bluuebunny/crossref_metadata_2025 huggingface dataset:
Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C
Authors: Manzoni Francesco , Saraboji Kadhirvel , Sprenger Janina , Kumar Rohit , Noresson Ann-Louise , Nilsson Ulf J. , Leffler Hakon , Fisher S. Zoë , Schrader Tobias E. , Ostermann Andreas , Coates Leighton , Blakeley Matthew P. , Oksanen Esko , Logan Derek T.
Published: October 2016

Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described. The larger crystals resulted in improved data quality and reduced data-collection times. Furthermore, protocols for complete removal of the lactose that is necessary for the production of large crystals of apo galectin-3C suitable for neutron diffraction are described. Five data sets have been collected at three different neutron sources from galectin-3C crystals of various volumes. It was possible to merge two of these to generate an almost complete neutron data set for the galectin-3C–lactose complex. These data sets provide insights into the crystal volumes and data-collection times necessary for the same system at sources with different technologies and data-collection strategies, and these insights are applicable to other systems.
Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase
Authors: Ruf Armin , Tetaz Tim , Schott Brigitte , Joseph Catherine , Rudolph Markus G.
Published: October 2016

Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connectedviathe minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements. Self-Patterson function analysis and various intensity statistics revealed the presence of pseudo-translation and the absence of twinning. The space group isP41212, but structure determination was also possible in space groupsP43212,P4122 andP4322. All solutions have the same arrangement of threeC2-symmetric dimers spaced by 1/3 along an NCS axis parallel to thecaxis located at (1/4, 1/4,z), which is therefore invisible in a self-rotation function analysis. The solutions in the four space groups are related to one another and emulate a body-centred lattice. If all NCS elements were crystallographic, the space group would beI4122 with acaxis three times shorter and a single FBPase subunit in the asymmetric unit.I4122 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.
Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations
Authors: Drozdzal Pawel , Gilski Miroslaw , Jaskolski Mariusz
Published: October 2016

The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2′-deoxyribose (the natural enantiomer) and L-2′-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form withC2/csymmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to anRfactor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg2+sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA–Mg2+structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG)2duplex with those of other homochiral and heterochiral Z-DNA structures.
1-[(E)-(3-Hydroxy-4-methoxybenzylidene)amino]-3-methylthiourea
Authors: Arafath Md. Azharul , Adam Farook , Razali Mohd. R.
Published: October 2016

In the title thiosemicarbazone Schiff base compound, C10H13N3O2S, the dihedral angle between the benzene ring and methyl carbothioamide side arm was found to be 17.4 (4)°. The presence of two intramolecular hydrogen bonds is noted, namely hydroxy-O—H...O(methoxy) and amine-N—H...N(imine). In the crystal, pairwise amine-N—H...S hydrogen bonds give rise to centrosymmetric {...HNCS}2 synthons, which lead to dimeric aggregates.
(E)-4-(Benzo[d]thiazol-2-yl)-N-(pyridin-3-ylmethylidene)aniline hemihydrate
Authors: Hong Li , Xin Zhang
Published: October 2016

The title compound, C19H13N3S·0.5H2O, is a benzothiazole derivative that crystallized as a hemihydrate, the water O atom being situated on a twofold rotation axis. The dihedral angles between the central benzene ring and the benzothiazole (r.m.s. deviation = 0.012 Å) and pyridine rings are 3.57 (6) and 10.12 (8)°, respectively, indicating that the molecule is nearly planar. The conformation about the N=C bond is E. In the crystal, molecules are linked by Owater—H...Npyridine hydrogen bonds, forming dimers, which in turn are linked by C—H...O hydrogen bonds into layers parallel to the ab plane. The layers are linked by offset π–π interactions, forming a three-dimensional network [shortest intercentroid distance = 3.721 (2) Å].
2,5-Bis[(dimethylamino)methyl]-1H-pyrrole
Authors: Guo Zhiqiang , Li Pengxiang , Feng Pengcheng , Liu Kai , Wei Xuehong
Published: October 2016

The asymmetric unit contains two independent molecules, C10H19N3, which are linked into dimers by two Npyrrole—H...Namine hydrogen bonds.
(E)-4-({[4-(Benzo[d]thiazol-2-yl)phenyl]imino}methyl)-N,N-diethylaniline
Authors: Yao Shun , Zhang Xin
Published: October 2016

The title benzothiazole derivative molecule, C24H23N3S, is almost planar with the central benzene ring being inclined to the benzothiazole ring and the diethylaniline ring by 4.05 (13) and 5.05 (13)°, respectively. The conformation about the N=C bond is E. In the crystal, molecules are linked by C—H...π interactions, forming layers parallel to the ab plane.
5,31-Diaza-2,8,15,18,21,28,34,41,44,47-decaoxaheptacyclo[46.4.0.04,32.06,30.09,14.022,27.035,40]dopentaconta-1(48),4,6(30),9(14),10,12,22(27),23,25,31,35(40),36,38,49,51-pentadecaene monohydrate
Authors: Kim Jong Sik , Lee Jai Young , Lee So Yeon , Lee Tae Yeon , Sim Wonbo
Published: October 2016

In the title compound, C40H40N2O10·H2O, each dual 17-crown-5 unit crystallizes with one solvent water molecule. The crown units are connected by a pyrazine ring. One oxo group in a crown moiety is disordered over two sites, with a refined occupancy ratio close to 1:1. The water molecule is linked to the crown unit by bifurcated O—H...O hydrogen bonds. In the crystal, molecules are linked by weak C—H...N and C—H...O interactions for the packing.
2-(2-Isopropylphenoxy)acetic acid
Authors: Mohammed Yasser Hussein Issa , Naveen S. , Mamatha S. V. , Jyothi Mahima , Khanum Shaukath Ara , Lokanath N. K.
Published: October 2016

In the title compound, C11H14O3, the pendant –OCH2COOH chain is in an extended conformation and almost lies in the plane of the benzene ring, as indicated by the dihedral angle of 2.61 (5)°. In the crystal, molecules are linked by a pair of O—H...O hydrogen bonds, forming classical carboxylic acid inversion dimers, with an R
2
2(8) loop. The crystal structure of this compound have been reported previously [Smith et al. (1992). Aust. J. Chem.
45, 1101–1108], however, in that report, the unit-cell dimensions differ significantly from those of the title structure and the carboxyl H atom was disordered within a cyclic hydrogen-bonded dimer.
(E)-N′-[4-(Dimethylamino)benzylidene]propionohydrazide monohydrate
Authors: Naveen S. , Samshuddin Seranthimata , Rodrigues Manuel , Arunkumar Dandavathi , Lokanath N. K. , Warad Ismail
Published: October 2016

In the title hydrated hydrazine compound, C12H17N3O·H2O, the C=N bond adopts an E conformation. In the crystal, water molecules bridge the hydrazine molecules, via N—H...O and O—H...O hydrogen bonds, forming sheets parallel to the bc plane. There are C—H...π interactions present within the sheets, and further C—H...π interactions link the sheets to form a three-dimensional structure.
A lexicon based approach for classifying Arabic multi-labeled text
Authors: Hmeidi Ismail , Al-Ayyoub Mahmoud , Mahyoub Nizar A. , Shehab Mohammed A.
Published: October 2016

Purpose

Multi-label Text Classification (MTC) is one of the most recent research trends in data mining and information retrieval domains because of many reasons such as the rapid growth of online data and the increasing tendency of internet users to be more comfortable with assigning multiple labels/tags to describe documents, emails, posts, etc. The dimensionality of labels makes MTC more difficult and challenging compared with traditional single-labeled text classification (TC). Because it is a natural extension of TC, several ways are proposed to benefit from the rich literature of TC through what is called problem transformation (PT) methods. Basically, PT methods transform the multi-label data into a single-label one that is suitable for traditional single-label classification algorithms. Another approach is to design novel classification algorithms customized for MTC. Over the past decade, several works have appeared on both approaches focusing mainly on the English language. This work aims to present an elaborate study of MTC of Arabic articles.

Design/methodology/approach

This paper presents a novel lexicon-based method for MTC, where the keywords that are most associated with each label are extracted from the training data along with a threshold that can later be used to determine whether each test document belongs to a certain label.

Findings

The experiments show that the presented approach outperforms the currently available approaches. Specifically, the results of our experiments show that the best accuracy obtained from existing approaches is only 18 per cent, whereas the accuracy of the presented lexicon-based approach can reach an accuracy level of 31 per cent.

Originality/value

Although there exist some tools that can be customized to address the MTC problem for Arabic text, their accuracies are very low when applied to Arabic articles. This paper presents a novel method for MTC. The experiments show that the presented approach outperforms the currently available approaches.
Learning to rank with click-through features in a reinforcement learning framework
Authors: Keyhanipour Amir Hosein , Moshiri Behzad , Piroozmand Maryam , Oroumchian Farhad , Moeini Ali
Published: October 2016

Purpose

Learning to rank algorithms inherently faces many challenges. The most important challenges could be listed as high-dimensionality of the training data, the dynamic nature of Web information resources and lack of click-through data. High dimensionality of the training data affects effectiveness and efficiency of learning algorithms. Besides, most of learning to rank benchmark datasets do not include click-through data as a very rich source of information about the search behavior of users while dealing with the ranked lists of search results. To deal with these limitations, this paper aims to introduce a novel learning to rank algorithm by using a set of complex click-through features in a reinforcement learning (RL) model. These features are calculated from the existing click-through information in the data set or even from data sets without any explicit click-through information.

Design/methodology/approach

The proposed ranking algorithm (QRC-Rank) applies RL techniques on a set of calculated click-through features. QRC-Rank is as a two-steps process. In the first step, Transformation phase, a compact benchmark data set is created which contains a set of click-through features. These feature are calculated from the original click-through information available in the data set and constitute a compact representation of click-through information. To find most effective click-through feature, a number of scenarios are investigated. The second phase is Model-Generation, in which a RL model is built to rank the documents. This model is created by applying temporal difference learning methods such as Q-Learning and SARSA.

Findings

The proposed learning to rank method, QRC-rank, is evaluated on WCL2R and LETOR4.0 data sets. Experimental results demonstrate that QRC-Rank outperforms the state-of-the-art learning to rank methods such as SVMRank, RankBoost, ListNet and AdaRank based on the precision and normalized discount cumulative gain evaluation criteria. The use of the click-through features calculated from the training data set is a major contributor to the performance of the system.

Originality/value

In this paper, we have demonstrated the viability of the proposed features that provide a compact representation for the click through data in a learning to rank application. These compact click-through features are calculated from the original features of the learning to rank benchmark data set. In addition, a Markov Decision Process model is proposed for the learning to rank problem using RL, including the sets of states, actions, rewarding strategy and the transition function.
Exchange rate interest rate linkages in India: an empirical investigation
Authors: Shastri Shruti , Shastri Swati
Published: October 2016

Purpose

The purpose of the paper is to examine the linkages between exchange rate and interest rate in India using quarterly data from Q1 of 1996 to Q4 of 2014.

Design/methodology/approach

Stationarity properties of data are checked using the Augmented Dickey–Fuller (ADF), Dickey–Fuller test with GLS de-trending (DF-GLS) and Kwiatkowski-Phillips-Schmidt-Shin (KPSS) tests and Perron’s unit root test with structural breaks. Johansen Juselius and Gregory Hansen tests are applied to assess cointegration, and block exogeneity test is used to detect causality among variables.

Findings

The study finds long-run relationship among interest rate, rupee–dollar exchange rate, capital flows, intervention, inflation differential, money supply differentials, output differentials and trade-balance differentials. However, the interest rate does not explain movements in the exchange rate, directly and indirectly, via capital flows. Intervention by the Central Banks to stabilize exchange rate does not have implications for movements in interest rate.

Research limitations/implications

The study finds capital flows to be insensitive with respect to interest rates and hence thwarts International Monetary Fund ’s (IMF) claim of using interest rates as a tool to stabilize exchange rate. The much-debated conflict between exchange-rate stabilization and control over interest rates also does not hold up to the empirical reality of India.

Originality/value

The study augments the existing literature by taking into account the problem of structural break in the relationship between interest rate and exchange rate. Three measures of interest rate are used to assess the robustness of results adding to their credibility compared to previous studies.
Beggaring thy neighbor at the state and local level
Authors: Murphy Ryan H.
Published: October 2016

Purpose

This paper aims to address a growing empirical literature which measures the size of the fiscal multiplier at the state and local levels. This literature generally fails to consider the reaction function of the central bank, which typically should be expected to offset local increases in spending by reducing it elsewhere in the currency area. This is true under rather orthodox assumptions, such as an inflation targeting central bank meeting its target.

Design/methodology/approach

The author reviews prominent examples of the literature and establishes the extent to which the empirical methodology avoids the issue he raises. Subsequently, the author discusses its importance.

Findings

Certain papers in the literature, especially Nakamura and Steinsson (2014), are careful about the issue. Most papers reviewed, however, are not.

Practical implications

There are severe limitations to papers using these methodologies. They are either contingent on very specific assumptions regarding central banks or lack policy relevance. Earlier methodologies, such as vector autoregression and the “narrative” method, deserve higher relative credence among methodologies applied to studying the size of the fiscal multiplier.

Originality/value

The current literature either entirely ignores the issue raised here or it is very briefly brushed aside. Considering the orthodoxy of the assumptions, at the very least, the issue deserves far greater recognition in the future. It may demand a broader re-evaluation of the family of methods.
Macroeconomic uncertainty and “global” economic performance
Authors: Abaidoo Rexford , Ellis Florence
Published: October 2016

Purpose

This study aims to explore potential paradigm shift in how “global economies” react to adverse macroeconomic conditions from key dominant economies such as the US and the Chinese economies. This is done by examining how economic activities within key economies around the world react to, or are impacted by, modeled adverse macroeconomic condition emanating from the Chinese and the US economies.

Design/methodology/approach

To verify potential paradigm shift in how external macroeconomic uncertainty impacts “global” industrial productivity and overall gross domestic product (GDP) growth within selected economies, this study opts for seemingly unrelated regression (SUR) model. Adoption of this method has been influenced by the potential for correlated error terms between modeled adverse macroeconomic condition, industrial productivity and GDP growth variables being tested in a two-equation system.

Findings

Empirical results based on SUR analysis find no evidence of this potential paradigm shift within the time frame examined in the study. Estimated results suggest that notwithstanding the recent growth surge of the Chinese economy, macroeconomic happenings within the US economy still exert significantly more influence on key economies around the world. For instance, this study finds that macroeconomic uncertainty associated with the US economy significantly constrains both industrial productivity and overall GDP growth within most of the economies tested, whereas the same condition emanating from the Chinese economy seems to rather have a weak positive impact on the same macroeconomic variables.

Research limitations/implications

Research results are strictly limited to the focus time frame for this study; it is likely that expanded data involving more years beyond what was analyzed in this study could yield different results.

Originality/value

This study is an original research based on data from a reputable US federal institution.
Transforming South Africa’s health sector
Authors: Katuu Shadrack
Published: October 2016

Purpose

The purpose of this paper is to explore the challenges of transforming South Africa’s health sector through the country’s eHealth Strategy and particularly one of its key components, the implementation of an integrated Electronic Document and Records Management System (EDRMS).

Design/methodology/approach

The study conducted an extensive review of literature and used it as a basis to analyse the challenges as well as opportunities in South Africa’s transformation path within its health sector based on the nation’s eHealth Strategy.

Findings

South Africa’s health sector faces three main transformation challenges: inequity, legacy of fragmentation and a service delivery structure biased towards curative rather than preventive services. Health information systems provide a solid platform for improving efficiency but, within South Africa, these systems have been highly heterogeneous. A recent study showed the country had more than 40 individual health information systems scattered in all provinces, with over 50 per cent not adhering to any national or international standards and more than 25 per cent being stand-alone applications that shared information neither locally nor externally. The eHealth Strategy offers a robust platform to start addressing the legacy of fragmentation and lack of interoperability. However, it also raises a few other concerns, including the use of different terminology such as Electronic Medical Record (EMR) interchangeable with Electronic Health Record (EHR), or EDRMS parallel with Electronic Content Management (ECM). In addition, there is the opportunity to explore the use of the maturity model concept in the EDRMS implementation experiences within South Africa.

Originality/value

This paper demonstrated the complex nature of the legacy of fragmentation in South Africa’s health information systems and explored three aspects relating to terminology as well as maturity models that should be considered in the country’s future eHealth Strategy.
Factors affecting the diffusion and success of collaborative interactions between university and industry
Authors: Capaldo Guido , Costantino Nicola , Pellegrino Roberta , Rippa Pierluigi
Published: October 2016

Purpose

This paper aims to investigate factors and weaknesses influencing university–industry interactions diffusion and success by focusing on the research services initiatives because there are limited studies in literature focusing on this specific form of interaction between the two actors.

Design/methodology/approach

The authors carried an explorative research based on multiple case studies referring to research services experienced between two big Italian universities and small and medium-sized enterprises located in the same area.

Findings

By conducting a cross-case analysis, the authors highlight categories of data in terms of factors influencing interactions’ diffusion and success, as perceived by researchers and by firms; and weaknesses in the interactions process to identify suggestions for improving interactions’ diffusion and success, from researchers and firms.

Practical implications

The outcomes provide managerial implications useful for agencies supporting the diffusion of innovation among firms and firms’ systems for defining new policies and action plans aimed at making the university–industry interactions faster and more effective, improving the innovation processes within firms.

Originality/value

This paper gives new insight in the analysis of factors enhancing university–industry relationships with a focus on research services collaborations and focusing both on university and industry, where large contributions focus predominantly on both groups.
The Key Role of Education in Reducing Poverty in South Sudan
Authors: Shimeles Abebe , Verdier‐Chouchane Audrey
Published: October 2016

Based on the 2009 National Baseline Household Survey (NBHS), the objective of the paper is to analyse the education sector in South Sudan and to highlight its key role in reducing poverty and inequality in the country. The first estimation highlights the role of educational attainment on the risk of poverty based on a Probit model with marginal effects. The second performs estimates of returns for each level of schooling using an extended Mincerian earnings equation. The third estimation uses benefit concentration curves to assess progressivity of education subsidy. Results confirm the negative correlation between education and poverty. For instance, someone with a primary level of education earns 36.5 per cent more than someone with no schooling and this figure increases until 188.6 per cent for university graduates, highlighting a convexity trend of private returns to education. The education challenge is enormous in post‐conflict South Sudan where more than 70 per cent of the population is illiterate and many children don't attend school. In terms of policy recommendations, the welfare analysis shows that subsidizing primary education is a pro‐poor policy in South Sudan. However, the government would also need to focus its action in the rural areas where the challenges are even more salient than in urban areas.
Critical Election in the Wake of an Economic and Political Crisis: Realignment of Icelandic Party Voters?
Authors: Önnudóttir Eva H. , Schmitt Hermann , Harðarson Ólafur Þ.
Published: October 2016

A critical election is generally defined as one in which the decisive results of voting reveal a sharp alternation of pre‐existing cleavage(s) and voting patterns, and the dealignment or realignment made between parties is lasting. A critical election can be caused by various factors and in this article the authors analyse whether the global credit crunch in 2008 set things in motion in Iceland, resulting in the 2009 election as a critical election. In that election, the electoral relevance of voters’ psychological attachment to parties and of ideological distances to them weakened, whereas party competence perceptions increased in importance for vote choices. Attachment to parties and ideological distances are factors that are generally stable and change slowly over time, while party competence is influenced by which issues are of importance at the time of the election. This indicates that, in 2009, a restructuring of the determinants of the vote occurred; a pattern of changes that is typical for a critical election. Evidence is found that the importance of party sympathy increases again in the 2013 election, indicating a realignment, rather than a dealignment, occurring in the wake of the 2009 election.
A narrative analysis of the birth stories of early‐age mothers
Authors: Carson Anna , Chabot Cathy , Greyson Devon , Shannon Kate , Duff Putu , Shoveller Jean
Published: October 2016

The telling of birth stories (i.e. stories that describe women's experiences of giving birth) is a common and important social practice. Whereas most research on birth narratives reflects the stories of middle‐class, ‘adult’ women, we examine how the birth stories told by early‐age mothers interconnect with broader narratives regarding social stigma and childbearing at ‘too early’ an age. Drawing on narrative theory, we analyse in‐depth interviews with 81 mothers (ages 15–24 years) conducted in Greater Vancouver and Prince George, Canada, in 2014–15. Their accounts of giving birth reveal the central importance of birth narratives in their identity formation as young mothers. Participants’ narratives illuminated the complex interactions among identity formation, social expectations, and negotiations of social and physical spaces as they narrated their experiences of labour and birth. Through the use of narrative inquiry, we examine the ways in which re‐telling the experience of giving birth serves to situate young mothers in relation to their past and future selves. These personal stories are also told in relation to a meta‐narrative regarding social stigma faced by ‘teenage’ mothers, as well as the public's ‘gaze’ on motherhood in general – even within the labour and delivery room.
A New Approach of Juvenile Age Estimation using Measurements of the Ilium and Multivariate Adaptive Regression Splines (MARS) Models for Better Age Prediction
Authors: Corron Louise , Marchal François , Condemi Silvana , Chaumoître Kathia , Adalian Pascal
Published: October 2016

Juvenile age estimation methods used in forensic anthropology generally lack methodological consistency and/or statistical validity. Considering this, a standard approach using nonparametric Multivariate Adaptive Regression Splines (MARS) models were tested to predict age from iliac biometric variables of male and female juveniles from Marseilles, France, aged 0–12 years. Models using unidimensional (length and width) and bidimensional iliac data (module and surface) were constructed on a training sample of 176 individuals and validated on an independent test sample of 68 individuals. Results show that MARS prediction models using iliac width, module and area give overall better and statistically valid age estimates. These models integrate punctual nonlinearities of the relationship between age and osteometric variables. By constructing valid prediction intervals whose size increases with age, MARS models take into account the normal increase of individual variability. MARS models can qualify as a practical and standardized approach for juvenile age estimation.
Adsorption of Shiga Toxin to Poly‐γ‐Glutamate Precipitated
Authors: Goto Tsukie , Tsuji Makiko , Kanemaru Kaori , Yokoigawa Kumio
Published: October 2016

We screened foods containing indigestible ingredients in the ability to adsorb Shiga toxin (Stx). When 5 mg of foods and dietary fibers such as dry vegetables and inulin were mixed and incubated with 0.5 mL of Stx solution (100 ng/mL) containing 0.5% bovine serum albumin, both Stx1 and Stx2 seemed to be adsorbed by only a fermented food, natto (a traditional Japanese food prepared from steamed soybeans by the biological action of Bacillus subtilis). We purified the Stx‐adsorbing substance from natto by extraction with H2O, acid treatment, Proteinase K treatment, and an ion exchange chromatography. The purified substance showed an average molecular mass of about 600 kDa. We identified it as poly‐γ‐glutamate (PGA) by amino acid analysis of its hydrolysate and peptide analysis after its treatment with Proteinase K. Purified PGA (MW: molecular weight = about 600 kDa) was considered to adsorb both Stx1 and Stx2 when we separated adsorbed and unadsorbed Stxs (MW = about 72 kDa) by an ultrafiltration method with a centrifugal filter unit (MWCO: molecular weight cut‐off = 100 K). However, PGA with the ability to adsorb Stx was an insoluble form precipitated in the filter unit during centrifugation. PGA precipitated beyond the saturated density was also confirmed to well adsorb both Stx1 and Stx2 by an equilibrated dialysis method. To the best of our knowledge, this is the 1st report on food‐adsorbing Stx.
Influence of Intestinal Microbiota on the Catabolism of Flavonoids in Mice
Authors: Lin Weiqun , Wang Wenting , Yang Hai , Wang Dongliang , Ling Wenhua
Published: October 2016

Although in vitro studies have shown that flavonoids are metabolized into phenolic acids by the gut microbiota, the biotransformation of flavonoids by intestinal microbiota is seldom studied in vivo. In this study, we investigated the impact of the gut microbiota on the biotransformation of 3 subclasses of flavonoids (flavonols, flavones, and flavanones). The ability of intestinal microbiota to convert flavonoids was confirmed with an in vitro fermentation model using mouse gut microflora. Simultaneously, purified flavonoids were administered to control and antibiotic‐treated mice by gavage, and the metabolism of these flavonoids was evaluated. p‐Hydroxyphenylacetic acid, protocatechuic acid, p‐hydroxybenzoic acid, vanillic acid, hydrocaffeic acid, coumaric acid, and 3‐(4‐hydroxyphenyl)propionic acid were detected in the serum samples from the control mice after flavonoid consumption. The serum flavonoid concentrations were similar in both groups, whereas the phenolic metabolite concentrations were lower in the antibiotic‐treated mice than in the control mice. We detected markedly higher flavonoids excretion in the feces and urine of the antibiotic‐treated mice compared to the controls. Moreover, phenolic metabolites were upregulated in the control mice. These results suggest that the intestinal microbiota are not necessary for the absorption of flavonoids, but are required for their transformation.
Strain improvement of Pichia kudriavzevii TY13 for raised phytase production and reduced phosphate repression
Authors: Qvirist Linnea , Vorontsov Egor , Veide Vilg Jenny , Andlid Thomas
Published: October 2016

In this work, we present the development and characterization of a strain of Pichia kudriavzevii (TY1322), with highly improved phytate‐degrading capacity. The mutant strain TY1322 shows a biomass‐specific phytate degradation of 1.26 mmol g−1 h−1 after 8 h of cultivation in a high‐phosphate medium, which is about 8 times higher compared with the wild‐type strain. Strain TY1322 was able to grow at low pH (pH 2), at high temperature (46°C) and in the presence of ox bile (2% w/v), indicating this strain's ability to survive passage through the gastrointestinal tract. The purified phytase showed two pH optima, at pH 3.5 and 5.5, and one temperature optimum at 55°C. The lower pH optimum of 3.5 matches the reported pH of the pig stomach, meaning that TY1322 and/or its phytase is highly suitable for use in feed production. Furthermore, P. kudriavzevii TY1322 tolerates ethanol up to 6% (v/v) and shows high osmotic stress tolerance. Owing to the phenotypic characteristics and non‐genetically modified organisms nature of TY1322, this strain show great potential for future uses in (i) cereal fermentations for increased mineral bioavailability, and (ii) feed production to increase the phosphate bioavailability for monogastric animals to reduce the need for artificial phosphate fortification.
Microbial copper resistance: importance in biohydrometallurgy
Authors: Martínez‐Bussenius Cristóbal , Navarro Claudio A. , Jerez Carlos A.
Published: October 2016

Industrial biomining has been extensively used for many years to recover valuable metals such as copper, gold, uranium and others. Furthermore, microorganisms involved in these processes can also be used to bioremediate places contaminated with acid and metals. These uses are possible due to the great metal resistance that these extreme acidophilic microorganisms possess. In this review, the most recent findings related to copper resistance mechanisms of bacteria and archaea related to biohydrometallurgy are described. The recent search for novel metal resistance determinants is not only of scientific interest but also of industrial importance, as reflected by the genomic sequencing of microorganisms present in mining operations and the search of those bacteria with extreme metal resistance to improve the extraction processes used by the biomining companies.
Intellectual Property & Global Policy
Authors: David Matthew , Halbert Debora J.
Published: October 2016

This article discusses Intellectual Property Rights (IPR) and in particular globalIPRexpansion. That globally protected intellectual property (IP) is more valuable than ever must be set against the fact that today's global network capitalism, in whichIPis so valuable, also enables information to circulate beyondIPcontrol. Similarly, globalIPexpansion and its resistance go hand in hand, as globalIPexpansionist policy contains but also encourages infringement. We document this conflict, the paradoxical space affording it, the boundary disputes that manifest it, and the globalIPexpansionist policy ‘ratchet’ designed, but which fails, to contain it. We then evaluate globalIPRs and the case for extensions, as manifested in treaties such asACTA,TPPandTTIP. This evaluation is undertaken though specific examinations of copyright, patent and trademark laws. Claims for the overall social benefit of globalIPharmonisation and expansion policies are rejected.
Effects of high‐dose ethanol intoxication and hangover on cognitive flexibility
Authors: Wolff Nicole , Gussek Philipp , Stock Ann‐Kathrin , Beste Christian
Published: October 2016

The effects of high‐dose ethanol intoxication on cognitive flexibility processes are not well understood, and processes related to hangover after intoxication have remained even more elusive. Similarly, it is unknown in how far the complexity of cognitive flexibility processes is affected by intoxication and hangover effects. We performed a neurophysiological study applying high density electroencephalography (EEG) recording to analyze event‐related potentials (ERPs) and perform source localization in a task switching paradigm which varied the complexity of task switching by means of memory demands. The results show that high‐dose ethanol intoxication only affects task switching (i.e. cognitive flexibility processes) when memory processes are required to control task switching mechanisms, suggesting that even high doses of ethanol compromise cognitive processes when they are highly demanding. The EEG and source localization data show that these effects unfold by modulating response selection processes in the anterior cingulate cortex. Perceptual and attentional selection processes as well as working memory processes were only unspecifically modulated. In all subprocesses examined, there were no differences between the sober and hangover states, thus suggesting a fast recovery of cognitive flexibility after high‐dose ethanol intoxication. We assume that the gamma‐aminobutyric acid (GABAergic) system accounts for the observed effects, while they can hardly be explained by the dopaminergic system.
Association of vitamin D status with semen quality and reproductive hormones in Iranian subfertile men
Authors: Abbasihormozi Sh. , Kouhkan A. , Alizadeh A.R. , Shahverdi A.H. , Nasr‐Esfahani M.H. , Sadighi Gilani M.A. , Salman Yazdi R. , Matinibehzad A. , Zolfaghari Z.
Published: October 2016

Although vitamin D deficiency is one of the most common health problems throughout the world, including Iran, conflicting information exists on the potential association between serum vitamin D levels and semen quality. This study intended to evaluate the association between serum vitamin D [25(OH) D3] with semen quality and hormones in Iranian subfertile men. We also compared mean vitamin D and hormone levels in normospermic men with oligoasthenoteratozoospermia (OAT) men. This cross‐sectional study was conducted on 278 men who were referred to Royan Infertility Clinic (Tehran, Iran) from March to September 2014. The participants were categorized into two groups; of 186 normospermic and 92 OAT patients according to World Health Organization 2010 criteria. Each participant provided informed consent prior to launching research. Participants completed two general questionnaires of nutritional status. Blood and semen samples were obtained for assessment, and all data were adjusted for age, body mass index (BMI), and season. Vitamin D levels were classified according to Institute of Medicine guidelines. Vitamin D deficiency, insufficiency, and normal levels were observed in 8.6%, 43.6%, 47.8% of participants, respectively. No association was found between daily dietary intake of vitamin D and calcium with sperm parameters. Serum vitamin D was inversely correlated with PTH (p < 0.045). In normospermic men, serum vitamin D levels categorized were not correlated with semen parameters and reproductive hormones (FSH, LH, testosterone(T), and FT), whereas sperm motility showed a positive correlation with vitamin D categorized in OAT men (rs = 0.131, p = 0.028). In conclusion, there was a high incidence of deficiency and insufficiency 25(OH) D Levels (<20ng/ml) observed in Iranian men (52.2%). Moreover, our findings showed a correlation between vitamin D levels and sperm motility in OAT men, which requires further studies.
A data‐driven search for semen‐related phenotypes in conception delay
Authors: Patel C. J. , Sundaram R. , Buck Louis G. M.
Published: October 2016

Sperm count, morphology, and motility have been reported to be predictive of pregnancy, although with equivocal basis prompting some authors to question the prognostic value of semen analysis. To assess the utility of including semen quality data in predicting conception delay or requiring >6 cycles to become pregnant (referred to as conception delay), we utilized novel data‐driven analytic techniques in a pre‐conception cohort of couples prospectively followed up for time‐to‐pregnancy. The study cohort comprised 402 (80%) male partners who provided semen samples and had time‐to‐pregnancy information. Female partners used home pregnancy tests and recorded results in daily journals. Odds ratios (OR), false discovery rates, and 95% confidence intervals (CIs) for conception delay (time‐to‐pregnancy > 6 cycles) were estimated for 40 semen quality phenotypes comprising 35 semen quality endpoints and 5 closely related fecundity determinants (body mass index, time of contraception, lipids, cotinine and seminal white blood cells). Both traditional and strict sperm phenotype measures were associated with lower odds of conception delay. Specifically, for an increase in percent morphologically normal spermatozoa using traditional methods, we observed a 40% decrease in conception delay (OR = 0.6, 95% CI = 0.50, 0.81; p = 0.0003). Similarly, for an increase in strict criteria, we observed a 30% decrease in odds for conception delay (OR = 0.7, 95% CI = 0.52, 0.83; p = 0.001). On the other hand, an increase in percent coiled tail spermatozoa was associated with a 40% increase in the odds for conception delay (OR = 1.4, 95% CI = 1.12, 1.75; p = 0.003). However, our findings suggest that semen phenotypes have little predictive value of conception delay (area under the curve of 73%). In a multivariate model containing significant semen factors and traditional risk factors (i.e. age, body mass index, cotinine and ever having fathered a pregnancy), there was a modest improvement in prediction of conception delay (16% increase in area under the curve, p < 0.0002).
Hepatocellular carcinoma recurrence in patients with curative resection or ablation: impact of HCV eradication does not depend on the use of interferon
Authors: Petta S. , Cabibbo G. , Barbara M. , Attardo S. , Bucci L. , Farinati F. , Giannini E. G. , Tovoli F. , Ciccarese F. , Rapaccini G. L. , Di Marco M. , Caturelli E. , Zoli M. , Borzio F. , Sacco R. , Virdone R. , Marra F. , Felder M. , Morisco F. , Benvegnù L. , Gasbarrini A. , Svegliati‐Baroni G. , Foschi F. G. , Olivani A. , Masotto A. , Nardone G. , Colecchia A. , Persico M. , Boccaccio V. , Craxì A. , Bruno S. , Trevisani F. , Cammà C. ,   the Italian Liver Cancer (ITA.LI.CA) Group
Published: October 2016

Background

In HCV‐infected cirrhotic patients with successfully treated early hepatocellular carcinoma (HCC), the time to HCC recurrence and the effects of sustained viral eradication (SVR) by interferon (IFN)‐based or IFN‐free regimens on HCC recurrence remain unclear.

Aim

To perform an indirect comparison of time to recurrence (TTR) in patients with successfully treated early HCC and active HCV infection with those of patients with SVR by IFN‐based and by IFN‐free regimens.

Methods

We evaluated 443 patients with HCV‐related cirrhosis and Barcelona Clinic Liver Cancer Stage A/0 HCC who had a complete radiological response after curative resection or ablation. Active HCV infection was present in 328, selected from the Italian Liver Cancer group cohort; 58 patients had SVR achieved by IFN‐free regimens after HCC cure, and 57 patients had SVR achieved by IFN‐based regimens after HCC cure. Individual data of patients in the last two groups were extracted from available publications.

Results

TTR by Kaplan–Meier curve was significantly lower in patients with active HCV infection compared with those with SVR both by IFN‐free (P = 0.02) and by IFN‐based (P < 0.001) treatments. TTR was similar in patients with SVR by IFN‐free or by IFN‐based (P = 0.49) strategies.

Conclusion

In HCV‐infected, successfully treated patients with early HCC, SVR obtained by IFN‐based or IFN‐free regimens significantly reduce tumour recurrence without differences related to the anti‐viral strategy used.
All‐oral direct‐acting antiviral therapy in HCV‐advanced liver disease is effective in real‐world practice: observations through HCV‐TARGET database
Authors: Reddy K. R. , Lim J. K. , Kuo A. , Di Bisceglie A. M. , Galati J. S. , Morelli G. , Everson G. T. , Kwo P. Y. , Brown R. S. , Sulkowski M. S. , Akuschevich L. , Lok A. S. , Pockros P. J. , Vainorius M. , Terrault N. A. , Nelson D. R. , Fried M. W. , Manns M. P. ,   the HCV‐TARGET Study Group
Published: October 2016

Background

Chronic hepatitis C virus therapy in patients with advanced liver disease remains a clinical challenge. HCV‐TARGET collects data in patients treated at tertiary academic and community centres.

Aim

To assess efficacy of all‐oral HCV therapy in advanced liver disease.

Methods

Between December 2013 and October 2014, 240 patients with a MELD score of ≥10 initiated HCV treatment with an all‐oral regimen. Data from the 220 patients who completed 12‐week follow‐up were analysed.

Results

Genotype 1 (GT1) patients had higher sustained virological response (SVR) when treated with sofosbuvir plus simeprevir ± ribavirin than with sofosbuvir plus ribavirin (66–74% vs. 54%); GT1b vs GT1a (84% vs. 64%). SVR for GT2 was 72% with sofosbuvir plus ribavirin, while GT3 patients had a substantially lower response (35%). A decrease in MELD score was not clearly related to SVR over the short course of follow‐up although some had improvements in MELD score, serum bilirubin and albumin. A predictor of virological response was albumin level while negative predictors were elevated bilirubin level and GT1a. Most patients with GT1 were treated with approximately 12‐week duration of sofosbuvir and simeprevir ± ribavirin therapy while GT2 and GT3 patients were treated with approximately 12 and 24 weeks of sofosbuvir plus ribavirin respectively.

Conclusions

All‐oral therapies are effective among patients with advanced liver disease with high levels of success in GT2 and GT1b, and may serve to reduce the severity of liver disease after SVR. Treatment for GT3 patients remains an unmet need.

Clinical trial number: NCT01474811
Body mass index greater than 35 is associated with severe Clostridium difficile infection
Authors: Mulki R. , Baumann A. J. , Alnabelsi T. , Sandhu N. , Alhamshari Y. , Wheeler D. S. , Perloff S. , Katz P. O.
Published: October 2016

Background

Obesity has been implicated in the acquisition of Clostridium difficile infections (CDI), however, no study has investigated whether there is a correlation between body mass index (BMI) and CDI severity.

Aim

To determine whether obesity, as measured by BMI correlates with severe hospital‐onset or community‐onset CDI.

Methods

Patients admitted with CDI at a tertiary‐care center from January 2013 to June 2015 were identified. The cohort was stratified by onset of disease using the National Healthcare Safety Network criteria, and by severity using the 2013 American College of Gastroenterology guidelines. Multivariate logistic regression was used to determine independent predictors of severe CDI.

Results

A total of 196 met the inclusion criteria, of which 57.1% (112) met criteria for severe disease. Overall, BMI >35 kg/m2 was 1.7‐fold more likely to be associated with severe CDI compared to a BMI 20–35 kg/m2 (P < 0.005), and was an independent predictor of severe CDI (P = 0.038). In patients with community‐onset‐CDI and hospital‐onset‐CDI, a BMI >35 kg/m2 was associated with a 1.96‐fold and 1.48 greater rate of severe CDI compared to a BMI 20–35 kg/m2 (P = 0.004 and 0.048), and was an independent predictor of severe CDI in these cohorts (P = 0.039 and 0.027) respectively.

Conclusion

This study has identified an association between body mass index and Clostridium difficile infection severity. A BMI>35 kg/m2 is an independent risk factor for severe community‐onset and hospital‐onset Clostridium difficile infections.