned to 4 groups in a 2‐by‐2 factorial design. Patients received 4 sessions of ABM (control or real training) combined with 2 mA tDCS (active: 20 minutes or sham: 30 seconds) over the left dorsolateral prefrontal cortex. Alcohol bias and craving were assessed, and treatment outcome was measured as relapse after 1 year.ResultsAttentional bias scores indicated that during the training only the group with active tDCS and real ABM displayed an overall avoidance bias (p < 0.05). From pre‐ to postassessment, there were no main or interaction effects of tDCS and ABM on the bias scores, craving, or relapse (p > 0.2). However, effects on relapse after active tDCS were in the expected direction.ConclusionsThere was no evidence of a beneficial effect of tDCS or ABM or the combination. Whether the absence of effect was due to issues with the outcome measurements (e.g., lack of craving, high dropout, and unreliable measurements) or aspects of the intervention should be further investigated.
Modulation of serotonin and noradrenaline in the BLA by pindolol reduces long‐term ethanol intake
Authors: Patkar Omkar L. , Belmer Arnauld , Holgate Joan Y. , Klenowski Paul M. , Bartlett Selena E. 
Published: July 2018

AbstractRepeated cycles of binge‐like alcohol consumption and abstinence change the activity of several neurotransmitter systems. Some of these changes are consolidated following prolonged alcohol use and are thought to play an important role in the development of dependence. We have previously shown that systemic administration of the dual beta‐adrenergic antagonist and 5‐HT1A/1B partial agonist pindolol selectively reduces long‐term but not short‐term binge‐like consumption of ethanol and alters excitatory postsynaptic currents in basolateral amygdala (BLA) principal neurons. The aim of this study was to investigate the effects of pindolol microinfusions in the BLA on long‐term ethanol intake using the drinking‐in‐the‐dark paradigm in mice. We also microinfused RU24969 (5‐HT1A/1B receptor partial agonist) and CGP12177 (β1/2 adrenergic antagonist) following long‐term ethanol intake and determined the densities of 5‐HT1A/1B receptors and β1/2 adrenergic in the BLA following short‐term (4 weeks) and long‐term ethanol (12 weeks) consumption. We show that intra‐BLA infusion of pindolol (1000 pmol/0.5 μl), RU24969 (0.3 and 3 pmol/0.5 μl) and CGP12177 (500 pmol/0.5 μl) produce robust decreases in long‐term ethanol consumption. Additionally, we identified reduced β1/2 adrenergic receptor expression and no change in 5‐HT1A/1B receptor density in the BLA of long‐term ethanol‐consuming mice. Collectively, our data highlight the effects of pindolol on voluntary, binge‐like ethanol consumption behavior following long‐term intake.