bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation and mitigation of GHG emissions from ruminant livestock in Pakistan
Authors: Habib Ghulam
Published: December 2018

The study examined baseline emissions of greenhouse gases from ruminant livestock in Pakistan for the year 2014 and evaluated feasible interventions for mitigating the sector emissions. Total emissions (as CO2-equivalents) from livestock supply chain from cradle to farm gate were estimated at 431007 × 103 t. Major part (77%) of the emissions was produced by the mixed system and the remaining 23% was contributed by the grazing system. Methane emissions were 62.5% of the total emissions, followed by N2O at 29.4% and CO2 at 8.1%. Bulk of milk (87.6%) and meat (59.4%) was produced by the mixed system, which was associated with three-fold higher emissions at 332248 × 103 t than when they were produced by the grazing system. The emission intensity (kg CO2-eq/kg protein) of milk and meat averaged 183.4 and 443.2 respectively, and ranked higher than the global average values. Buffaloes were responsible for the major proportion of emissions, followed by cattle. Average emissions per animal in buffalo, cattle, sheep and goat were 4.27, 3.27, 0.28 and 0.25 t CO2-eq/year respectively. The emission intensities (kg CO2-eq/kg commodity protein) of both milk and meat remained lower in cattle than buffalo and were calculated as 166.1 and 299.7 in cattle and 189.5 and 527.9 in buffaloes respectively. The carbon footprint of milk and meat in sheep and goats also remained high and averaged 189.0 and 472.6 kg CO2-eq/kg protein respectively. Overall, the emission intensity of meat was slightly higher in the grazing system than mixed system, but remained much higher in non-dairy herds than in dairy herds (1006.6 vs 46.6 kg CO2-eq/kg meat protein). Interventions such as improving diet quality through increased fodder supply, vaccination for adequate health control and genetic improvement reduced emission intensities of milk (kg CO2-eq/kg protein), varying from 20.3% to 36.8% compared with the baseline in dairy cows and buffaloes and this was associated with a positive productivity outcome of enhanced milk production by 25–50%. More significant reduction in emission intensities of milk between 48.1% and 53.1%, together with a 100% increase in milk yield above baseline, resulted from combined application of the three interventions as a single package.
Electrochemical Detection of Explosive Compounds in an Ionic Liquid in Mixed Environments: Influence of Oxygen, Moisture, and Other Nitroaromatics on the Sensing Response
Authors: Lee Junqiao , Silvester Debbie S.
Published: December 2018

From a security point of view, detecting and quantifying explosives in mixed environments is required to identify potentially concealed explosives. Electrochemistry offers a viable method to detect nitroaromatic explosive compounds owing to the presence of easily reducible nitro groups that give rise to a current signal. However, their reduction potentials can overlap with interfering species, making it difficult to distinguish particular compounds. We have therefore examined the effect of oxygen, moisture, and other nitroaromatic species on the cyclic voltammetry and square wave voltammetry of nitroaromatic compounds of a range of mixed environments, focussing on 2,4,6-trinitrotoluene (TNT) and 2,4-dinitrotoluene (DNT) as model analytes, and using the hydrophobic room-temperature ionic liquid (RTIL) [P14,6,6,6][NTf2] as the solvent. Oxygen (0–20% vol.) minimally affected the current of the first reduction peak of TNT in [P14,6,6,6][NTf2], but significantly affects the current for DNT. The impact of water (0 to 86% relative humidity), however, was much more dramatic – even in the hydrophobic RTIL, water significantly affected the currents of the analyte peaks for TNT and DNT, and gave rise to additional reduction features, further contributing to the current. Additionally, the voltammetry of other related di- and tri-nitro compounds (2,6-dinitrotoluene, 1,3-dinitrobenzene, 2,4,6-trinitrotoluene, 1,3,5-trinitrobenzene, and musk xylene) was also studied to understand how different substituents on the aromatic ring may affect the reduction potentials. A 50:50 mixture of TNT and DNT revealed that both analytes could be separately identified and quantified using square wave voltammetry. Overall, this information is useful in determining the effect of other species on the current signals of electrochemical explosive sensors, and reveals that it may be necessary to dry the aprotic RTIL electrolyte when used in humid environments.
Effects of abiotic stress on anthocyanin accumulation and grain weight in purple wheat
Authors: Li Xiaolan , Lv Xiang , Wang Xiaohong , Wang Liaohong , Zhang Mingsheng , Ren Mingjian
Published: December 2018

This study explored the effects of abiotic stress on anthocyanin accumulation and grain weight of purple wheat (Triticum aestivum L. cv. Guizi 1). Plants were treated with five abiotic stress factors at different developmental periods of the grain, then mature grains were analysed for anthocyanin content and 1000-grain weight (TGW). Stresses included temperature (cold and heat), light (shading irradiance and continuous irradiance), drought (20 and 40mm PEG 6000), salinity (100 and 200mm NaCl), and wounding (four types). Of all treatments, 25% tended to increase both anthocyanin content and TGW, although only 5% reached a significant level, 27.5% decreased both, 40% increased anthocyanins but decreased TGW, and 7.5% increased TGW but decreased anthocyanins. Heat stress tended to increase anthocyanin content and decrease TGW, whereas cold stress increased anthocyanins only at 15 days post-anthesis (DPA) and decreased both traits at other times. Shading irradiance decreased anthocyanins but had little effect on TGW. Continuous irradiance increased anthocyanins and TGW at 35 DPA but decreased both at 10 DPA. The lower levels of drought (20mm PEG 6000) and salinity (100mm NaCl) stress tended to increase anthocyanins and decrease TGW; however, the effects of 40mm PEG 6000 and 200mm NaCl were different, and were period-dependent. The four types of wounds increased anthocyanins and TGW at 30 DPA, but their individual effects were different in the other four periods. The results quantified the effects of five abiotic stress factors on anthocyanin accumulation and grain weight, and provide the foundation for further study of defence-responsive molecular mechanisms of abiotic stress in purple wheat.
Fenestrations control resting-state block of a voltage-gated sodium channel
Authors: Gamal El-Din Tamer M. , Lenaeus Michael J. , Zheng Ning , Catterall William A.
Published: December 2018

Potency of drug action is usually determined by binding to a specific receptor site on target proteins. In contrast to this conventional paradigm, we show here that potency of local anesthetics (LAs) and antiarrhythmic drugs (AADs) that block sodium channels is controlled by fenestrations that allow drug access to the receptor site directly from the membrane phase. Voltage-gated sodium channels initiate action potentials in nerve and cardiac muscle, where their hyperactivity causes pain and cardiac arrhythmia, respectively. LAs and AADs selectively block sodium channels in rapidly firing nerve and muscle cells to relieve these conditions. The structure of the ancestral bacterial sodium channel Na
V
Ab, which is also blocked by LAs and AADs, revealed fenestrations connecting the lipid phase of the membrane to the central cavity of the pore. We cocrystallized lidocaine and flecainide with Na
v
Ab, which revealed strong drug-dependent electron density in the central cavity of the pore. Mutation of the contact residue T206 greatly reduced drug potency, confirming this site as the receptor for LAs and AADs. Strikingly, mutations of the fenestration cap residue F203 changed fenestration size and had graded effects on resting-state block by flecainide, lidocaine, and benzocaine, the potencies of which were altered from 51- to 2.6-fold in order of their molecular size. These results show that conserved fenestrations in the pores of sodium channels are crucial pharmacologically and determine the level of resting-state block by widely used drugs. Fine-tuning drug access through fenestrations provides an unexpected avenue for structure-based design of ion-channel–blocking drugs.
Gender, number and inflectional class in some Northern Italian dialects
Authors: Baldi Benedetta , Franco Ludovico
Published: December 2018

In many Northern Italian varieties the plural inflection ‑i has a restricted distribution, targeting feminine class nouns, determiners and adjectives. The ‑i morpheme also occurs with clitic pronouns, both subjects and objects. The crucial point we address is the relation between the plural specialized morpheme ‑i and its distribution among noun classes. We account for the distribution of the inflection ‑i on the basis of a theoretical treatment of the internal structure of the noun, along the lines of Manzini and Savoia (2017a, b).
Notes on infinitival relatives in Italian
Authors: Cinque Guglielmo , Benincà Paola
Published: December 2018

Here certain properties of Italian infinitival relatives will be discussed which to our knowledge have not been addressed in previous work on this topic (Napoli 1976; Cinque 1988: § 1.1.5; Bianchi 1991, 2007). In particular, we will point out a distinction between two ‘da + infinitive’ relative constructions and a difference between da infinitival relatives and infinitival relatives introduced by relative pronouns; furthermore, we will illustrate the bounded vs unbounded nature of relativization under restructuring, and the properties of restrictive vs non-restrictive infinitival relatives.
Negation and negative copulas in Bantu
Authors: Cocchi Gloria
Published: December 2018

The main aim of this work is to further speculate on the many syntactic similarities, already discussed in previous work, which may be observed in Bantu and Romance languages. In particular, this work analyses the expression of negation in Bantu, a phenomenon which involves different elements and multiple positions. Crucially, Bantu negation is generally encoded in a specialized prefix, which shows up at the left edge of the complex verbal form; however, negation may also interfere either with tense feature – at least in languages, like Swahili, which exhibit morphologically different tense/aspect infixes in affirmative and negative clauses – or with modality, encoded in the final inflection. This recalls the situation observed also in Romance varieties and especially in Northern Italian dialects.
On gender and number
Authors: Lorusso Paolo
Published: December 2018

In the theory of agreement developed by Chomsky (2000, 2001) φ features are undifferentiated, they are organized in a bundle of features, despite the intrinsically different information that each of them carries. However, while person is found to have an autonomous status in many psycholinguistic studies, number and gender show contrasting results: some studies show a crucial difference in the processing of number and gender, others, mainly ERP, do not. We will review the different psycholinguistic findings and we will propose that number and gender simply denote different nominal classes. The difference found in some experiments for number and gender maybe linked to when the feature is made available in the comprehension of the sentence (early/late cues).
Micro‑ and macro-variation
Authors: Rita Manzini M.
Published: December 2018

Manzini and Savoia (2005, 2017) argue that morphophonology is involved in enclisis/proclisis alternations only in so far as it externalizes the syntactico-semantic category of non-veridicality, as outlined here in Section 1. In Section 2 we review typological literature reporting that the irrealis category governs the alternation between different pronominal series cross-linguistically. This evidence potentially fulfills a prediction issuing from the treatment of Romance. What is more, comparison between treatments of Romance microvariation and of typological macrovariation reveals a propensity to treat the former in terms of morphophonological organization and the latter in terms of conceptual systems. If Manzini and Savoia are correct, efforts at defining opposed notions of macro‑ and micro-parametrization are not warranted by the evidence (Section 3).
Concealed pseudo-clefts? Evidence from a Lombard dialect
Authors: Pescarini Diego , Donzelli Giulia
Published: December 2018

This paper focuses on the syntax of clefts in the Lombard dialect of Comun Nuovo (Bergamo). In this dialect, clefts are highly constrained (in particular, they are ungrammatical in questions) and, in the contexts where clefts and pseudo-clefts alternate, the distinction between the two is often blurred. We argue that Comunuovese clefts are better analysed as concealed pseudo-clefts (Paul 2001 a.o.).
Negation patterns across dialects
Authors: Poletto Cecilia , Oliviéri Michèle
Published: December 2018

In this work we consider two opposite sorts of Romance varieties with respect to the negative marker, i.e. an Occitan variety where the preverbal negative marker alone is so much reduced that it can nowadays only occur in some specific syntactic contexts and two Venetan varieties where the preverbal negative marker is so widespread that it even displays strict negative concord. We will show that despite being so different, both types of dialects are sensitive to the modal environment and that the presence of the preverbal negative marker is tied to a subset of non-veridical contexts, i.e. those that contain a [−realis] verbal form.
A note on left-peripheral maps and interface properties
Authors: Rizzi Luigi
Published: December 2018

The cartographic analysis of the left periphery leads to the identification of invariant and variable properties in the syntactic expression of scope-discourse configurations, such as topic-comment and focus-presupposition. One notable property is that languages typically permit a unique focus in the left periphery of a clause, whereas left-peripheral topics may proliferate in many languages. A comparative analysis of Italian and Gungbe reveals that Italian disallows distinct LP foci also in distinct clauses of complex sentences, an option which is permitted in Gungbe. The proposal developed in this paper capitalizes on computational mechanisms applying at the interfaces with sound and meaning to capture the invariant core and the variability in these left-peripheral properties across languages.
Overabundance in Hungarian accusative pronouns
Authors: Grossmann Maria , Thornton Anna M.
Published: December 2018

Overabundance is defined as the situation in which more than one inflected form is available to realize a single cell of an inflectional paradigm (Thornton 2011, 2012). Hungarian pronominal paradigms host several cases of overabundance in the accusative forms. Quantitative data from both diachronic and synchronic corpora are presented, showing that 1/2/3sg.acc forms have an unbalanced distribution while 1pl.acc and 2pl.acc forms have a very balanced distribution, close to a 1:1 ratio between the two competing forms. One of the factors mentioned in the literature as favoring one of the two 1pl.acc and 2pl.acc forms, i.e., usage in emphatic / focus position, is illustrated and briefly discussed on the basis of corpus data.
Phonological correlates of syntactic structure
Authors: Ledgeway Adam
Published: December 2018

The present article considers the syntactic constraints operative on the distribution of a phonological fortition process, raddoppiamento fonosintattico ‘phonosyntactic doubling’, in the Calabrian dialect of Cosenza. It is shown that the relevant locality restrictions are best understood, not in terms of the three core structural configurations Spec-Head, Head-Head and Head-Comp, but in terms of phasal domains, highlighting how different phonological realizations represent the spell-out of deep syntactic differences mapped at the syntax-phonology interface. At the same time, the theoretical assumptions assumed here provide us with the key to understanding some intriguing empirical generalizations about the distribution of Cosentino RF which, in turn, throw new light on some current theoretical assumptions about clause structure and the nature of phases.
Metaphony as magnetism
Authors: van Oostendorp Marc , D’Alessandro Roberta
Published: December 2018

Metaphony in Romance poses a well-known problem for Element Theory, as it seems to involve lowering. [D’Alessandro and van Oostendorp (2016)] propose to solve this by assuming some suffixes are ‘ |A| Eaters’, absorbing the |A| element from the stem vowel without getting phonetically realized themselves. This paper points to some problems with this analysis, and shows that Magnetic Grammar, a framework in which all linguistic variation is encoded in features, might help to solve them.
Remarks on the vulnerability of grammar
Authors: Marotta Giovanna
Published: December 2018

This paper deals with the special status of morphological features in a series of contexts that are crucial for the understanding of the architecture of human grammar: language pathology and impairment, L1/L2 acquisition, language evolution, language contact. The critical review of data referring to different domains and to different languages enlightens the special vulnerability of morphology. In language impairments, as well as in communicative exchanges occurring in multilingual contexts, morphological categories are not perfectly acquired. Empirical evidence relative to atypical contexts shows a peculiar asymmetry in the structure of language: alongside early development and strength of lexicon and phonology, late appearance and vulnerability of morphology. However, the weakness of morphology does not imply a minor role of this component into the grammar.
Levitated electromechanics: all-electrical cooling of charged nano- and micro-particles
Authors: Goldwater Daniel , Stickler Benjamin A , Martinetz Lukas , Northup Tracy E , Hornberger Klaus , Millen James
Published: December 2018

We show how charged levitated nano- and micro-particles can be cooled by interfacing them with an RLC circuit. All-electrical levitation and cooling is applicable to a wide range of particle sizes and materials, and will enable state-of-the-art force sensing within an electrically networked system. Exploring the cooling limits in the presence of realistic noise we find that the quantum regime of particle motion can be reached in cryogenic environments both for passive resistive cooling and for an active feedback scheme, paving the way to levitated quantum electromechanics.
The class of the affine line is a zero divisor in the Grothendieck ring: Via 𝐺₂-Grassmannians
Authors: Ito Atsushi , Miura Makoto , Okawa Shinnosuke , Ueda Kazushi
Published: December 2018

Motivated by [J. Algebraic Geom. 27 (2018), pp. 203–209] and [C. R. Math. Acad. Sci. Paris 354 (2016), pp. 936–939], we show the equality

(
[
X
]
−
[
Y
]
)

⋅
[

A

1

]
=
0

\left ( [ X ] - [ Y ] \right ) \cdot [ \mathbb {A} ^{ 1 } ] = 0

in the Grothendieck ring of varieties, where

(
X
,
Y
)

( X, Y )

is a pair of Calabi-Yau 3-folds cut out from the pair of Grassmannians of type

G

2

G _{ 2 }

.
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks
Authors: Hanson Jack , Paliwal Kuldip , Litfin Thomas , Yang Yuedong , Zhou Yaoqi
Published: December 2018

Motivation

Sequence-based prediction of one dimensional structural properties of proteins has been a long-standing subproblem of protein structure prediction. Recently, prediction accuracy has been significantly improved due to the rapid expansion of protein sequence and structure libraries and advances in deep learning techniques, such as residual convolutional networks (ResNets) and Long-Short-Term Memory Cells in Bidirectional Recurrent Neural Networks (LSTM-BRNNs). Here we leverage an ensemble of LSTM-BRNN and ResNet models, together with predicted residue-residue contact maps, to continue the push towards the attainable limit of prediction for 3- and 8-state secondary structure, backbone angles (θ, τ, ϕ and ψ), half-sphere exposure, contact numbers and solvent accessible surface area (ASA).

Results

The new method, named SPOT-1D, achieves similar, high performance on a large validation set and test set (≈1000 proteins in each set), suggesting robust performance for unseen data. For the large test set, it achieves 87% and 77% in 3- and 8-state secondary structure prediction and 0.82 and 0.86 in correlation coefficients between predicted and measured ASA and contact numbers, respectively. Comparison to current state-of-the-art techniques reveals substantial improvement in secondary structure and backbone angle prediction. In particular, 44% of 40-residue fragment structures constructed from predicted backbone Cα-based θ and τ angles are less than 6 Å root-mean-squared-distance from their native conformations, nearly 20% better than the next best. The method is expected to be useful for advancing protein structure and function prediction.

Availability and implementation

SPOT-1D and its data is available at: http://sparks-lab.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.
MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment
Authors: Burgin Josephine , Molitor Corentin , Mohareb Fady
Published: December 2018

Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research.

Availability and implementation

MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM).

Supplementary information

Supplementary data are available at Bioinformatics online.
SPRING: a next-generation compressor for FASTQ data
Authors: Chandak Shubham , Tatwawadi Kedar , Ochoa Idoia , Hernaez Mikel , Weissman Tsachy
Published: December 2018

Motivation

High-Throughput Sequencing technologies produce huge amounts of data in the form of short genomic reads, associated quality values and read identifiers. Because of the significant structure present in these FASTQ datasets, general-purpose compressors are unable to completely exploit much of the inherent redundancy. Although there has been a lot of work on designing FASTQ compressors, most of them lack in support of one or more crucial properties, such as support for variable length reads, scalability to high coverage datasets, pairing-preserving compression and lossless compression.

Results

In this work, we propose SPRING, a reference-free compressor for FASTQ files. SPRING supports a wide variety of compression modes and features, including lossless compression, pairing-preserving compression, lossy compression of quality values, long read compression and random access. SPRING achieves substantially better compression than existing tools, for example, SPRING compresses 195 GB of 25× whole genome human FASTQ from Illumina’s NovaSeq sequencer to less than 7 GB, around 1.6× smaller than previous state-of-the-art FASTQ compressors. SPRING achieves this improvement while using comparable computational resources.

Availability and implementation

SPRING can be downloaded from https://github.com/shubhamchandak94/SPRING.

Supplementary information

Supplementary data are available at Bioinformatics online.
GlycanFormatConverter: a conversion tool for translating the complexities of glycans
Authors: Tsuchiya Shinichiro , Yamada Issaku , Aoki-Kinoshita Kiyoko F
Published: December 2018

Motivation

Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide variety glycans. However, WURCS uses a complicated nomenclature, so it is not human-readable. Therefore, we aimed to support the interpretation of WURCS by converting WURCS to the most basic and widely used format IUPAC.

Results

In this study, we developed GlycanFormatConverter and succeeded in converting WURCS to the three kinds of IUPAC formats (IUPAC-Extended, IUPAC-Condensed and IUPAC-Short). Furthermore, we have implemented functionality to import IUPAC-Extended, KEGG Chemical Function (KCF) and LinearCode formats and to export WURCS. We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool.

Availability and implementation

https://github.com/glycoinfo/GlycanFormatConverter.git

Supplementary information

Supplementary data are available at Bioinformatics online.
Methane inhalation reduces the systemic inflammatory response in a large animal model of extracorporeal circulation
Authors: Bari Gábor , Érces Dániel , Varga Gabriella , Szűcs Szilárd , Varga Zoltán , Bogáts Gábor , Boros Mihály
Published: December 2018

OBJECTIVES

Extracorporeal circulation induces cellular and humoral inflammatory reactions, thus possibly leading to detrimental secondary inflammatory responses. Previous data have demonstrated the bioactive potential of methane and confirmed its anti-inflammatory effects in model experiments. Our goal was to investigate the in vivo consequences of exogenous methane administration on extracorporeal circulation-induced inflammation.

METHODS

Two groups of anaesthetized Vietnamese minipigs (non-treated and methane treated, n = 5 each) were included. Standard central cannulation was performed, and extracorporeal circulation was maintained for 120 min without cardiac arrest or ischaemia, followed by an additional 120-min observation period with haemodynamic monitoring. In the methane-treated group, 2.5% v/v methane–normoxic air mixture was added to the oxygenator sweep gas. Blood samples through the central venous line and tissue biopsies from the heart, ileum and kidney were taken at the end point to determine the whole blood superoxide production (chemiluminometry) and the activity of xanthine-oxidoreductase and myeloperoxidase, with substrate-specific reactions.

RESULTS

Methane treatment resulted in significantly higher renal blood flow during the extracorporeal circulation period compared to the non-treated group (63.9 ± 16.4 vs 29.0 ± 9.3 ml/min). Whole blood superoxide production (548 ± 179 vs 1283 ± 193 Relative Light Unit (RLU)), ileal myeloperoxidase (2.23 ± 0.2 vs 3.26 ± 0.6 mU/(mg protein)) and cardiac (1.5 ± 0.6 vs 4.7 ± 2.5 pmol/min/mg), ileal (2.2 ± 0.6 vs 7.0 ± 3.4 pmol/min/mg) and renal (1.2 ± 0.8 vs 13.3 ± 8.0 pmol/min/mg) xanthine-oxidoreductase activity were significantly lower in the treated group.

CONCLUSIONS

The addition of bioactive gases, such as methane, through the oxygenator of the extracorporeal circuit represents a novel strategy to influence the inflammatory effects of extracorporeal perfusion in cardiac surgical procedures.
Assessing middle atmosphere weather models using infrasound detections from microbaroms
Authors: Hupe Patrick , Ceranna Lars , Pilger Christoph , de Carlo Marine , Le Pichon Alexis , Kaifler Bernd , Rapp Markus
Published: December 2018

The nonlinear interaction of ocean surface waves produces coherent infrasound noise—microbaroms—between 0.1 and 0.5 Hz. Microbaroms propagate through the atmosphere over thousands of kilometres due to low absorption and efficient ducting between the ground and the stratopause. These signals are globally and permanently detected by the International Monitoring System (IMS) infrasound network, which has been established to monitor compliance with the Comprehensive Nuclear-Test-Ban Treaty. At the International Data Centre (IDC) in Vienna, where IMS data are routinely processed, microbarom detections appear in overlapping frequency bands, and are treated as false alarms. Therefore, understanding the variability in microbarom detections is essential to support the IDC in the reduction of the false alarm rate. In this study, microbarom amplitudes and the direction of arrivals at the German infrasound station IS26 were modelled. For the simulations, the source was described by an operational ocean wave interaction model, and the signal amplitude was modelled using a semi-empirical attenuation relation. This relation strongly depends on middle atmosphere (MA; i.e. 15–90 km altitude) dynamics; however, vertical temperature and wind profiles, provided by numerical weather prediction (NWP) models, exhibit significant biases and differences when compared with high-resolution light detection and ranging instrument (lidar) soundings in altitudes where infrasound signals propagate. To estimate uncertainties in the modelled amplitude, a fully autonomous lidar for MA temperature measurements was installed at IS26. Temperature and wind perturbations, considering observed biases and deviations, were added to the operational high-resolution atmospheric model analysis produced by the European Centre for Medium-Range Weather Forecasts. Such uncertainties in horizontal winds and temperature strongly impact propagation conditions, explaining almost 97 per cent of the actual detections, compared to 77 per cent when using the direct output of the NWP model only. Incorporating realistic wind and temperature uncertainties in NWP models can thus significantly improve the understanding of microbarom detections as well as the detection capability of a single station throughout the year.
The contribution of drug-related deaths to the US disadvantage in mortality
Authors: Barbieri Magali
Published: December 2018

Background

The USA ranks last in life expectancy among high-income countries. Since 2000, excess US mortality has been particularly concentrated in the working ages, which are also the ages hardest hit by the increase in drug deaths. This study measures the effect of drug-related mortality on the gap in life expectancy between the USA and other countries.

Methods

Data from the Human Mortality Database and the World Health Organization were combined to construct age-standardized mortality rates for 2000–14 in 12 high-income countries and the USA for seven broad causes of death, including drug use. The contribution of each cause to the difference in life expectancy between the USA and the other 12 countries was estimated.

Results

In 2014, the increase in drug-related deaths accounted for 10–15% of the US disadvantage in mortality, but with marked differences by age group. For working-age men, the increase in drug-related deaths accounted for up to 38% of the difference. Overall, American mortality is higher than the comparison countries across a wide range of causes.

Conclusions

The severity of the drug epidemic appears to be specific to the USA, but it only partly contributes to the American shortfall in mortality.
Stability and Hopf bifurcation analysis of lac Operon model with distributed delay and nonlinear degradation rate
Authors: Alrikaby Zenab
Published: December 2018

We propose a simple model of lac operon that describes the expression of B-galactosidase from lac Z gene in Escherichia coli, through the interaction among several identical mRNA. Our goal is to explore the complex dynamics (i.e. the oscillation phenomenon) of this architecture mediated by this interaction. This model was theoretically and numerically investigated using distributed time delay. We considered the average delay as a bifurcation parameter and the nonlinear degradation rate as a control parameter. Sufficient conditions for local stability were gained by using the Routh–Hurwitz criterion in the case of a weak delay kernel. Then we proved that Hopf bifurcation happened and the direction of the periodic solution was determined using multiple time scale technique. Our results suggest that the interaction among several identical mRNA plays the main role in gene regulation.
Game-theoretic semantics for non-distributive logics
Authors: Hartonas Chrysafis
Published: December 2018

We introduce game-theoretic semantics for systems without the conveniences of either a De Morgan negation, or of distribution of conjunction over disjunction and conversely. Much of game playing rests on challenges issued by one player to the other to satisfy, or refute, a sentence, while forcing him/her to move to some other place in the game’s chessboard-like configuration. Correctness of the game-theoretic semantics is proven for both a training game, corresponding to Positive Lattice Logic and for more advanced games for the logics of lattices with weak negation and modal operators (Modal Lattice Logic).
AFF3-DNA methylation interplay in maintaining the mono-allelic expression pattern of XIST in terminally differentiated cells
Authors: Zhang Yue , Wang Chao , Liu Xiaoxu , Yang Qian , Ji Hongliang , Yang Mengjun , Xu Manman , Zhou Yunyan , Xie Wei , Luo Zhuojuan , Lin Chengqi
Published: December 2018

X chromosome inactivation and genomic imprinting are two classic epigenetic regulatory processes that cause mono-allelic gene expression. In female mammals, mono-allelic expression of the long non-coding RNA gene X-inactive specific transcript (XIST) is essential for initiation of X chromosome inactivation upon differentiation. We have previously demonstrated that the central factor of super elongation complex-like 3 (SEC-L3), AFF3, is enriched at gamete differentially methylated regions (DMRs) of the imprinted loci and regulates the imprinted gene expression. Here, we found that AFF3 can also bind to the DMR downstream of the XIST promoter. Knockdown of AFF3 leads to de-repression of the inactive allele of XIST in terminally differentiated cells. In addition, the binding of AFF3 to the XIST DMR relies on DNA methylation and also regulates DNA methylation level at DMR region. However, the KAP1-H3K9 methylation machineries, which regulate the imprinted loci, might not play major roles in maintaining the mono-allelic expression pattern of XIST in these cells. Thus, our results suggest that the differential mechanisms involved in the XIST DMR and gDMR regulation, which both require AFF3 and DNA methylation.
A role for 3′ exonucleases at the final stages of chromosome duplication in Escherichia coli
Authors: Midgley-Smith Sarah L , Dimude Juachi U , Rudolph Christian J
Published: December 2018

Chromosome duplication initiates via the assembly of replication fork complexes at defined origins, from where they proceed in opposite directions until they fuse with a converging fork. Recent work highlights that the completion of DNA replication is highly complex in both pro- and eukaryotic cells. In this study we have investigated how 3′ and 5′ exonucleases contribute towards the successful termination of chromosome duplication in Escherichia coli. We show that the absence of 3′ exonucleases can trigger levels of over-replication in the termination area robust enough to allow successful chromosome duplication in the absence of oriC firing. Over-replication is completely abolished if replication fork complexes are prevented from fusing by chromosome linearization. Our data strongly support the idea that 3′ flaps are generated as replication fork complexes fuse. In the absence of 3′ exonucleases, such as ExoI, these 3′ flaps can be converted into 5′ flaps, which are degraded by 5′ exonucleases, such as ExoVII and RecJ. Our data support the idea that multiple protein activities are required to process fork fusion intermediates. They highlight the complexity of fork fusions and further support the idea that the termination area evolved to contain fork fusion-mediated pathologies.
Heterogeneous Impacts of Concentrated Poverty During Adolescence on College Outcomes
Authors: Levy Brian L
Published: December 2018

This research analyzes how living in concentrated poverty during adolescence affects future college outcomes. Using Add Health data and propensity score methods to explore effect heterogeneity, I find that concentrated poverty has little direct impact on college matriculation. It does, however, strongly reduce the odds of graduating from college for adolescents least likely to reside in concentrated poverty. This indicates an advantage-leveling model in which individuals with prior advantages have the most to lose from neighborhood disadvantage during adolescence. I assess neighborhood socialization, school effects, and peer effects as potential explanations for the neighborhood effect. Supporting collective socialization theory, neighborhood economic opportunity and resource deprivation are key aspects of poverty-saturated neighborhoods that influence college graduation odds. Schools also play an important role in the relationship between neighborhoods and college outcomes. Main effects are likely to be causal as they are highly robust to unobserved confounding.
Assessors assemble: the need for harmonised external quality assessment schemes for emerging diagnostic methodologies in the field of parasitology
Authors: Shrivastava Jaya
Published: December 2018

Global travel and migration trends have meant a huge increase in the numbers of people exposed to tropical parasitic diseases. Thus, there is an increasing need for robust, reproducible and reliable diagnostic techniques in the field.

Advanced molecular and lateral flow techniques have pushed the boundaries of clinical parasite diagnostics with their enhanced sensitivities and specificities. These emerging technologies are, however, not without their challenges, and recently there has been multiple evidence of a lack of consensus among protocols and results obtained by quality assessment of these novel technologies.

This commentary discusses findings from some recent quality assessment studies in the field of blood and faecal parasitology. The article also makes recommendations for a unified and harmonised approach towards delivering high-quality clinical parasitology diagnoses, especially through the use of proficiency testing.
The Language of First-Trimester Nonviable Pregnancy
Authors: Clement Elizabeth G. , Horvath Sarah , McAllister Arden , Koelper Nathanael C. , Sammel Mary D. , Schreiber Courtney A.
Published: December 2018

OBJECTIVE:

To document the terminology patients hear during the treatment course for a nonviable pregnancy and to ask patients their perceived clarity and preference of terminology to identify a patient-centered lexicon.

METHODS:

We performed a preplanned substudy survey of English-speaking participants in New York, Pennsylvania, and California at the time of enrollment in a randomized multisite trial of medical management of first-trimester early pregnancy loss. The six-item survey, administered on paper or an electronic tablet, was developed and piloted for internal and external validity. We used a visual analog scale and quantified tests of associations between participant characteristics and survey responses using risk ratios.

RESULTS:

We approached 155 English-speaking participants in the parent study, of whom 145 (93.5%) participated. In the process of receiving their diagnosis from a clinician, participants reported hearing the terms “miscarriage” (n=109 [75.2%]) and “early pregnancy loss” (n=73 [50.3%]) more than “early pregnancy failure” (n=31 [21.3%]) and “spontaneous abortion” (n=21 [14.4%]). The majority selected “miscarriage” (n=79 [54.5%]) followed by “early pregnancy loss” (n=49 [33.8%]) as their preferred term. In multivariable models controlling for study site, ethnicity, race, history of induced abortion, and whether the current pregnancy was planned, women indicated that “spontaneous abortion” and “early pregnancy failure” were significantly less clear than “early pregnancy loss” (53/145, adjusted risk ratio 0.12, 95% CI 0.07–0.19 and 92/145, adjusted risk ratio 0.38, 95% CI 0.24–0.61, respectively, as compared with 118/145 for “early pregnancy loss”). “Miscarriage” scored similarly to “early pregnancy loss” in clarity (119/145, adjusted risk ratio 1.05, 95% CI 0.62–1.77).

CONCLUSION:

The terminology used to communicate “nonviable pregnancy in the first trimester” is highly variable. In this cohort of women, most preferred the term “miscarriage” and classified both “miscarriage” and “early pregnancy loss” as clear labels for a nonviable pregnancy. Health care providers can use these terms to enhance patient–clinician communication.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT02012491.
Reasons why the diagnosis of serrated polyposis syndrome is missed
Authors: van Herwaarden Yasmijn J. , Pape Simon , Vink-Börger Elisa , Dura Polat , Nagengast Fokko M. , Epping Ludger S.M. , Bisseling Tanya M. , Nagtegaal Iris D.
Published: December 2018

Objectives

Serrated polyposis syndrome (SPS) is a relatively new and under-recognized colorectal cancer (CRC) predisposition syndrome. Previous studies have reported miss-rates of SPS diagnosis varying from 40 to 82%. As SPS patients and their first-degree relatives have an increased risk of CRC, early recognition is important. We aimed to determine the miss-rate of SPS and to determine the reasons for missed diagnosis.

Patients and methods

We retrospectively identified all patients diagnosed with at least one colorectal polyp or carcinoma detected at our tertiary referral center between January 1986 and July 2013 using the nationwide pathology registry. On the basis of cumulative polyp count with size and location, SPS patients were identified. We checked whether the SPS diagnosis was made in the medical files and, if not, what might have been the reason for missing the diagnosis.

Results

We randomly assessed 5000 patients, of whom 25 patients fulfilled the WHO criteria for SPS. In six patients, no previous SPS diagnosis had been made, leading to a miss-rate of 24.0% (95% confidence interval: 7.3–40.7). The reasons for missed diagnosis were polyps removed before establishment of the WHO criteria, unavailable pathology reports, and failure to apply the criteria by the clinician.

Conclusion

The miss-rate for the diagnosis of SPS is considerable, even during longer follow-up with repeated colonoscopies. A preventable reason for missing SPS cases is failure to apply the WHO criteria. Awareness of this CRC predisposition syndrome needs to be raised to decrease the miss-rate of SPS.
Intravenous thrombolysis and mechanical thrombectomy in patients with minor or rapidly improving neurological deficits
Authors: Ferrari Julia , Krebs Stefan , Sykora Marek
Published: December 2018

Purpose of review

A substantial proportion of patients with ischemic stroke present with mild neurological deficits ('Stroke with mild symptoms,’ SMS). Treating these patients with thrombolysis or with thrombectomy is controversial and clinical practice is different. We will highlight the importance of these treatment decisions by reviewing the recent advances in this area.

Recent findings

Intravenous thrombolysis with recombinant tissue plasminogen activator in patients with SMS showed a significant reduction in functional disability after 3 months. Treatment with tenecteplase seems to be a pharmacologically superior and possibly safer thrombolytic agent making it ideal for use in this patient group. Imaging criteria to select the profiting patients are evolving. Thrombectomy in patients with a large vessel occlusion and minor deficits are showing promising results in cohort studies so far, however, randomized controlled trials are lacking.

Patients with acute ischemic stroke and minor or rapidly improving symptoms should be carefully treated the same way as more severe strokes are treated as neurological deterioration is not infrequent. Nevertheless, treatment decisions should be individualized dependent on clinical and radiological features.
Monitoring Neural Activity During Exposure to Drugs of Abuse With In Vivo Fiber Photometry
Authors: Rinker Jennifer A. , Gioia Dominic , Braunscheidel Kevin M. , Wayman Wesley N. , Hoffman Michaela , Passarella Linsey , Calipari Erin S. , Mulholland Patrick J. , Woodward John J.
Published: December 2018

Drugs of abuse are known to alter activity in areas of brain associated with reward, cognition and decision making. Changes in neural activity in these regions that follow repeated exposures to abused substances may underlie the development of addictive behaviors and contribute to the high rates of relapse associated with drug use. Measuring real-time changes in neural activity during drug seeking and taking is important for correlating changes in behavior with alterations in neuronal signaling typically measured using ex vivo electrophysiological recordings. In this study, C57BL/6J mice or Sprague-Dawley rats were injected in different brain areas with adeno-associated viruses (AAV) encoding the calcium sensor GCaMP6f along with an optical fiber. Calcium-dependent fluorescence was monitored in the nucleus accumbens core or mPFC during and following exposure to toluene vapor and in the medial prefrontal cortex (mPFC) and orbitofrontal cortex (OFC) during ethanol drinking. Toluene vapor, at concentrations previously shown to induce conditioned place preference, produced a rapid decrease in the frequency of calcium transients in the NAc core of rats that recovered following washout of the toluene vapor. In a probabilistic risk task, GCaMP6 signals in rat mPFC increased just prior to lever pressing and showed decreases during the reward phase that were proportional to reward size. Toluene pretreatment elevated the signal during the decision-making period while post-lever responses were independent of reward size. Using the drinking in the dark (DID) protocol in mice, we observed a consistent increase in GCaMP6 fluorescence during the period leading up to an ethanol drinking bout, a decrease during consumption and a rebound increase following the bout. The initial increase in signal prior to consumption was greater for ethanol and sucrose than water. GCaMP6 signals in the lateral OFC also decreased during ethanol consumption and increased following bout completion while no increase in activity was noted prior to bout initiation. Following repeated cycles of chronic intermittent ethanol (CIE) exposure that enhanced ethanol consumption, OFC calcium signals during and after ethanol drinking were similar to those in air-treated animals. Addition of quinine to the ethanol solution augmented the decrease in signal during consumption in both air and CIE mice while having no effect on the magnitude of the rebound in activity. Conversely, when sucrose was added to the ethanol solution, air exposed mice showed blunted changes in GCaMP6 signals while those in CIE mice were enhanced. Overall, the results from these experiments complement and extend data from prior behavioral and electrophysiological studies and support the use of in vivo fiber photometry in the study of effects of abused substances on brain function.