bluuebunny/crossref_metadata_2025 huggingface dataset:
Sophisticated collaboration is common among Mexican-heritage US children
Authors: Alcalá Lucía , Rogoff Barbara , López Fraire Angélica
Published: November 2018

In light of calls for improving people’s skill in collaboration, this paper examines strengths in processes of collaboration of Mexican immigrant children. Sibling pairs (6–10 years old) in California were asked to collaborate in planning the shortest route through a model grocery store. On average, 14 sibling pairs with Mexican Indigenous-heritage backgrounds engaged together collaboratively as an ensemble, making decisions in common and fluidly building on each other’s ideas, more often than 16 middle-class European American sibling pairs, who on average more often divided decision making into a solo activity (often ignoring the other or simply bossing the other). Siblings who spent more time collaborating fluidly as an ensemble in the shared planning task were also more likely to collaborate with initiative at home, according to their mothers, which suggests that family socialization practices may contribute to cultural differences in collaboration.
Bulk electronic transport impacts on electron transfer at conducting polymer electrode–electrolyte interfaces
Authors: Wijeratne Kosala , Ail Ujwala , Brooke Robert , Vagin Mikhail , Liu Xianjie , Fahlman Mats , Crispin Xavier
Published: November 2018

Significance

Spreading electrochemical technologies, such as energy, bioelectrochemical devices, and industrial electrochemical synthesis, require low-cost large area electrodes. Conducting polymers possess a unique combination of properties compared with most of the inorganic electrodes: acid resistance, the absence of surface-insulating oxide, low temperature and solution processability, a high natural abundance of their elements, molecular porosity. Conducting polymers are inhomogeneous conductors composed of ordered and disordered regions through which electronic transport takes place via percolation paths. We discovered that the density of percolation paths in the bulk of the material dictates the rate of electron transfer at the electrolyte–polymer electrode interface. This reveals one of the key parameters of designs to achieve efficient electrochemical technologies based on polymer electrodes.
Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes
Authors: Kubitza Christian , Bittner Florian , Ginsel Carsten , Havemeyer Antje , Clement Bernd , Scheidig Axel J.
Published: November 2018

Significance

The involvement of biotransformation enzymes in drug metabolism is one of the most crucial objectives during preclinical research, since they ultimately determine the bioavailability of medicinal drugs. The mARC N-reductive enzyme system was found to be a highly effective counterpart to one of the most prominent biotransformation enzymes, CYP450, and is involved in activation of amidoxime prodrugs as well as inactivation of other drugs containing N-hydroxylated functional groups. Owing to its potent N-reductive capacity toward a broad range of compounds, including mutagenic N-oxygenated nucleobase analogs, mARC plays a crucial role in pharmacology. Our crystal structure of human mARC forms the basis for predictions on the metabolism of drug candidates and structure–activity relationships. Moreover, it indicates the evolutionary development of different molybdoenzyme families.
Engineering the protein secretory pathway of
Saccharomyces cerevisiae
enables improved protein production
Authors: Huang Mingtao , Wang Guokun , Qin Jiufu , Petranovic Dina , Nielsen Jens
Published: November 2018

Significance

Recombinant proteins production by cell factories for medical and industrial use is one of the most prominent achievements in the modern biotech industry. It is constantly necessary to explore the underlying mechanisms of protein secretion to identify new targets for design and construction of improved cell factories. Here, we identified several gene targets, most of which are involved in the trafficking and secretory pathways, that could improve protein production by
Saccharomyces cerevisiae
to the gram per liter level. We also found that intracellular retention of recombinant proteins can be significantly reduced by engineering the endosome-to-Golgi trafficking. Genes and pathways identified here may provide general guidelines for engineering other cell factories for efficient protein secretion.
Arabidopsis thaliana
NGATHA1 transcription factor induces ABA biosynthesis by activating
NCED3
gene during dehydration stress
Authors: Sato Hikaru , Takasaki Hironori , Takahashi Fuminori , Suzuki Takamasa , Iuchi Satoshi , Mitsuda Nobutaka , Ohme-Takagi Masaru , Ikeda Miho , Seo Mitsunori , Yamaguchi-Shinozaki Kazuko , Shinozaki Kazuo
Published: November 2018

Significance

The plant hormone abscisic acid (ABA) is essential for drought-stress responses in plants, and its functions have been well studied; however, the detailed molecular mechanisms of ABA biosynthesis during early drought stress need to be further explored. The present study identified a transcription factor, NGTHA1 (NGA1), which positively regulates ABA accumulation during dehydration stress by activating the
NCED3
gene encoding a key ABA biosynthetic enzyme. We also identified a
cis
-acting element bound by NGA1 in the 5′ untranslated region (5′ UTR) of the
NCED3
promoter. The NGA1 protein was degraded under nonstressed conditions, but it was stabilized during dehydration stress in an ABA-independent pathway.
Awareness of what is learned as a characteristic of hippocampus-dependent memory
Authors: Smith Christine N. , Squire Larry R.
Published: November 2018

Significance

Knowledge (or awareness) of what has been learned has been described as a key feature of hippocampus-dependent memory or as unhelpful for understanding hippocampal function. We recorded eye movements while memory-impaired patients with hippocampal lesions and controls viewed familiar scenes or familiar scenes that had been altered. Controls preferentially looked at the altered regions of the scenes, but only when they knew what had changed and where the change occurred. Patients had difficulty distinguishing altered and unaltered scenes and, overall, did not direct their viewing toward the altered regions. Nonetheless, they did exhibit this effect on the few occasions when they were aware of the change. The results indicate the importance of conscious awareness for understanding hippocampal function.
Inclusive fitness consequences of dispersal decisions in a cooperatively breeding bird, the long-tailed tit (
Aegithalos caudatus
)
Authors: Green Jonathan P. , Hatchwell Ben J.
Published: November 2018

Natal dispersal is a demographic trait with profound evolutionary, ecological, and behavioral consequences. However, our understanding of the adaptive value of dispersal patterns is severely hampered by the difficulty of measuring the relative fitness consequences of alternative dispersal strategies in natural populations. This is especially true in social species, in which natal philopatry allows kin selection to operate, so direct and indirect components of inclusive fitness have to be considered when evaluating selection on dispersal. Here, we use lifetime reproductive success data from a long-term study of a cooperative breeder, the long-tailed tit
Aegithalos caudatus
, to quantify the direct and indirect components of inclusive fitness. We show that dispersal has a negative effect on the accrual of indirect fitness, and hence inclusive fitness, by males. In contrast, the inclusive, predominantly direct, fitness of females increases with dispersal distance. We conclude that the conflicting fitness consequences of dispersal in this species result in sexually antagonistic selection on this key demographic parameter.
Split coordination in English
Authors: Taylor Ann , Pintzuk Susan
Published: November 2018

In this article we provide a practical demonstration of how syntactically annotated corpora (treebanks), particularly the English
Historical Parsed Corpora Series, can be used to investigate research questions with a diachronic depth and synchronic breadth
that would not otherwise be possible. The phenomenon under investigation is split coordination, in which two parts of a conjoined
constituent appear separated in the clause (e.g., and this is where my aunt lives and my
uncle
). It affects every type of coordinated constituent (subject/object DPs, predicate and attributive ADJPs,
ADVPs, PPs and DP objects of P) in Old English (OE); and it, or a superficially similar construction, occurs continuously
throughout the attested period from approximately 800 to the present day. Despite its synchronic range and diachronic persistence,
split coordination has received surprisingly little attention in the diachronic literature, with the exception of Perez Lorido’s (2009) limited study of split subjects in eight OE texts. Its modern
counterpart is most frequently analysed as Bare Argument Ellipsis (BAE). Although the OE and Present-Day English constructions
appear superficially similar, we show that not all of the OE data is amenable to a BAE analysis. We bring to bear different types
of evidence (structural, discourse/performance effects, rate of change, etc.) to argue that split coordination in fact represents
two different constructions, one of which remains stable over time while the other is lost in the post-Middle English
period.
Non-configurationality in diachrony
Authors: Ponti Edoardo Maria , Luraghi Silvia
Published: November 2018

Non-configurationality is a linguistic property associated with free word order, discontinuous constituents, including NPs, and null anaphora of referential arguments. Quantitative metrics, based both on local networks (syntactic trees and word order within sentences) and on global networks (incorporating the relations within a whole treebank into a shared graph), can reveal correlations among these features. Using treebanks we focus on diachronic varieties of Ancient Greek and Latin, in which non-configurationality tapered off over time, leading to the largely configurational nature of the Romance languages and of Modern Greek. A property of global networks (density of their spectra around zero eigenvalues) measuring the regularity in word order is shown to be strengthened from classical to late varieties. Discontinuous NPs are traced by counting the words creating non-projectivity in dependency trees: these drop dramatically in late varieties. Finally, developments in the use of null referential direct objects are gauged by assessing the percentage of third-person personal pronouns among verb objects. All three features turn out to change over time due to the decay of non-configurationality. Evaluation of the strength of their pairwise correlation shows that null direct objects and discontinuous NPs are deeply intertwined.
Spoken Latin behind written texts
Authors: Korkiakangas Timo
Published: November 2018

This study uses treebanking to investigate how spoken language infiltrated legal Latin in early medieval Italy. The documents used are always formulaic, but they also always contain a ‘free’ part where the case in question is described in free prose. This paper uses this difference to measure how ten linguistic features, representative of the evolution that took place between Classical and Late Latin, are distributed between the formulaic and free parts. Some variants are attested equally often in both parts of the documents, while perceptually or conceptually salient variants appear to be preserved in their conservative form mainly in the formulaic parts.
Metaphoric moral framing and image-text relations in the op-ed genre
Authors: Abdel-Raheem Ahmed
Published: November 2018

This article examines the role of visual metaphor for moral-political cognition. It makes use of a large corpus of 250 multimodal op-eds about the Euro crisis and lays the foundation for establishing a general system of image-text relations in the op-ed genre. Specifically, the paper addresses the following questions: Is there a difference between a cartoon and an illustration? Why do not op-ed illustrations have captions? What role does layout play in conveying meaning? How do ‘op-ed’ and ‘illustration’ relate to each other in terms of the metaphors and moral values employed in both of them? What is the nature of the relationship between the two? How does the illustrating process work? Should the text and image be considered as a single unit or as two separate (though related) units? Moreover, the results of this research will show that visual metaphors can exert a strong effect on individuals’ moral-political cognition.
The‘listen to characters thinking’novel
Authors: Pascual Esther , Królak Emilia
Published: November 2018

This article explores direct speech involvingfictive interaction, that is not functioning as an ordinary quote (e.g. “a look of‘I told you so’”;Pascual, 2006,2014). We specifically deal with its use as a literary strategy, in which different fictive speech constructions may serve to: (i) give access to characters’ mental worlds; (ii) show the relationships and non-verbal communication between characters; (iii) create new semantic categories; and (iv) produce such rhetorical effects as vividness or humor. Special emphasis is placed on a comparative analysis of the English fictive direct speech plus noun construction (e.g. “the‘why bother?’attitude”) with its translations into Polish and Spanish. We show that the construction proves a challenge to translators, since neither of these languages has an exact syntactic equivalent. This study is based on an extensive and heterogeneous database that includes 30 bestselling novels from different genres, published between 1935 and 2013.
On metaphorical views, dynamite, and doodlings
Authors: Reijnierse W. Gudrun , Burgers Christian , Krennmayr Tina , Steen Gerard J.
Published: November 2018

This paper offers a systematic, bottom-up, investigation of the role of adjectives as metaphor signals in metaphorical domain constructions (MDCs) such as ‘budgetary anorexia’ and ‘economic crash’ within the framework of Deliberate Metaphor Theory (e.g.,Steen, 2017). To this end, we analyse all MDCs in the VU Amsterdam Metaphor Corpus. Results of our analyses demonstrate that domain adjectives in MDCs do not by definition constitute signals of metaphor, and that not all nouns in MDCs are identified as potentially deliberate metaphors. We identify three different functions of domain adjectives: (1) signal of novel metaphor; (2) signal of conventional metaphor; (3) non-signal. The analyses in this paper provide new insights into both the role of domain adjectives in MDCs, and the position of MDCs as a typical manifestation of potentially deliberate metaphor.
Reconstructing social emotions across languages and cultures
Authors: Krawczak Karolina
Published: November 2018

The present study investigates the adjectival profiling ofshamefrom a cross-linguistic and cross-cultural perspective. This concept, overarching the field of negative self-evaluative emotions, is operationalized through two lexical categories (‘shame’ and ‘embarrassment’) that are comparable in the languages under investigation. The usage of the adjectival exponents of these categories is analyzed in four communities of British English, American English, French, and Polish. The study has two goals, one descriptive, the other methodological. Firstly, it aims to identify the conceptual structuring of the two lexical categories relative to their respective socio-cultural contexts. The result will be four sets of culture-sensitive usage profiles. Secondly, the study further advances corpus-driven quantitative methodology for the description of intersubjectively-grounded abstract concepts. The results obtained here provide partial evidence for the existence of a cultural continuum ranging from the Anglo-Saxon communities, through France to Poland along the descriptive dimension of individualism-collectivism.
On objective and subjective epistemic modality again
Authors: Olbertz Hella , Hattnher Marize Mattos Dall'Aglio
Published: November 2018

This aim of this chapter is to prove the linguistic reality of the distinction between objective and subjective epistemic modality as made in FDG, according to which the former modifies the Episode and the latter the Propositional Content. The chapter studies the two basic Spanish modal auxiliaries poder ‘can, may’ and deber ‘must’ and its Portuguese cognates dever and poder in order to see (i) which of the criteria (proposed by Hengeveld (1988) for the lexical expression of this distinction) yield testable criteria for the grammatical expression of epistemic modality and (ii) if the objective-subjective dichotomy somehow relates to the degrees of possibility and necessity expressed by these modal auxiliaries. With respect to (i), it is argued that there are two testable criteria, i.e. non-locatability in time and space and the boundedness to the ‘locutionary agent’ of propositions, for the identification of subjective auxiliary expressions. As for (ii), it turns out that the expressions of auxiliaries of necessity are prone to express subjective epistemic modality, whereas those of probability and possibility generally express objective epistemic modality.
Subject expression in Brazilian Portuguese
Authors: Peres de Oliveira Taísa
Published: November 2018

This chapter analyzes the expression of subjects with identifiable referents in Brazilian Portuguese, using the multi-level architecture of Functional Discourse Grammar (Hengeveld & Mackenzie 2008) and the notions of transparency and opacity as conceived of by this theory. The aim of the chapter is to show that in regard to subject expression, Brazilian Portuguese grammar may be developing into a more transparent system in comparison to its earlier stages and other Romance languages. It is shown that in many cases there is no verbal morphology to cross-reference the argument on the predicate with subjects being expressed by means of a single morphosyntactic unit; since this morphological unit corresponds to single units at higher levels of representation, subject expression involves a one-to-one relation between levels, resulting in a transparent system.
Measuring polysynthesis
Authors: Genee Inge
Published: November 2018

This chapter proposes a framework for a quantitative approach to the typology of polysynthesis based in Functional Discourse Grammar (FDG). FDG’s strict separation between the Interpersonal, Representational and Morphosyntactic Levels of analysis combined with its approach to morpheme types allows for a detailed examination of the scalar nature of polysynthesis. The analysis refines FDG’s treatment of morphological typology, which characterizes languages according to two parameters, viz. transparency and synthesis. Inspired by recent FDG treatments of transparency (esp. Leufkens 2015; Hengeveld & Leufkens 2018), and building on FDG work by Fortescue (2007) and Smit (2005), I propose the following set of parameters: (1) (verbal) lexical density (qualitative and quantitative); (2) anisomorphism between Formulation and Encoding levels; (3) anisomorphism within the Morphosyntactic Level (word-internal layering in the verbal word); (4) alignment restrictions; (5) optionality (availability of analytic alternative). This quantitative approach is intended to complement the qualitative typology developed by Mattissen (2004, 2017).
3D genomic architecture reveals that neocentromeres associate with heterochromatin regions
Authors: Nishimura Kohei , Komiya Masataka , Hori Tetsuya , Itoh Takehiko , Fukagawa Tatsuo
Published: November 2018

The centromere is an important genomic locus for chromosomal segregation. Although the centromere is specified by sequence-independent epigenetic mechanisms in most organisms, it is usually composed of highly repetitive sequences, which associate with heterochromatin. We have previously generated various chicken DT40 cell lines containing differently positioned neocentromeres, which do not contain repetitive sequences and do not associate with heterochromatin. In this study, we performed systematic 4C analysis using three cell lines containing differently positioned neocentromeres to identify neocentromere-associated regions at the 3D level. This analysis reveals that these neocentromeres commonly associate with specific heterochromatin-rich regions, which were distantly located from neocentromeres. In addition, we demonstrate that centromeric chromatin adopts a compact structure, and centromere clustering also occurs in vertebrate interphase nuclei. Interestingly, the occurrence of centromere–heterochromatin associations depend on CENP-H, but not CENP-C. Our analyses provide an insight into understanding the 3D architecture of the genome, including the centromeres.
Reduction of water hardness from groundwater in Puerto Princesa City, Palawan, Philippines using electrocoagulation
Authors: Cabiguen M L , Soriano A N , Adornado A P
Published: November 2018

Reduction of water hardness from groundwater is extremely important to prevent corrosion, scale and hard foam formation, clogging, decline in efficiency, and lathering of soap before it can be used for industrial and domestic consumptions. In this study, water hardness caused by the presence of high concentration of minerals mainly calcium (Ca) and magnesium (Mg) is reduced by electrocoagulation (EC) with iron (Fe) and aluminum (Al) electrodes. The effects of the following parameters: initial pH, current intensity, electrolysis time, and conductivity by supporting electrolyte concentration were studied. Reduction efficiencies of both Fe and Al electrodes are satisfactory. Under favorable conditions, using Fe and Al electrodes, the water hardness was reduced of about 98.12% and 97.57%, respectively.
Biosorption of lead and chromium in surface water using Philippine mud crab (Scylla serrata) and tahong (Perna viridis) shells
Authors: Esguerra M J S , Manguiam V L R , Cabanban S K V , Gala M J A L , Limos M J N A , Tella-in J M J , Adornado A P
Published: November 2018

This study aimed to prove the feasibility of Philippine mud crab (Scylla serrata) and tahong (Perna viridis) shells in treating heavy metal content of surface water through the removal of lead (Pb) and chromium (Cr). Surface water samples were collected at Pasig River (at the deepest point at Guadalupe, Makati City, Philippines). The surface water samples were then treated with varying biosorbent dosages and contact time. Based on statistical tests, there was a significant difference in the Pb and Cr concentrations between treated and untreated surface water, this means that both S. serrata and P. viridis shells were effective in absorbing Pb and Cr. However, S. serrata shells were more effective in absorbing Pb while P. viridis shells proved to absorb more Cr content in surface water.
LCA-SEM Energy Petrochemical Product Structure: A Research on Optimization Model of Low Carbon Economy Urban Agglomeration Supply Chain
Authors: Yucong You , Luxia Yi
Published: November 2018

Nowadays, the carbon dioxide and other gases generated by human activities have caused problems such as the greenhouse effect and global warming. The construction of a low-carbon economy city gathering supply chain is one of the main ways to reduce greenhouse gases. This paper uses the concept of carbon footprint, takes a certain urban agglomeration as the research object, and applies the greenhouse gas emission of energy petrochemical product structure into consideration according to the principles of economic, social and environmental sustainable development, together with constructing the LCA-SEM supply chain optimization model. Taking the minimum net carbon emission of energy and petrochemical product structure in low-carbon economy urban agglomeration area as the optimization goal, combined with the optimization index analysis of energy and petrochemical product structure index system, the research conclusions show that the low-carbon supply chain plays a key role in the environment in terms of five supply chain links: energy petrochemical raw material production, energy and petrochemical raw material transportation, energy and petrochemical production, energy and petrochemical product storage, as well as energy petrochemical transportation. The list of environmental burdens À(X) on the contribution of greenhouse gases to global warming optimization model shows that the urban agglomeration area and the “core area” energy consumption carbon sink area bears a significantly positive correlation with both of the regional carbon intensity and energy intensity of different energy land.
Medication Management Capacity and Its Neurocognitive Correlates in Huntington’s Disease
Authors: Sumida Catherine A , Van Etten Emily J , Lopez Francesca V , Sheppard David P , Pirogovsky-Turk Eva , Corey-Bloom Jody , Filoteo J Vincent , Woods Steven P , Gilbert Paul E , Schmitter-Edgecombe Maureen
Published: November 2018

Objective

Although medication management is a necessary daily activity for individuals with Huntington’s disease (HD), medication management abilities and their relation to cognitive functioning have not been evaluated.

Method

Twenty individuals with HD and 20 healthy adults (HA) completed the Medication Management Abilities Assessment (MMAA). Individuals with HD also completed a self-report medication management measure and neuropsychological tests assessing executive function, retrospective memory, and prospective memory.

Results

Individuals with HD performed significantly poorer and made more undertaking errors on the MMAA as compared to HA. No group differences were found in overtaking errors. In the HD group, significant associations were found between undertaking errors and perceived medication management ability as well as between MMAA task performance and measures assessing prospective memory and executive functions.

Conclusions

Medication management capacity was negatively affected in individuals with HD and may be associated with difficulty remembering to take medications in the future.
Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis
Authors: Correa Marrero Miguel , Immink Richard G H , de Ridder Dick , van Dijk Aalt D J
Published: November 2018

Motivation

Predicting residue–residue contacts between interacting proteins is an important problem in bioinformatics. The growing wealth of sequence data can be used to infer these contacts through correlated mutation analysis on multiple sequence alignments of interacting homologs of the proteins of interest. This requires correct identification of pairs of interacting proteins for many species, in order to avoid introducing noise (i.e. non-interacting sequences) in the analysis that will decrease predictive performance.

Results

We have designed Ouroboros, a novel algorithm to reduce such noise in intermolecular contact prediction. Our method iterates between weighting proteins according to how likely they are to interact based on the correlated mutations signal, and predicting correlated mutations based on the weighted sequence alignment. We show that this approach accurately discriminates between protein interaction versus non-interaction and simultaneously improves the prediction of intermolecular contact residues compared to a naive application of correlated mutation analysis. This requires no training labels concerning interactions or contacts. Furthermore, the method relaxes the assumption of one-to-one interaction of previous approaches, allowing for the study of many-to-many interactions.

Availability and implementation

Source code and test data are available at www.bif.wur.nl/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Metabolic Consequences of Concomitant Strongyloides stercoralis Infection in Patients With Type 2 Diabetes Mellitus
Authors: Rajamanickam Anuradha , Munisankar Saravanan , Bhootra Yukthi , Dolla Chandrakumar , Thiruvengadam Kannan , Nutman Thomas B , Babu Subash
Published: November 2018

Background

Human and animal studies have demonstrated that helminth infections are associated with a decreased prevalence of type 2 diabetes mellitus (T2DM). However, very little is known about their biochemical and immunological interactions.

Methods

To assess the relationship between a soil-transmitted helminth, Strongyloides stercoralis (Ss), and T2DM, we examined analytes associated with glycemic control, metabolic processes, and T-cell–driven inflammation at the time of Ss diagnosis and 6 months after definitive anthelmintic treatment. We measured plasma levels of hemoglobin A1c, glucose, insulin, glucagon, adipocytokines, and T-helper (TH) 1-, 2-, and 17- associated cytokines in patients with T2DM with (INF group) or without (UN group) Ss infection. In INF individuals, we again assessed the levels of these analytes 6 months following anthelmintic treatment.

Results

Compared to UN individuals, INF individuals exhibited significantly diminished levels of insulin and glucagon that increased significantly following therapy. Similarly, INF individuals exhibited significantly diminished levels of adiponectin and adipsin that reversed following therapy. INF individuals also exhibited significantly decreased levels of the TH1- and TH17- associated cytokines in comparison to UN individuals; again, anthelmintic therapy augmented these levels. As expected, INF individuals had elevated levels of TH2-associated and regulatory cytokines that normalized following definitive therapy. Multivariate analysis revealed that these changes were independent of age, sex, body mass index, and liver and renal function.

Conclusions

Strongyloides stercoralis infection is associated with a significant modulation of glycemic, hormonal, and cytokine parameters in T2DM and its reversal following anthelmintic therapy. Hence, Ss infection has a protective effect on diabetes-related parameters.
Aequatus: an open-source homology browser
Authors: Thanki Anil S , Soranzo Nicola , Herrero Javier , Haerty Wilfried , Davey Robert P
Published: November 2018

Background

Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterization enables the identification of syntenic blocks, which can then be visualized with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.

Findings

We present Aequatus, an open-source web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualizations. It relies on precalculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfills the visualization aspects of Aequatus, available within the Galaxy web platform as a visualization plug-in, which can be used to visualize gene trees generated by the GeneSeqToFamily workflow.
Transfer learning improves resting-state functional connectivity pattern analysis using convolutional neural networks
Authors: Vakli Pál , Deák-Meszlényi Regina J , Hermann Petra , Vidnyánszky Zoltán
Published: November 2018

Background

Deep learning is gaining importance in the prediction of cognitive states and brain pathology based on neuroimaging data. Including multiple hidden layers in artificial neural networks enables unprecedented predictive power; however, the proper training of deep neural networks requires thousands of exemplars. Collecting this amount of data is not feasible in typical neuroimaging experiments. A handy solution to this problem, which has largely fallen outside the scope of deep learning applications in neuroimaging, is to repurpose deep networks that have already been trained on large datasets by fine-tuning them to target datasets/tasks with fewer exemplars. Here, we investigated how this method, called transfer learning, can aid age category classification and regression based on brain functional connectivity patterns derived from resting-state functional magnetic resonance imaging. We trained a connectome-convolutional neural network on a larger public dataset and then examined how the knowledge learned can be used effectively to perform these tasks on smaller target datasets collected with a different type of scanner and/or imaging protocol and pre-processing pipeline.

Results

Age classification on the target datasets benefitted from transfer learning. Significant improvement (~9%–13% increase in accuracy) was observed when the convolutional layers' weights were initialized based on the values learned on the public dataset and then fine-tuned to the target datasets. Transfer learning also appeared promising in improving the otherwise poor prediction of chronological age.

Conclusions

Transfer learning is a plausible solution to adapt convolutional neural networks to neuroimaging data with few exemplars and different data acquisition and pre-processing protocols.
Services Deepening and the Transmission of Monetary Policy
Authors: Galesi Alessandro , Rachedi Omar
Published: November 2018

The structural transformation from manufacturing to services comes with a process of services deepening: the services share of intermediate inputs rises over time. Moreover, inflation reacts less to monetary policy shocks in countries that are more intensive in services intermediates. We rationalize these facts using a two-sector New Keynesian model where trends in sectoral productivities generate endogenous variations in the Input–Output matrix. Services deepening reduces the contemporaneous response of inflation to monetary policy shocks through a marginal cost channel. Since services prices are stickier than manufacturing prices, the rise of services intermediates raises the sluggishness of sectoral marginal costs and inflation rates.
I-FABP Is Higher in People With Chronic HIV Than Elite Controllers, Related to Sugar and Fatty Acid Intake and Inversely Related to Body Fat in People With HIV
Authors: Cheru Lediya T , Park Elli A , Saylor Charles F , Burdo Tricia H , Fitch Kathleen V , Looby Sara , Weiner Jeffrey , Robinson Jake A , Hubbard Jane , Torriani Martin , Lo Janet
Published: November 2018

Background

Intestinal fatty acid binding protein (I-FABP) has been shown to be a marker of intestinal damage among people living with HIV. We hypothesized that I-FABP would be increased in chronically HIV-infected patents more than elite controllers and would relate to specific nutrient intake and body composition.

Methods

In an observational study, serum I-FABP was measured by enzyme-linked immunosorbent assay. Anthropometric measurements, dual-energy x-ray absorptiometry, and single-slice abdominal computed tomography were obtained to assess body composition, as well as visceral and subcutaneous adipose tissue areas (VAT and SAT). Dietary intake was assessed using 4-day food records.

Results

One hundred forty-nine people with chronic HIV (65% male, 47 ± 7 years of age, 54.7% white, and 14 ± 6 years of known HIV), 10 elite controllers (60% male, 53 ± 8 years, 60% white, and 20 ± 7 years of known HIV), and 69 HIV-negative controls (59.4% male, 46 ± 7 years, and 52.2% white) were included in the analysis. I-FABP was significantly higher in HIV progressors relative to HIV-negative controls and elite controllers. In the chronic HIV group, I-FABP was positively associated with dietary intake of added sugar and with saturated fatty acids. I-FABP was inversely associated with body mass index, VAT, and SAT. I-FABP also correlated with MCP-1, CXCL10, sCD163, and lipopolysaccharide (LPS) among all participants.

Conclusions

I-FABP was increased among chronically HIV-infected patients to a greater degree than in elite controllers and was related to nutrient intake and body composition in HIV progressors. Future studies to investigate the role of intestinal damage on nutrient absorption are needed to elucidate the mechanisms of these relationships.

Trial Registration Identifier

NCT00455793.
MONITORING OF HIGH-ENERGY PHOTON FLUENCE IN CLINAC USING Zn AND Cr PHOTOACTIVATION
Authors: Haddad Kh , Anjak O , Yousef B , Ammar M
Published: November 2018

Monitoring of high-energy photon dose in radiation therapy is crucial for radiation protection, as well as to estimate the radiation effects in the operating microelectronic devices. The aim of this work was to investigate the possibility of using the photoactivation technique to monitor the high-energy photon fluence in the Varian 21EX 23MV CLINAC. The 52Cr(γ,n)51Cr and 66Zn(γ,n)65Zn reactions were used. It was found that 51Cr and 65Zn can be used successfully to monitor the fluence for short term (80 days) and long term (110 days), respectively.
Developing Tomorrow’s Leaders: A Medical Student Distinction Track in Health System Transformation and Leadership
Authors: Lawson Luan , Lake Donna , Lazorick Suzanne , Reeder Timothy , Garris Jenna , Baxley Elizabeth G.
Published: November 2018

Problem

Calls for medical education reform focus on preparing physicians to meet the challenges of today’s complex health care system. Despite implementing curricula focused on health systems science (HSS), including quality improvement (QI), patient safety, team-based care, and population health, a significant gap remains in training students to meet the system’s evolving needs.

Approach

Brody School of Medicine redesigned its curriculum to prepare leaders to effect health system change. This included development of a distinction track in health system transformation and leadership, known as the Leaders in INnovative Care (LINC) Scholars Program. Selected LINC scholars spend eight weeks in a summer immersion experience designed to provide foundational knowledge and practical application.

Outcomes

Two cohorts (15 LINC scholars) completed the summer immersion in 2015 and 2016. Participants demonstrated significant improvement in knowledge and confidence and continue to be engaged in ongoing QI projects throughout the health system. All scholars have presented their work at local, regional, or national meetings. Students rated patient navigation experiences, health system leader interviews, QI project application, and interprofessional experiences as most valuable and recommended adoption in the curriculum for all students.

Next Steps

A distinction track with an immersion component can be an effective method to pilot innovative HSS components for the entire curriculum while preparing a cadre of learners with advanced expertise. To longitudinally measure HSS knowledge change, behavioral impact, and organization-level outcomes, next steps must focus on development of workplace-based assessments, establishment of learner portfolios, and longitudinal tracking of student outcomes, including career trajectory.
Cochlear Reflectance and Otoacoustic Emission Predictions of Hearing Loss
Authors: Neely Stephen T. , Fultz Sara E. , Kopun Judy G. , Lenzen Natalie M. , Rasetshwane Daniel M.
Published: November 2018

Objectives:

Cochlear reflectance (CR) is the cochlear contribution to ear-canal reflectance. CR is a type of otoacoustic emission (OAE) that is calculated as a transfer function between forward pressure and reflected pressure. The purpose of this study was to compare wideband CR to distortion-product (DP) OAEs in two ways: (1) in a clinical-screening paradigm where the task is to determine whether an ear is normal or has hearing loss and (2) in the prediction of audiometric thresholds. The goal of the study was to assess the clinical utility of CR.

Design:

Data were collected from 32 normal-hearing and 124 hearing-impaired participants. A wideband noise stimulus presented at 3 stimulus levels (30, 40, 50 dB sound pressure level) was used to elicit the CR. DPOAEs were elicited using primary tones spanning a wide frequency range (1 to 16 kHz). Predictions of auditory status (i.e., hearing-threshold category) and predictions of audiometric threshold were based on regression analysis. Test performance (identification of normal versus impaired hearing) was evaluated using clinical decision theory.

Results:

When regressions were based only on physiological measurements near the audiometric frequency, the accuracy of CR predictions of auditory status and audiometric threshold was less than reported in previous studies using DPOAE measurements. CR predictions were improved when regressions were based on measurements obtained at many frequencies. CR predictions were further improved when regressions were performed on males and females separately.

Conclusions:

Compared with CR measurements, DPOAE measurements have the advantages in a screening paradigm of better test performance and shorter test time. The full potential of CR measurements to predict audiometric thresholds may require further improvements in signal-processing methods to increase its signal to noise ratio. CR measurements have theoretical significance in revealing the number of cycles of delay at each frequency that is most sensitive to hearing loss.
Increasing melanoma incidence in the elderly in North-East Hungary: is this a more serious problem than we thought?
Authors: Janka Eszter A. , Kékedi Kriszta , Várvölgyi Tünde , Gellén Emese , Kiss Borbála , Remenyik Éva , Emri Gabriella
Published: November 2018

There is a great need for efficient and cost-effective melanoma screening, but this is not yet solved. Epidemiological studies on trends in melanoma incidence by tumour thickness, anatomical site and demographical data can help to improve public health efforts regarding earlier melanoma diagnosis. We aimed to study the trends in the incidence and characteristics of patients and their melanoma in North-East Hungary from 2000 to 2014. Data were obtained from a university hospital-based registry. A total of 1509 cutaneous invasive melanomas of 1464 patients were included in the study. A moderate but significant increase in incidence was observed in the region [average annual percentage change: 3.04 (0.07; 6.11); P = 0.045], with a breakpoint in 2007. From 2001 to 2007, the trend was increasing [APC: 9.84 (3.52; 16.55); P=0.006], but it stalled from 2007 [APC: −2.45 (−5.99; 1.23); P = 0.164]. However, in the age groups over the age of 60 years, where the standardised incidence was the highest, the incidence continued to rise. Furthermore, older age, male sex and trunk or lower extremity localization were found to be associated with thicker melanomas. Our results support that regular screening examination for melanoma would be desirable for people over the age of 60 years.
Cruciferous vegetable intake and colorectal cancer risk: Japan public health center-based prospective study
Authors: Mori Nagisa , Sawada Norie , Shimazu Taichi , Yamaji Taiki , Goto Atsushi , Takachi Ribeka , Ishihara Junko , Iwasaki Motoki , Inoue Manami , Tsugane Shoichiro
Published: November 2018

We aimed to assess the association between cruciferous vegetable intake and colorectal cancer (CRC) development among Japanese adults aged between 45 and 74 years in the Japan Public Health Center-based Prospective Study. During 1 325 853 person-years of follow-up, 2612 CRC cases were identified. The association of cruciferous vegetable intake with CRC risk was assessed using a Cox proportional hazard regression model to compute hazard ratios (HRs) and 95% confidence intervals (CIs), adjusted for potential confounders. No significant association was observed between the highest cruciferous vegetable intake quartile (compared with the lowest) and CRC risk in men (multivariate HRs: 1.08; 95% CI: 0.91, 1.29) and women (multivariate HRs: 0.99; 95% CI: 0.80, 1.22) and its subsites. Women showed a marginal negative association between cruciferous vegetable intake and the risk of colon cancer (CC) after excluding participants who developed CC in the first 3 years of follow-up (P for trend = 0.08); a positive association was found with proximal CC in men. Cruciferous vegetable intake does not have a significant association with CRC risk in the Japanese general population.
Pericoital contraception
Authors: Cahill Erica P. , Blumenthal Paul D.
Published: November 2018

Purpose of review

To evaluate the literature on repeat use of emergency contraception and pericoital approaches to contraception.

Recent findings

Women are very interested in an oral, on-demand contraceptive option, were one available. Ulipristal acetate and a combination of levonorgestrel (LNG) and meloxicam (a cyclo-oxygenase-2 inhibitor) both appear to be more effective at disrupting ovulation than LNG alone. Recent advisories from the United Kingdom regarding daily dosing of ulipristal for fibroids emphasize the need for more safety data.

Repeat pericoital dosing of 1.5-mg LNG is approximately as effective as other on-demand contraceptive methods and is overall very safe. The most common side effect is irregular bleeding. Repeat on-demand ulipristal acetate or meloxicam/other cyclo-oxygenase-2 inhibitors have potential as an on-demand option either alone or in combination but have not been evaluated for contraceptive efficacy in a large-scale study. Given the high unmet need for contraception, even among women with access to available options, there is a distinct need for options that address needs of women who are interested in an on-demand option. On-demand oral contraception has the potential to expand the convenience of contraceptive options and overall contraceptive use.
Cystoscopy at the time of incontinence and prolapse surgery
Authors: Stewart Lauren E. , Hall Evelyn , Carberry Cassandra L.
Published: November 2018

Purpose of review

This article provides an update on the use of cystoscopy at the time of prolapse and incontinence surgery.

Recent findings

Iatrogenic lower urinary tract injury is a known complication of antiincontinence procedures and surgical repair of pelvic organ prolapse. Intraoperative cystoscopy improves detection of lower urinary tract injuries in women undergoing pelvic floor surgery. The pelvic surgeon has a number of agents available to aid in the cystoscopic visualization of ureteral efflux. When injuries of the urinary tract are identified and treated intraoperatively, there is decreased morbidity, lower healthcare costs, and a lower risk of litigation than when detection is delayed. Therefore, many organizations, including the American College of Obstetricians and Gynecologists (ACOG), the American Urogynecologic Society (AUGS), and the American Urological Association (AUA) recommend cystoscopy at the time of pelvic floor surgery.

Cystoscopy should be universally employed at the time of prolapse and incontinence surgery, except in instances of isolated repair of the posterior compartment.